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• Collateral damage
  - Nature (London) 466(7310):1023 (2010)
  Nature | Editorial Collateral damage Journal name:NatureVolume:466,Page:1023Date published:(26 August 2010)DOI:doi:10.1038/4661023aPublished online25 August 2010 An investigation at Harvard University highlights the human cost of scientific misconduct. Article tools * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg In the dark story of Marc Hauser, the evolutionary psychologist who was last week revealed to have committed scientific misconduct, there is perhaps one bright light: the courage of the young researchers who alerted the university to their concerns over how the professor was interpreting his data. Hauser is a star in his field and an intellectual celebrity. Members of his lab at Harvard University in Cambridge, Massachusetts, took a huge professional risk to raise complaints against such a formidable figure. Graduate students and postdocs are often in the best position to witness misconduct. Unfortunately, their careers are also the most vulnerable to collateral damage from such transgressions, particularly when the accused is a mentor. A young scientist's reputation is tethered to the successes and failures of his or her adviser, and when that adviser is accused of misconduct, trainees can also be viewed with suspicion. The dozens of graduates and postdocs who have passed through Hauser's hands now face an uncertain future. Some have had to switch labs. Others are ready to look for faculty positions, but don't know how to explain their status to hiring committees. Should they openly discuss Harvard's three-year investigation? Some are new faculty members anxiously applying for grants. How should they list their publications with Hauser? When will it be safe for them to submit papers co-authored with him? These are the dilemmas that play out behind the headlines in nearly every misconduct case. In the days following the first reports of the Hauser investigation in mid-August, Harvard's refusal to release its findings only increased the pressure on these young scientists. The university offered no clues as to whether other researchers or publications would be implicated. Fortunately, the silence did not last, and on Friday Harvard released a summary of the conclusions reached by its internal investigation. The report found problems with the way that Hauser, whose work connects the observed behaviour of non-human primates to the evolution of key human characteristics such as morality, handled data and reported results. The university's statement stressed that Hauser alone was responsible for the eight instances of misconduct uncovered, and listed only three papers tarnished by the discovery. Harvard had been pummelled in the press for its reticence, but it is common and sometimes necessary for universities to sit on the results of internal misconduct investigations. This is particularly true when the case is complex — as they often are — and the findings subject to challenge, or when other researchers have been implicated. Indeed, the US Office of Research Integrity (ORI), which monitors investigations of researchers who are funded by the National Institutes of Health, asks institutions not to make their investigations public until the ORI has completed its own assessment. This can delay a verdict for weeks or even years after the university completes its own investigation. There is a practical reason for this secrecy: if the ORI needs to convene a hearing, the office does not want potential witnesses to be tainted by exposure to prior conclusions. In this case, following two weeks of pressure from scientists and the press, Harvard was right to release key details of its investigation ahead of schedule. The move does not entirely lift the burden on Hauser's young associates, but it can perhaps ease their load until a full account of his misconduct is brought to light. Such relief is a welcome reward. At a laboratory where there are now question marks over both animal and human behaviour, the young researchers acted as true scientists should. Additional data
• Australia's mixed climate
  - Nature (London) 466(7310):1023 (2010)
  Nature | Editorial Australia's mixed climate Journal name:NatureVolume:466,Page:1023Date published:(26 August 2010)DOI:doi:10.1038/4661023bPublished online25 August 2010 A coalition government could be what the country needs to make headway on an emissions policy. Article tools * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg At first glance, there are notable parallels between the outcomes of the Australian general election last weekend and the British election held in May. Both electorates rejected the incumbent party, but failed to endorse the main opposition in sufficient numbers to hand them a majority. As Nature went to press, the power-broking in Australia was yet to resolve into a clear picture of the likely political landscape, although, as in Britain, the expected outcome is a coalition government. Science barely featured in either election, but the issue of climate change lurked behind the scenes. Both elections returned historic representation from the Green party. Australia's politicians have failed its people on climate change. Despite opinion polls that consistently indicated popular support for policies to tackle greenhouse-gas emissions, the country's two main parties have both weakened their stance on the issue of late. The conservative Liberals ousted former leader Malcolm Turnbull last year over his support for a planned emissions-trading scheme, and replaced him with climate sceptic Tony Abbott. Soon after, the Labor party dumped the scheme altogether, followed by Prime Minister Kevin Rudd. The lukewarm approach to climate by his successor, Julia Gillard, seems to have contributed to the electoral success of the Australian Greens. By contrast, Britain's three big parties raced to outdo each other on ambitious climate pledges in the lead-up to the election, a political arms race that leaves the resulting Conservative–Liberal union ahead of much of the public when it comes to support for policies to restrict emissions. However, consistent failure to deliver the promised action over the years shows that the UK model is no guarantee of success. Australia's current political turmoil could yet benefit the climate. A coalition government will be forced to compromise and cooperate, and must look for popular support. Renewed focus on climate change would be a good start. Additional data
• Evolutionary biology: Lice in hiding
  - Nature (London) 466(7310):1024 (2010)
  
• Applied physics: Record data storage
  - Nature (London) 466(7310):1024 (2010)
  
• Neuroscience: Quick mood lift
  - Nature (London) 466(7310):1024 (2010)
  
• Astronomy: Exploding computer models
  - Nature (London) 466(7310):1024 (2010)
  
• Animal behaviour: Genetics and culture clash
  - Nature (London) 466(7310):1024 (2010)
  
• Astronomy: Brown dwarf spotted
  - Nature (London) 466(7310):1024 (2010)
  
• Developmental biology: Live-action embryos
  - Nature (London) 466(7310):1025 (2010)
  
• Cancer biology: Muscling in on cancer
  - Nature (London) 466(7310):1025 (2010)
  
• Neurodegeneration: Cell respiration ruin
  - Nature (London) 466(7310):1025 (2010)
  
• Astronomy: Oldest rock
  - Nature (London) 466(7310):1025 (2010)
  
• Journal club
  - Nature (London) 466(7310):1025 (2010)
  
• News briefing: 20–26 August 2010
  - Nature (London) 466(7310):1026 (2010)
  The week in science. Download a PDF of this article. Policy|Research|Events|Business|Business watch|People|The week ahead|Number crunch|Sound bites Harvard University in Cambridge, Massachusetts, has acknowledged that it has found famed evolutionary psychologist Marc Hauser responsible for eight counts of scientific misconduct. Michael Smith, dean of the Faculty of Arts and Sciences, confirmed the findings in a letter to his faculty on 20 August. Smith cited "problems involving data acquisition, data analysis, data retention, and the reporting of research methodologies and results" in three of Hauser's publications. He did not elaborate further (see Editorial, page 1023). A US district court has blocked the current policy for federal funding of human embryonic stem-cell research. The suit was brought against the Department of Health and Human Services by Christian groups and researchers last August, after US President Barack Obama lifted the previous administration's restrictions on embryonic stem-cell studies (see go.nature.com/RyW82Y). The judge agreed with the plaintiffs, who contend that the research violates federal law by destroying human embryos. See go.nature.com/O341gd for more. Ten months after committing US$230 million to fund 14 research teams developing stem-cell-based therapies (see Nature 462, 22; 2009), the California Institute for Regenerative Medicine in San Francisco has earmarked $243 million to fund 12 more such translational grants. The scheme, approved on 19 August by the state stem-cell agency's governing body, will give out planning grants (for which applications begin in November), before full awards are approved in 2012. As flood surges in Pakistan continued to destroy homes and farmland last week, engineers warned that water diverted from the swollen Indus River was swamping irrigation canals. The practice could affect irrigation infrastructure in the long term, making severe food shortages even more likely over the coming months. Farmland will probably not be ready for rice planting later this year, says Etienne Labande, deputy chief of the Preparedness and Response Branch of the United Nations World Food Programme. See go.nature.com/pZXTJc for more. Almost four decades after construction began, Iran opened its first nuclear reactor on 21 August. The 1,000-megawatt, Russian-built pressurized water reactor is located at a power plant near Bushehr, in southwestern Iran. It is not considered a proliferation risk because Russia will supply the fuel and repatriate the waste that the plant produces. Engineers have begun to load the reactor with fuel, and the process should be completed by early September. Extra data can be more of a hindrance than a help, according to the Journal of Neuroscience. In a notice published in its 11 August issue, editor-in-chief John Maunsell announced that the journal won't be accepting supplementary material for review, nor including it online with papers it publishes (see go.nature.com/Xs7sX6). Maunsell says that a massive influx of supplementary material was making peer review difficult. The journal will go back to basics from 1 November. The European Space Agency (ESA) is working to regain data transmission from its gravity-field and steady-state ocean circulation explorer satellite (GOCE). Since launching in 2009, the low-flying satellite has mapped Earth's gravity, providing data sets that can be used for global estimates of sea level and improved models of ocean circulation. It emerged last week that ESA suspended telemetry in July while troubleshooting GOCE's computer systems. Project scientists are patching software and hope to resume transmitting data by mid-September. The US National Institutes of Health has announced the details of a US$10-million project to study the long-term health effects of the oil spill in the Gulf of Mexico. From October, researchers will start recruiting people who live in the nearby community, or who were involved in the clean-up operation, to take part in the study. They hope to monitor the cardiovascular, respiratory, reproductive and mental health of around 50,000 people. AP/PRESS ASSOCIATION IMAGES Japan's mission to study an asteroid suffered many technical glitches, but its much publicized troubles have only helped its celebrity status. The Japanese space agency (JAXA) says that more than 100,000 people have crowded into exhibitions throughout the country to see the plucky Hayabusa spacecraft's recovery capsule (pictured), which may have returned with a dust sample. Fans have also paid tribute to the craft in online music videos (see go.nature.com/dukEgl). The capsule's next appearance is at a Tokyo museum on 26 August. JAXA has not yet announced whether the mission succeeded in bringing asteroid dust back to Earth. Research-services giant Life Technologies of Carlsbad, California, announced on 17 August that it plans to acquire start-up gene-sequencing company Ion Torrent, based in Guilford, Connecticut, for US$375 million in cash and stock. The start-up's shareholders are eligible for another $350 million if it meets certain milestones by the end of 2012. Ion Torrent's sequencing machines use semiconductor chips to detect hydrogen ions that are released as nucleotides are added to a DNA strand. The machines, which Life Technologies plans to launch later this year, will cost less than $100,000, making them accessible to researchers as well as diagnostic labs. The United States needs to revamp its system for quickly producing medicines and supplies in response to medical emergencies, says a report released on 19 August by the Department of Health and Human Services. The review was commissioned last year, when the country struggled with vaccine production during the flu pandemic. It recommends boosting the science and regulatory capacity of the Food and Drug Administration, as well as providing support for small biotech companies, which are often first to heed the call of medical emergencies but have trouble attracting investors to fund their therapies. SOURCE: LUX RESEARCH The United States, Japan and Germany together accounted for 65% of worldwide government funding and corporate investment in nanotechnology in 2009, according to an 18 August report from Lux Research, a business consultancy in Boston, Massachusetts. US government and corporations spent the most: US$2.5 billion and $3.2 billion, respectively (see graph). US-based researchers were also awarded the largest number of patents, 2,378, by a wide margin. The country takes top spot in nanotech research and development not just because of healthy government funding, but also because of its strong private sector, robust patenting system and a culture of innovation, says David Hwang, a research associate at Lux. "With Germany, Japan and South Korea, it doesn't look like their growth rates are so much faster than the United States that they're going to overtake it any time soon," he says. Although nanotechnology research publications generally correlate with funding, last year Chinese scientists put out 13,049 papers to the United States's 11,818. Still, Hwang says that China seems to be focusing more on manufacturing than on nanotech innovation. But as it develops its private sector and shores up its patenting system, China has a good chance of overtaking the United States in the next 10–20 years, Hwang says. REUTERS Four mathematicians were awarded the Fields Medal, the discipline's most prestigious prize, on 19 August at the quadrennial International Congress of Mathematics, held this year in Hyderabad, India. Elon Lindenstrauss, of the Hebrew University of Jerusalem, won for his work on ergodic theory; Ngô Bảo Châu (pictured, above right), who works at the Institute for Advanced Study in Princeton, New Jersey, for his proof of the Fundamental Lemma; Stanislav Smirnov, of the University of Geneva, Switzerland, for his work on lattice models in statistical physics; and Cédric Villani, of the École Normale Supérieure in Lyon, France, for his work on the Boltzmann equation. Lawrence Tabak will become the new principal deputy director of the National Institutes of Health (NIH) in Bethesda, Maryland. Tabak, who has spent the past ten years as director of the NIH's dental research institute, will become the number-two official at the US$31-billion agency. His research focuses on the biosynthesis and function of mucin glycoproteins. Tabak also oversaw the recent reshaping of the NIH's peer-review system, and shepherded through the spending of $10.4 billion in agency economic-stimulus funds. He replaces Raynard Kington, who became president of Grinnell College in Iowa on 1 August. Five teams of neuroscientists compete to find the best computer algorithms for mapping a nerve cell in three dimensions. The finals of the Diadem Challenge take place at the Howard Hughes Medical Institute's Janelia Farm Research Campus in Ashburn, Virginia. → http://diademchallenge.org The effects of acupuncture and studies of pain in newborns are on the agenda of the 13th World Congress on Pain in Montreal, Canada. → go.nature.com/KObh8T The InterAcademy Council will release its eagerly awaited review into the processes and procedures of the Intergovernmental Panel on Climate Change (IPCC). It will deliver its report to IPCC chair Rajendra Pachauri and UN secretary-general Ban Ki-moon in New York City. → go.nature.com/fbSFDo Number of days that a colony of cyanobacteria from Britain's sea cliffs survived in space — the record for a fully functional photosynthetic organism. Source: BBC News Bob Brown, Australian Greens party leader, on the election of six new Greens senators to Australia's upper house on 22 August (see Editorial, page 1023). Source: Sydney Morning Herald 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.
• Big science feels the pinch in Europe
  - Nature (London) 466(7310):1028 (2010)
  Financial hard times in member states are fuelling calls for budget savings across the board. Researchers at CERN have been asked to hunt high and low for budget cuts.C. MARCELLONI/M. BRICE/CERN Long insulated by multi-year budgets and treaties, Europe's multinational research organizations and the glittering scientific projects they fund are finally feeling the financial pain of their member states. This week, representatives from the 20 nations involved in CERN, Europe's particle-physics laboratory near Geneva, Switzerland, meet to discuss budget cuts for the laboratory over the next five years. In the next few months, Nature has learned, other organizations are facing decisions on whether to delay new projects, put upgrades on hold or make cuts in an attempt to appease their struggling member states. "We are all very worried about the financial situation." "We are all very worried about the financial situation," says Francesco Sette, director of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. For decades, the nations of Europe have built impressive scientific facilities through cooperation. Money from across the continent has gone to construct the Large Hadron Collider (LHC), the world's most powerful particle accelerator, which is located at CERN. Similar efforts have created the world-class European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, a series of massive telescopes in the Chilean desert and spacecraft to observe Earth and beyond. Extraordinary measures In the European fashion, financing for these projects is agreed through painstaking, multi­lateral negotiations. Most organizations are overseen by independent councils composed of scientists and bureaucrats from the member governments. Budget negotiations can be long, but usually result in stable funding that stretches years into the future (see 'Steady as they go?'). The organizations operate under treaties that ensure committed funding is rarely pulled, providing an extra level of security. Click for a larger version. At CERN, the budget process often generates debate. But as the organization planned its latest five-year budget this spring, it met un­usually strong resistance from member states, notably the United Kingdom. As a result, the CERN council rejected the five-year budget and asked the laboratory to come up with a plan to save money. The new strategy will be discussed at an extraordinary meeting of the organization's financial council on 25 August and includes plans to suspend activities at CERN's smaller accelerators during a 2012 shutdown of the LHC, delay renovating the lab's ageing buildings, and slow down development of the Compact Linear Collider advanced accelerator technology. "CERN is in some sense a bellwether," says John Womersley, director of science programmes at the UK Science and Technology Facilities Council, which oversees many of Britain's subscriptions to international research bodies. Britain's newly elected coalition government is planning deep cuts in public spending to cope with a growing budget deficit, and Womersley says that his council is facing a difficult choice: fund projects abroad or support scientists at home. In the coming months, as more of Europe's treaty organizations bring budgets up for review, Womersley says that Britain will be calling for tough savings across the board. The United Kingdom is usually the third-largest contributor to cooperative efforts, behind France and Germany, and its hard line is creating difficulties. At the synchrotron facility in Grenoble, Sette says that the British delegation to the governing council has asked it to outline the consequences of three scenarios: a flat budget, a 10% cut and a budget for minimal operations. The timing couldn't be worse for the ESRF, which is just embarking on a seven-year, €100-million (US$127-million) upgrade to its facilities. "We are today at a very critical stage," he says. "A major cut would imply a complete rethinking of the medium- and long-term strategy for the lab." Britain is not the only European state with financial difficulties. Italy and Spain, among others, are also facing domestic budget crises that are causing trouble. Iain Mattaj, director of the EMBL, says that several countries unexpectedly announced in June that they might have trouble paying their dues in the coming year. Mattaj declined to name which nations were struggling. "The situation is not easy for anyone," says Franco Bonacina, a spokesperson for the European Space Agency in Paris. As a result of the downturn, the agency has decided to put its plans for new missions largely on hold. Fresh projects are normally agreed during triennial meetings of research ministers, but there will be no meeting in 2011. Instead, the agency hopes that a lower-key delegation can approve two critical starts — an extension to the International Space Station programme until 2020, and funding to develop the next generation of the Ariane 5 rocket. A stimulating solution Not all plans for the future are on hold, however. Budget cuts have "never been something that's been asked of us," says Colin Carlile, director of the European Spallation Source, a new neutron-scattering facility to be located in Lund, Sweden. Carlile says that the Scandinavian member states who originally backed the Lund site have so far remained committed, as have other partners, including Spain. At present, the €1.5-billion facility is still on track to begin construction in 2013, he says, noting that the distant start date has insulated his group somewhat from the current financial problems. Tim de Zeeuw, director-general of the European Southern Observatory, headquartered in Garching, Germany, says that in the next financial year he plans to ask for funds to start developing the European Extremely Large Telescope, a 42-metre-diameter behemoth. De Zeeuw points out that much of the telescope's €1-billion budget will go to high-tech companies in Europe, which will design its optics and instrumentation. "If we want to stimulate our economy, this is a fine way of doing it," he says. ADVERTISEMENT Womersley says that Britain hopes to participate in the new telescope, although the fiscal realities the country now faces may prove to be an obstacle. More generally, he hopes that Europe's patchwork of international partnerships will be able to negotiate the crisis. "We certainly don't want to see long-term damage to the future prospects of these organizations," he says. 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.
• Sugar synthesis speeds up
  - Nature (London) 466(7310):1029 (2010)
  Automated synthesizers can make complex carbohydrates on demand. When biologists need a particular peptide or strand of DNA, they ask a machine to make it for them. Automation gives fast, inexpensive access to these molecules, and it has helped turbocharge biology. But constructing complex carbohydrates from sugar building blocks still needs expert chemists, with researchers spending weeks — and tens of thousands of dollars — forging molecules by hand. Two groups of chemists now say they have independently developed automated carbohydrate synthesizers with the aim of making the molecules on demand. One machine is already churning out carbohydrates for clients, and the other will be available for labs to buy next year. Advocates say the machines could unplug a major bottleneck in the field of glycobiology, which studies the sugar chains (glycans) present on many proteins and lipids. The main problem with carbohydrate synthesis is that sugar building blocks attach to each other in myriad ways to create a dazzling variety of branched structures — in contrast to peptides, which are made from a linear chain of amino acids linked by identical chemical bonds. Making the right carbohydrate means avoiding all the unwanted possibilities. Click for a larger version. In 2001, chemist Peter Seeberger, who now directs the Max Planck Institute of Colloids and Interfaces in Potsdam, Germany, published the outline of a carbohydrate synthesizer that attached sugars one by one to a resin-linked chain (O. J. Plante, E. R. Palmacci and P. H. Seeberger Science 291, 1523–1527; 2001). The idea was based on solid-phase peptide synthesis, which won biochemist Bruce Merrifield the Nobel Prize in Chemistry in 1984; the resin holds on to the growing peptide or carbohydrate chain, with unreacted building blocks being washed away. But many researchers believed the chemistry behind Seeberger's proposal would be too complicated to be reliable, and the number of different sugars needed too great to manufacture. So Seeberger has spent the past decade completely remodelling his machine — overhauling the chemistry that links the sugars to the resin, for example. Commercial machines will be available next year, he says. The device is being tested at Leiden University in the Netherlands and the University of Alberta in Edmonton, Canada. It is also being used by Ancora Pharmaceuticals, based in Medford, Massachusetts, a company co-founded by Seeberger to design and test carbohydrate-based vaccines. Seeberger says that 90% of known mammalian carbohydrates can be constructed using just 35 building blocks, which he plans to supply in bulk. Seeberger presented the early fruits of research using his machines at this week's American Chemical Society meeting in Boston, Massachusetts. For example, he is imaging sugar-covered bacterial cells — and targeting drugs at them — by attaching a variety of glycans to nanoparticles. ADVERTISEMENT Not everyone thinks Seeberger's technology is currently versatile enough to make a wide range of carbohydrates on demand. "I don't think the chemistry is sufficiently well developed," says Geert-Jan Boons at the University of Georgia in Athens. But it could build libraries of carbohydrates using well-established synthetic routes, he adds. Meanwhile, a complementary system is already delivering shorter carbohydrates than those targeted by Seeberger. Developed by Nicola Pohl of Iowa State University in Ames, it uses a hydrophobic fluorocarbon tag, rather than a resin, to anchor growing sugar chains in solution. Pohl's company, LuCella Biosciences in Ames, has been filling orders to build carbohydrates since November 2009. Pohl hopes that automated machines will persuade more biologists to study glycans rather than being deterred by their complexity. "A lot of our early work is about educating the biologists that these carbohydrates are now readily available," she says. 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.
• G-whizzes disagree over gravity
  - Nature (London) 466(7310):1030 (2010)
  Recent measurements of gravitational constant increase uncertainty over accepted value. A model of Henry Cavendish's torsion balance (left) and its latest successor, a laser interferometer.SCIENCE MUSEUM; H. PARKS/JILA The Newtonian constant of gravitation — known in the finely tuned business of metrology as 'big G' — has come a long way since British physicist Henry Cavendish first measured the gravitational attraction of Earth in 1798. Although G derived from Cavendish's measurements had an uncertainty of about 1%, modern measurements have tightened that to just a couple of tens of parts per million. But the relentless honing of G may have hit a stumbling block. Two recent experiments are in striking disagreement with earlier findings, and the overall uncertainty in the value of the constant may be set to increase. In Newton's equations of gravity, G represents the size of the gravitational force. The constant is involved in the quest to unify the theories of gravity and quantum mechanics, and efforts to determine G have contributed to progress in areas of experimental physics: elements of the apparatus first developed to measure the constant, for example, are now used in gravitational-wave detectors. But for some researchers, measuring G is an end in itself. "It's the ultimate precision experiment," says James Faller, a physicist at the University of Colorado at Boulder. Metrologists have traditionally measured G using a torsion balance — a rod suspended from a wire. When masses are placed near the ends of the rod, their minute gravitational pull causes it to rotate by an amount proportional to G. In 2000, Jens Gundlach and Stephen Merkowitz at the University of Washington in Seattle used a new torsion-balance method to make the most precise measurement to date1: 6.674215 × 10−11 cubic metres per kilogram per square second, with an uncertainty of 14 parts per million (p.p.m.). But that value is being challenged by two different methods that have now been developed to a level of precision comparable to Gundlach and Merko­witz's. In a paper accepted by Physical Review Letters2, Faller and Harold Parks at Sandia National Laboratories in Albuquerque, New Mexico, used a laser interferometer to measure the displacement of pendulum bobs by various masses. Their result (6.67234 × 10−11 m3 kg−1 s−2, with an uncertainty of 21 p.p.m.) is an enormous 10 standard deviations lower than the value measured by Gundlach and Merko­witz. And in a paper3 published in 2009 in Physical Review Letters, researchers led by Jun Luo of Huazhong University of Science and Technology in Wuhan, China, measured G by comparing the time it took for a torsion pendulum to swing past masses placed at varying distances from it. They obtained a value of 6.67349 × 10−11 m3 kg−1 s−2, with an uncertainty of 26 p.p.m., about three standard deviations be! low Gundlach and Merkowitz's value. Metrologists had expected much smaller disagreements among the results — probably no more than a couple of standard deviations. Stephan Schlamminger of the University of Washington, who measured G while at the University of Zurich in Switzerland and reported4 a result consistent with that of Gundlach and Merkowitz, says he cannot explain the inconsistency. It may be down to systematic error, which is why it is so important to measure G in a variety of ways, he says. "People are obviously overlooking effects and not taking that into account in their experiments," adds Barry Taylor of the National Institute of Standards and Technology in Gaithersburg, Maryland. ADVERTISEMENT The latest results mean that the Paris-based Committee on Data for Science and Technology (CODATA), which recommends values of physical constants every four years (see 'A changing constant'), will probably revise G in its next set of values, finalized in early 2011. "Those new values will pull the value down," says Taylor, who sits on the committee. "The final uncertainty will be the same or larger." Faller says the fear of being wrong can cause investigators to wait many years before publishing results that don't agree with previous measurements. He and Parks ran their experiment in 2004, and have spent the time since then searching for effects they might have missed. But he's sure their measurement is sound: "I feel like I've checked everything and I have to wash my hands." * References * Gundlach, J. H. & Merkowitz, S. M. Phys. Rev. Lett.85, 2869 (2000). | Article | PubMed | ISI | ChemPort | * Parks, H. V. & Faller, J. E. Phys. Rev. Lett.http://xxx.lanl.gov/abs/1008.3203 (2010). * Luo, J. et al. Phys. Rev. Lett.102, 240801 (2009). | Article | PubMed | ChemPort | * Schlamminger, S. et al. Phys. Rev. D74, 082001 (2006). | Article | ChemPort | 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.
• Key Alzheimer's findings questioned
  - Nature (London) 466(7310):1031 (2010)
  Conflicting results cloud link to prion protein. Plaques can destroy nerve cells and cause the brain to shrink in Alzheimer's disease (left) — but how?PASIEKA/SPL When Stephen Strittmatter discovered an unexpected link between key proteins in two devastating brain maladies1 — Alzheimer's disease and Creutzfeldt–Jakob disease (CJD) — researchers in the field agreed that he was on to something big. But a year on, conflicting results, including findings published in Nature this month2, have clouded that rosy picture and highlight the challenge faced by researchers seeking a way to arrest Alzheimer's disease progression. Strittmatter, a neurologist at Yale University in New Haven, and his team were trying to understand how the protein fragment amyloid-β causes damage when it forms plaques in the brains of people with Alzheimer's disease. They found that cellular prion protein, whose abnormal, infectious form is infamously associated with CJD, can bind readily to amyloid-β, suggesting that it may act as a receptor that kicks off a chain of events leading to neuronal destruction1. "It really was a spectacular finding," says Bart De Strooper, who studies neurodegenerative diseases at the Catholic University of Leuven in Belgium. So far, therapies that directly target amyloid-β have not performed well (see 'Clinical trial disappoints'). The prospect of targeting prions instead was a cause for excitement. "It could make a fast jump to a real therapy, if it were a real target," says Dominic Walsh, who studies Alzheimer's disease at University College Dublin. But the disparate experimental methods used by researchers often lead to contradictory conclusions. "There's just a history of this in the field," says Roberto Malinow, an electrophysiologist at the University of California, San Diego. "There are these spectacular results and they have a half-life of six months to a couple of years." Strittmatter and his team speculated that the prion protein, which is present on the surfaces of neurons, might activate a cell-damaging pathway when bound and activated by amyloid-β. To test that idea, they injected amyloid-β into mice and measured the electrical changes that take place in the brain during memory retrieval. The electrical signatures were unaffected in mice that lacked the prion protein — suggesting that the prion protein mediates damage caused by amyloid-β. Yet when others in the field rushed to build on the work, the results differed. Gianluigi Forloni, an Alzheimer's researcher at the Mario Negri Institute for Pharmacological Research in Milan, Italy, and his team also injected amyloid-β into mice lacking the prion protein, but found that the mice suffered memory deficits even in the absence of the prion protein3. In Switzerland, Adriano Aguzzi, a prion-protein researcher at University Hospital Zürich, and his group reached the same conclusion4 using mice that were genetically engineered to produce copious amounts of amyloid-β. And Malinow and his colleagues closely replicated the brain measurements of Strittmatter and his team, but failed to replicate their findings2. Strittmatter cautions that differences in the groups' animal models, memory tests and methods of preparing and administering amyloid-β may explain the conflicting results. Forloni takes a more negative view. "If it depends so much on the original experimental conditions, then the findings become no longer necessarily relevant." In more recent work5, Strittmatter and his colleagues report that a lack of prion protein staved off memory loss due to amyloid-β accumulation in mice that are genetically different from those that Aguzzi used. And in July, a team lead by Michael Rowan, a neuropharmacologist at Trinity College Dublin, reported at the Federation of European Neuroscience Societies meeting in Amsterdam that antibodies that block access to the prion protein could reduce the effect of amyloid-β on electrical changes in the brain associated with memory, backing up the findings of Strittmatter and his team. ADVERTISEMENT Conflicting results are common in Alzheimer's disease research, says Sangram Sisodia, a neurobiologist at the University of Chicago in Illinois. Animal models are particularly contentious, he notes, because there is no single model that is universally perceived to be the best system in which to study the disease. And because each lab has invested its time, effort and reputation into its particular model system, this is unlikely to change, he adds. A consortium organized by the Cure Alzheimer's Fund, based in Boston, Massachusetts, is trying to unite members of the competitive and often contentious field. "But in terms of standardizing experimental approaches, that is a long ways off," says Sisodia. "I just don't see that happening." * References * Laurén, J. et al. Nature457, 1128-1132 (2009). | Article | PubMed * Kessels, H. W., Nguyen, L. N., Nabavi, S. & Malinow, R. Nature466, E3-E4 (2010). | Article | PubMed * Balducci, C. et al. Proc. Natl Acad. Sci. USA107, 2295-2300 (2010). | Article | PubMed * Calella, A. M. et al. EMBO Mol. Med.2, 306-314 (2010). | Article | PubMed * Gimbel, D. A. et al. J. Neurosci.30, 6367-6374 (2010). | Article | PubMed | ChemPort | 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.
• Battle to degas deadly lakes continues
  - Nature (London) 466(7310):1033 (2010)
  Funding shortage is biggest hurdle for those striving to disarm three rare but lethal geological hazards. A plume of gassy water spewing from Lake Nyos.M. HALBWACHS After nearly a decade, a scheme to suck a deadly build-up of carbon dioxide out of Lake Nyos is nearing its final stages, say project scientists. But two other African lakes may still harbour serious dangers — now or in the future. Located in a volcanic crater in a remote area of Cameroon, Lake Nyos captured the world's attention in 1986, when an explosive release of CO2 from the lake's depths asphyxiated 1,700 people in the surrounding villages. Gas had been seeping into the lake over decades or possibly centuries from the magma deep below. The dense, gas-filled water had been trapped in a layer near the lake bottom until an event, perhaps a landslide or heavy rainfall, stirred the lake and triggered release of the gas — a limnic eruption. The mass suffocation drew attention to a rare but lethal natural hazard and prompted scientists to consider ways of reducing the risk of it reoccurring. In 2001, a team led by the physicist and engineer Michel Halbwachs, then of the University of Savoie in Chambéry, France, inserted a long pipe into the middle of Lake Nyos and started to siphon up the gassy water from the lake depths. The siphoned water releases its CO2 as it spews champagne-like from the top of the pipe, then falls harmlessly back onto the lake. In this way, the size of the gas-charged layer below and the risk it poses steadily decrease. Despite setbacks, the basic strategy is working, says Halbwachs, who is now head of the gas-extraction company Data Environnement, based in Chambéry. But one pipe makes for a slow extraction, leaving villagers at risk. The plan called for more pipes to be installed, but funds were not forthcoming. After campaigning for more than a decade, Halbwachs says that he has secured donations of €1.4 million (US$1.8 million) from the United Nations Development Programme for two more pipes, which he hopes to deploy in Lake Nyos between November 2010 and February 2011. "The long delay is normal with international donors," says Halb­wachs, who estimates that new pipes should make the region around Lake Nyos safe from a limnic eruption within 5 years. Click for a larger version. "This is a big success story," says George Kling, a biogeochemist at the University of Michigan in Ann Arbor who has been studying the lake for decades. But he worries that the schedule may slip again. "I've heard lots of dates before about when the pipes are actually going in," he says. "For the sake of the people there, I hope something gets done sooner rather than later." Kling adds that other lakes still pose a threat. "We haven't solved all the problems. We need to remind government officials that scientists are still worried." At nearby Lake Monoun, where a similar limnic eruption killed 37 people in 1984, a pipe that Halb­wachs has been operating since 2003, along with two more added in 2006, has succeeded in degassing the deep waters. Halbwachs has declared the lake safe. But Kling suggests that new problems may lie ahead. Now that years of siphoning have effectively eliminated the separation of the lake's waters into layers, new gas entering from the lake bed could mix into a larger volume of water than before. According to Kling, it is harder to deal with more gas at a lower concentration because the gas pressure is insufficient to drive water up the pipes. Takeshi Ohba, a geochemist at Tokai University in Hiratsuka, Japan, is in the process of securing more than $4 million, half from the Japan Science and Technology Agency and half from the Japan International Cooperation Agency, to help create a more permanent solution for Lake Monoun. His team plans to visit the area in February 2011 to help train local scientists and develop a pump that can extract the gassy bottom waters. The problems are different at Lake Kivu, which borders Rwanda and the Democratic Republic of the Congo. Lake Kivu's deep waters hold CO2 and methane. Several commercial projects are under way to extract the methane and turn it into energy (see Nature 460, 321–323; 2009). So far, one 4‑megawatt power plant is up and running. A 3.6‑megawatt plant, which Halbwachs is heading up, has been rebuilt after the first collection platform sank in 2008. This plant was trialled successfully in June this year but is not yet in operation. Both are small demonstration projects compared with what may come: several hundred-megawatt-scale plants are being planned. ADVERTISEMENT Most of Lake Kivu is relatively stable, with the gas-rich waters sitting below 330 metres. But local regulations are urgently needed, says Kling, to ensure that the degassed water from the planned full-scale power plants is returned to the lake at places where it won't stir up the deep layers, increasing the risk of eruption. Care must also be taken not to threaten the resident fish — an important local food source — by disturbing nutrient and oxygen levels. A far greater threat lurks in the Gulf of Kabuno, which is connected to Lake Kivu by a narrow strait and holds a dangerous amount of gas just 12 metres below its surface. The World Bank has pledged $3 million to degas the gulf, but Halbwachs says his company would need perhaps $2 million more before work could start. "It contains ten times more carbon dioxide than Nyos and is located in a very populated area," says Halb­wachs. 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.
• Nuclear theory nudged
  - Nature (London) 466(7310):1034 (2010)
  Results from mothballed facility challenge established theory. Fund-starved ORELA could still spring a surprise.DOE, ORNL For 40 years, physicists at the Oak Ridge Electron Linear Accelerator (ORELA) at Oak Ridge National Laboratory in Tennessee fired bursts of neutrons at various targets to probe the structure of atomic nuclei. Now, with the facility effectively mothballed by a shortage of funds, a newly published result based on data gathered at ORELA has challenged a well-established theory of the nucleus. Independent experts say that further measurements should be made to follow up the tantalizing claim, which would involve putting the facility back on line. In 2002, Oak Ridge physicist Paul Koehler and his colleagues used the neutron beam to measure 'neutron resonances' in each of four different isotopes of platinum. The resonances are particular energies at which the neutrons are especially likely to be absorbed by the platinum nuclei. The motion of protons and neutrons inside the platinum nuclei affects the pattern of resonances. And according to random matrix theory, a mathematical theory that for decades has been crucial for calculating the behaviour of large nuclei, those motions should be chaotic. Yet, as Koehler and his colleagues report this month in Physical Review Letters (P. E. Koehler et al. Phys. Rev. Lett. 105, 072502; 2010), their analysis of the ORELA data found no sign that the nucleons in platinum were moving chaotically. By looking at the strength of the resonances, rather than just their spacing, the group rejects the applicability of random matrix theory with a 99.997% probability. Instead, the nucleons seem to move in a coordinated fashion. "There's no viable model of nuclear structure that could explain this," says Koehler. The resolution of the puzzle could have practical implications, as random matrix theory is currently used to estimate the probability that escaping neutrons will collide with nuclei, and from this to calculate the amount of shielding needed in nuclear reactors and stockpiles. "Engineers build in some extra shielding to cover the uncertainty, but if you were building 100 nuclear reactors you'd want the precision," says Gary Mitchell of North Carolina State University in Raleigh, co-author of a recent review article on random matrix theory (H. A. Weidenmüller and G. E. Mitchell Rev. Mod. Phys. 81, 539; 2009). Mitchell adds that further experiments on nuclei other than platinum are urgently needed to determine whether the theory has truly broken down in this experiment, as Koehler and colleagues suggest, or whether — as Mitchell suspects — the shape of the platinum nucleus is unusual in some way that would account for the result. "There's a lot of good physics we could do if we could run." Oriol Bohigas of the University of Paris-South, a leader in the field of random matrix theory, also recommends additional measurements. He says Koehler and his colleagues need to repeat measurements made at Columbia University in New York in the 1970s, which first contributed to the theory's acceptance, in order to see whether modern instruments and data-analysis methods give the same results. But additional measurements at ORELA seem unlikely. "It hasn't been adequately funded and it's on standby," says Jim Beene, director of the Physics Division at Oak Ridge National Laboratory. According to the US Department of Energy, Koehler and Beene received US$105,998 from the department's Office of Science for ORELA operations in fiscal year 2009, only about a tenth of what the researchers have said would be needed to run it. Beene explains that with the demise of the US fast-reactor programme in the 1980s, direct funding for ORELA dried up; the energy department says that other research efforts are a higher priority for the nuclear-science community. ADVERTISEMENT According to Koehler, the only other place in the world where similar measurements could be made is at the Geel Electron Linear Accelerator (GELINA) at Geel in Belgium, which has a flux, energy resolution and source brightness to rival ORELA. But, Koehler says, he'd love to take additional measurements himself. "There's a lot of good physics we could do if we could run," he says. 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.
• Genetics: Pet project
  - Nature (London) 466(7310):1036 (2010)
  Stymied in the search for genes underlying human neuropsychiatric diseases, some researchers are looking to dogs instead. David Cyranoski meets the geneticist's new best friend. Download a PDF of this story. Solo takes a double dose of Xanax (alprazolam) for his nerves during the 4 July festivities in the United States. That is in addition to the antidepressant, fluoxetine or amitriptyline, that the 11-year-old border collie takes year-round. Fireworks just set him off, as do thunderclaps, gunshots — practically any explosive sounds — sending him into nervous fits. Panting and drooling with eyes dilated, he desperately searches for a place to hide. If another dog is nearby, he might attack. "It's called anxiety redirection," says Melanie Chang, Solo's owner and an evolutionary biologist at the University of Oregon in Eugene. As a postdoctoral researcher at the University of California, San Francisco, Chang helped to collect hundreds of border-collie DNA samples, including Solo's, as part of a project studying the genes for noise phobia. She estimates that at least 50% of collies suffer from it, with 10% severely affected, sometimes injuring themselves or others in response to loud noises. Steven Hamilton, a psychiatrist at the University of California, San Francisco, who runs the project, says that he sees parallels between the dogs' panic and human anxiety. And the same drugs work in about the same proportion of cases for man and beast. "It is easy to see similarities," he says. A growing number of projects like Hamilton's are underway to both help suffering dogs and untangle the roots of human neuropsychiatric disease. The hunt for genes causing psychiatric problems in humans has been "hard work with slim pickings", says Jonathan Flint, a geneticist at the Wellcome Trust Centre for Human Genetics in Oxford, UK. This is partly because human genomes are complex and these disorders are hard to diagnose consistently. But owing to 200 years of selective inbreeding, dogs have a bevy of breed-specific behaviours, and their genomes make it relatively easy to track down the genes responsible. "They are the only naturally occurring models of psychiatric disorders, and perfect for genetic mapping and cloning. It's just beautiful," says Guoping Feng, a mouse geneticist at the Massachusetts Institute of Technology in Cambridge, who is setting up collaborations with dog researchers. "Dogs are the only naturally occurring models of psychiatric disorders." Border collies were bred to herd grazing animals and to hear the calls of their masters from great distances. This, some have reasoned, might have produced hearing so sensitive that loud noises overwhelm some of the animals — inducing something akin to an anxiety disorder in humans. "In general, a lot of anxiety probably resulted from a long period of selection for dogs that can respond to human social cues," says Chang. The provenance of other traits is less clear. Dobermann pinschers, for example, were bred to be faithful watchdogs but often have fixations and quirks akin to obsessive–compulsive behaviour. And Dalmatians, bred for speed and endurance — probably so they could run with horses — tend to be aggressive. Click for a larger version.J. DANIELS/ARDEA.COM Whether certain canine conditions arose by chance or are an unintentional outcome of selection for a specific quality is a matter of speculation. But behaviour problems are definitely frequent. Nicholas Dodman, an animal-behaviour specialist at Tufts University in North Grafton, Massachusetts, estimates that, at minimum, 40% of the 77.5 million dogs owned in the United States have some kind of behavioural disorder. Pet pharmaceuticals, including psychotropic drugs, are a thriving market. And sadly, many dogs with such problems are euthanized as a result of their temperament. Researchers have good reason to believe that dogs will give up their genetic secrets more easily than humans. A study this year, for example, showed that variants at six locations in the dog genome could explain 80% of the variation in dog body size1. In contrast, 294,831 common human variants, considered simultaneously, explained only 45% of height differences between humans2. But if the genetics of height is so different in dogs and humans, one might wonder why the genetics of anxiety, compulsion or aggression would be similar. Patrick Sullivan, a geneticist at the University of North Carolina in Chapel Hill, says that "behaviour that appears intriguingly similar in human and another species could have a completely different genetic architecture", meaning that the same trait could map to different genes or to different parts of the brain. Proponents of canine studies suggest, however, that dog genes might hint at the pathways involved in human disease, and that might be enough. Sleeping dogs don't lie At least one success story shows that studies in dogs can lead to answers in humans. For decades, researchers vainly sifted through the DNA of human narcoleptics to find the genes behind the sleep disorder. But many genes were involved, environmental factors were inconsistent and no clear mechanism emerged. "People were arguing whether it was an autoimmune disease, but no one knew what to do next. It was too difficult," says Emmanuel Mignot, a sleep researcher at the Stanford University School of Medicine in Redwood City, California, with a background in molecular pharmacology. But Dobermann pinschers are often susceptible to narcolepsy, and they held the key. In 1989, Mignot started to use classical genetic techniques to breed narcoleptic Dobermanns and trace the inheritance pattern of the disorder. Without the benefit of modern genetic and genomic tools it took him ten years to zero in on the mutation that caused the disease, in a gene called hypocretin receptor 2 (ref. 3), which regulates the brain's uptake of the neurotransmitter hypocretin, also known as orexin. Click for a larger version.J. DANIELS/ARDEA.COM Mignot did not find the same mutation in the corresponding human gene, but he did find changes in the hypocretin pathway4. "We started to measure hypocretin in cerebrospinal fluid. In narcoleptics, it was gone. It was striking," says Mignot. Researchers are homing in on human gene mutations that lead to hypocretin depletion and to narcolepsy5, and drug companies are targeting hypocretin as a possible lead in the search for insomnia treatments. Same dogs, new tricks Since Mignot published his studies, the canine genome has been sequenced6. That has ultimately allowed researchers to quickly and easily compare the genomes of hundreds of dogs by looking at single nucleotide polymorphisms (SNPs) — single-letter changes in the genome that act as markers for inherited blocks of DNA. The genome-wide association studies (GWAS) that researchers can carry out using these markers are much simpler in dogs than in humans. Most dog breeds are extremely homogeneous; individual animals in the same breed share significantly larger DNA blocks than are shared by any two humans. That means that researchers can look at fewer SNPs and fewer individuals to find a block of DNA that associates reliably with a disease7. According to Kerstin Lindblad-Toh of the Broad Institute in Cambridge, Massachusetts, human GWAS might require 5,000 individuals with a trait of interest and 5,000 controls without it to show that the trait is convincingly associated with a particular genome region. Dog studies can sneak by on as few as a hundred cases and a hundred controls. And a study requiring hundreds of thousands of SNPs in humans might need only 15,000 in canines. GWAS have proved successful in finding the genes for several dog traits that are relevant to human diseases, including the bone disorder osteogenesis imperfecta — pinned to the gene causing stubby legs in dachshunds8 — and the autoimmune disease systemic lupus erythematosus, which was shown in a study published this year to be controlled by five separate genes in Nova Scotia duck-tolling retrievers9. And more are coming. Anne-Sophie Lequarré, a veterinarian at the University of Liège in Belgium, coordinates the European dog-genetics initiative LUPA. The project, started in 2008 with a €12-million (US$15.4-million) budget, brings together some 100 researchers to study single-gene and complex disorders — including cancer, cardiovascular disease and neurological disorders — by genotyping 10,000 dogs. Researchers involved will soon publish findings on two mutations in dog genes that cause disorders corresponding with human disease, says Lequarré: "The first results ! really show that once you find a mutation [related to a disease] in dogs, 90% of the cases involve the same gene in humans." Compulsive disorders may be among the first successes in unravelling human behavioural conditions through dogs. More than 60 studies on genes in mice thought to have a role in human obsessive–compulsive disorder (OCD) have so far failed to find significant, reproducible associations10. But there are lots of dogs with obsessive behaviour. A high proportion of bull terriers, for example, chase their tails relentlessly. Many large-breed dogs, such as Dobermanns, German shepherds, Great Danes and golden retrievers, chew their flanks or lick their legs until they lose hair, develop lesions and in some cases cripple themselves — a habit some compare with obsessive hand washing and other rituals of people with OCD. Click for a larger version.J. BURTON/NATUREPL.COM In January, Lindblad-Toh and Dodman reported a link between canine compulsive disorder and a region on the dog's chromosome 7 (ref. 11). Their study was based on an analysis of 14,700 SNPs in the genomes of more than 90 compulsively chewing Dobermanns and about 70 controls. It linked the behaviour to variations in a 400-kilobase-long stretch of DNA. The connection between the variant that confers risk and the compulsive behaviour is not airtight, but it is good: 60% of the dogs that chewed their flanks, blankets and anything else they could get their teeth on had the variant, compared with 43% of those with milder chewing compulsion and just 22% of those with no signs of compulsive behaviour. One gene in the targeted region has already captured the imaginations of other researchers. CDH2 encodes the protein cadherin 2, which is involved in forming connections between neural cells. Deanna Benson, a neuroscientist at Mount Sinai School of Medicine in New York, says the possibility that cadherins are involved in OCD has inspired others. Feng, who makes mouse models for OCD, is exploring the link. Last autumn, he and Lindblad-Toh struck up a collaboration to find brain circuitry related to compulsion that is shared by mice, dogs and humans. Feng is now knocking out Cdh2 function in specific brain regions of mice to test whether that produces OCD-like behaviours. Dogged progress Lindblad-Toh is now seeking a tighter genetic fit to human OCD. Researchers approach dog genetic studies in two steps: first narrowing in on a large DNA chunk within one breed and then looking for overlap with that region in the DNA of dogs of other breeds with the same disease. Mignot used narcoleptic dachshunds to home in on the mutation expressed by his sleepy Dobermanns. And by comparing DNA loci in flank-sucking German shepherds and tail-chasing bull terriers, Lindblad-Toh hopes to narrow the implicated region on chromosome 7 to a more manageable 10 kilobases. Similarly, Hamilton intends to broaden his noise-phobia studies from border collies to bearded collies and Australian shepherds that show similar anxieties. "For 10,000 years, dog has been man's best friend. Now dog is serving man again by helping us identify genes." But canine genetics is challenged by some of the same issues that have foiled researchers studying human illnesses. Diagnoses for neuropsychiatric disease are slippery. Schizophrenia, for example, could represent a collection of many different disorders, each with separate genetic and environmental triggers. And if the subjects grouped by symptoms have different underlying diseases, GWAS can become confused. "A few dogs can spoil a cohort," says Lequarré. She cites an epilepsy study that was not delivering any significant correlations. The researchers later found that some of the dogs in the disease group actually had a form of late-onset epilepsy that was different from that being studied. "Phenotyping is crucial. You need to have dogs that have exactly the same disease," she says. LUPA is making an effort to clarify diagnosis. To identify neurological disorders consistently, the group selected veterinarians who follow standard procedures in parsing dog temperament. Standardization is the right approach, says Hamilton. For his work on collies, he leads owners through a 24-page questionnaire that elicits objective observations. "We don't ask, 'Is your dog aggressive?' We ask, 'When there is a thunderstorm, what does your dog do?'" LUPA's neurological-disorder division is focusing on aggression in the English cocker spaniel and English springer spaniel, both given to sudden fits of rage. The researchers hope that the studies will identify mutations in genes related to human bipolar disorder, schizophrenia and other mental disorders involving aggression. Click for a larger version.J.-M. LABAT/ARDEA.COM Excitement over dog models has been spreading. At the University of Tokyo's Laboratory of Veterinary Ethology, Yukari Takeuchi has collected DNA samples from 200 Japanese shiba inu and 200 labrador retrievers to look for the genes underlying the former's aggression and latter's lapses in concentration. It could help solve a practical problem, she says. Distracted retrievers do not make good guide dogs, and knowing the gene variant responsible could help breeders to limit the trait in their stocks12. ADVERTISEMENT Whether or not the dog studies live up to their promise for understanding and relieving human suffering, they are sure to benefit pets. Breeders are already taking notice of some of the gene variants that ravage certain breeds. For better and, in terms of scientific research, for worse, through screening and more selective breeding, the next generations of border collies will probably have fewer anxiety-ridden dogs such as Solo who can be studied. But Elaine Ostrander, dog geneticist at the National Human Genome Research Institute in Bethesda, Maryland, is confident that dogs have much to offer human health beyond the pleasure of warm fur and a cold, wet nose. "For 10,000 years, dog has been man's best friend. When we transitioned to hunter-gatherer, when we switched to agrarian, they were there. Now, in the genomic era, dog is serving man again by helping us identify genes," she says. David Cyranoski is Nature 's Asia–Pacific correspondent. * References * Boyko, A. R.et al. PLoS Biol.8, e1000451 (2010). * Yang, J.et al. Nature Genet.42, 565-569 (2010). * Lin, L.et al. Cell98, 365-376 (1999). * Nishino, S. , Ripley, B. , Overeem, S. , Lammers, G. J. & Mignot, E.Lancet355, 39-40 (2000). * Hallmayer, J.et al. Nature Genet.41, 708-711 (2009). * Lindblad-Toh, K.et al. Nature438, 803-819 (2005). * Karlsson, E.K. & Lindblad-Toh, K.Nature Rev. Genet.9, 713-725 (2008). * Drögemüller, C.et al. PLoS Genet.5, e1000579 (2009). * Wilbe, M.et al. Nature Genet.42, 250-254 (2010). * Wang, L. , Simpson, H.B. & Dulawa, S.C.Behav. Pharmacol.20, 119-133 (2009). * Dodman, N. H.et al. Mol. Psychiatr.15, 8-10 (2010). * Takeuchi, Y.et al. Animal Genet.40, 217-224 (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.
• Consumers have a right to affordable genetic testing
  - Nature (London) 466(7310):1040 (2010)
  There is no good reason for people to have access to their personal genetic information only through medical experts, as Arthur Beaudet suggests (Nature 466, 816–817; 2010). Such tests provide an incentive for consumers to learn about genetics and to support genetics research, while encouraging them to make reasonably informed decisions about their health.
• Misconduct: don't assume science is self-correcting
  - Nature (London) 466(7310):1040 (2010)
  Your Opinion pieces propose that research misconduct could be prevented either by financial incentives for teaching research integrity or by informal intervention (Nature 466, 436–4372010 and Nature 466, 438–440; 2010). Weak regulations and admonitions are unlikely to deter a prospective fraudster, as they are easily dodged.
• Misconduct: don't penalize the honest majority of scientists
  - Nature (London) 466(7310):1040 (2010)
  Sandra Titus and Xavier Bosch suggest that scientific misconduct will be solved by "mandatory and frequent" educational classes for all members of institutions that receive government research funding (Nature 466, 436–437; 2010). But it is far from clear that the behaviour of the research community has improved since these classes were introduced.
• Proposals for surface-temperature databank now open for scrutiny
  - Nature (London) 466(7310):1040 (2010)
  Our plan to create a suite of surface-temperature data sets for analysis by the international climate community (Nature 465, 158–159; 2010) is now under way. In the interest of transparency, we announce the publication of 12 white papers that are available until 1 September for public comment through a moderated blog (http://www.surfacetemperatures.org
• Clarifying knowledge ownership in Europe's medicines initiative
  - Nature (London) 466(7310):1040 (2010)
  Research organizations have criticized the intellectual-property policies of the Innovative Medicines Initiative (IMI) — a European public–private partnership to improve pharmaceutical research and development (Nature466, 306–307; 2010). This partly reflects a misunderstanding about how knowledge sharing is handled in collaborations between academia and industry.
• Mosquitoes: schemes to render them extinct are impracticable
  - Nature (London) 466(7310):1041 (2010)
  I was astonished by the hubris of the mosquito experts you interviewed who believe that the ecological consequences of an extinction would be minor, nil or quickly compensated (Nature466, 432–434; 2010). Leaving aside the ethical dilemma and immense technological challenge of extinguishing even one of the many thousands of species of mosquito, our meagre understanding of mosquito biology cannot justify this conclusion.
• Mosquitoes: first evaluate impacts of eradicating them
  - Nature (London) 466(7310):1041 (2010)
  We may find ways to limit or even eradicate certain groups of mosquitoes, and it is wise to evaluate the consequences in advance (Nature466, 432–434; 2010). We played God with smallpox.
• Mosquitoes: retain an ex situ population for ecological insurance
  - Nature (London) 466(7310):1041 (2010)
  You are wrong to dismiss our limited understanding of the consequences of deliberately wiping out 3,500 species of mosquitoes (Nature466, 432–434; 2010).I would not object in principle to some mosquito extinctions, but your arguments need better ecological insight.
• Mosquitoes: just how much biodiversity does humanity need?
  - Nature (London) 466(7310):1041 (2010)
  If a world without mosquitoes (Nature466, 432–434; 2010) would be better for humanity and inflict no more than "collateral damage" on ecosystems, then what else might we reasonably eliminate from the face of the planet — deadly snakes, plague locusts?Never mind that the collateral damage of eradicating mosquitoes might include the loss of a group of pollinators and a primary food source for many species.
• Disasters widen the rich–poor gap
  - Nature (London) 466(7310):1042 (2010)
  New Orleans's recovery five years on from Katrina is a harbinger of how climate change will drive a thicker wedge between the haves and the have-nots, says John Mutter.
• Save your census
  - Nature (London) 466(7310):1043 (2010)
  National censuses and surveys are threatened around the world by high costs and low response rates. The demographic data they yield are too valuable to lose, warn Stephen E. Fienberg and Kenneth Prewitt.
• Last days of the lone astronomer
  - Nature (London) 466(7310):1044 (2010)
  A celebratory account of the Sloan Digital Sky Survey highlights astronomy's culture shift to big science — but at what risk to individual ingenuity, asks Joss Bland-Hawthorn?
• Preserving social difference
  - Nature (London) 466(7310):1045 (2010)
  Every major war causes us to reflect on the meaning of the word civilization. The mayhem over the past decade in what was once Mesopotamia (now Iraq) is particularly provocative because the region is known as the historical birthplace of civilization.
• Japanese view of the natural world
  - Nature (London) 466(7310):1046 (2010)
  According to Japanese Shinto tradition, divine spiritual power infuses animate and inanimate objects, from humans and trees to rivers and rocks. Every pocket of spirit should be celebrated.
• Condensed-matter physics: The dance of electrons and holes
  - Nature (London) 466(7310):1047 (2010)
  How many pairs of electrons and 'missing electrons' can sustain collective motion in a semiconductor? The limits of this electron–hole dance are found by probing the dance floor using ultrashort laser pulses.
• Structural biology: Conservation in vesicle coats
  - Nature (London) 466(7310):1048 (2010)
  Coat proteins of vesicles involved in intracellular membrane trafficking have closely related molecular architectures. The structure of COPI extends known similarities, and strengthens the case for a common evolutionary origin.
• Astrophysics: Making black holes from scratch
  - Nature (London) 466(7310):1049 (2010)
  The means by which supermassive black holes form and grow have remained largely unclear. Numerical simulations show that the collision of massive galaxies can naturally lead to the creation of these objects.
• 50 & 100 years ago
  - Nature (London) 466(7310):1050 (2010)
  Interference between plant viruses was first demonstrated in plants infected with tobacco mosaic virus. Although several theories have been proposed to explain interference ... there is little evidence on the mechanisms involved.
• Cell cycle: Retinoblastoma, a trip organizer
  - Nature (London) 466(7310):1051 (2010)
  The retinoblastoma protein is essential for accurate DNA replication, and its loss is commonly associated with cancer. It emerges that this protein also regulates another stage of the cell cycle.
• Neurodegeneration: An expansion in ALS genetics
  - Nature (London) 466(7310):1052 (2010)
  Aggregates and mutations of the proteins ataxin-2 and TDP-43 have been implicated in distinct neurodegenerative disorders. An interplay between these proteins is now reported for amyotrophic lateral sclerosis.
• Quantum mechanics: The usefulness of uselessness
  - Nature (London) 466(7310):1053 (2010)
  A game for three or more players called 'guess your neighbour's input' reveals common ground between classical and quantum physics — at the expense of more exotic, super-quantum, theories of nature.
• Cancer: Viruses' backup plan
  - Nature (London) 466(7310):1054 (2010)
  Tumour viruses can cause cancer by altering gene expression and protein activity in the host cell. Tumour adenoviruses, however, seem to go to great lengths to ensure that one particular host cell protein, p53, is suppressed.
• Evidence for male allocation in pipefish?
  - Nature (London) 466(7310):E11 (2010)
  Nature | Brief Communication Arising Evidence for male allocation in pipefish? * Darryl T. Gwynne1 Search for this author in: * NPG journals * PubMed * Google Scholar * Kevin A. Judge2 Search for this author in: * NPG journals * PubMed * Google Scholar * Clint D. Kelly3 Search for this author in: * NPG journals * PubMed * Google Scholar * AffiliationsJournal name:NatureVolume:466,Page:E11Date published:(26 August 2010)DOI:doi:10.1038/nature09275Received11 April 2010Accepted14 June 2010 * Letter (March, 2010) * Brief Communication Arising (August, 2010) Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Arising from: K. A. Paczolt & A. G. Jones Nature464, 401–404 (2010); Paczolt & Jones reply Sexual differences in the extent and type of parental care lie at the heart of sexual selection theory1, and evolution resulting from parental conflict has produced some striking behavioural and morphological adaptations. In a study of male pregnancy in Gulf pipefish, Paczolt and Jones2 showed that more eggs were transferred to the male's brood pouch and more offspring survived following mating with large females (preferred by males) than with small (less preferred) females. Although the authors conclude that the lower survival of embryos from small females is most consistent with males actively removing resources from these offspring2, 3, 4, no data are presented to directly support this hypothesis (ref. 2, and Supplementary Information therein) and the data do not refute the alternative explanation that differential egg survival is caused by female effects mediated by variation in fecundity and egg size or quality. We argue that only by experimentally manipulating female! attractiveness separately from the quality of eggs deposited in the brood pouch can the extent of sexual conflict in this role-reversed system be assessed. View full text Subject terms: * Animal behaviour * Evolution Author information * Author information * Comments Affiliations * Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6. darryl.gwynne@utoronto.ca * Darryl T. Gwynne * Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4 * Kevin A. Judge * Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, Iowa 50011, USA * Clint D. Kelly Competing financial interests declared none. Additional data
• Paczolt & Jones reply
  - Nature (London) 466(7310):E12 (2010)
  Nature | Brief Communication Arising Paczolt & Jones reply * Kimberly A. Paczolt1 Search for this author in: * NPG journals * PubMed * Google Scholar * Adam G. Jones1 Search for this author in: * NPG journals * PubMed * Google Scholar * AffiliationsJournal name:NatureVolume:466,Page:E12Date published:(26 August 2010)DOI:doi:10.1038/nature09276 * Brief Communication Arising (August, 2010) Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Replying to: D. T. Gwynne, K. A. Judge & C. D. Kelly Nature466, 10.1038/nature09275 (2010) Our recent study of pre- and post-copulatory sexual selection in the sex-role-reversed Gulf pipefish indicates that males prefer to mate with larger females compared to smaller females, that larger females transfer more eggs per copulation than smaller females, that the eggs from larger females are more likely to result in viable offspring than eggs from smaller females, and that males experience fitness trade-offs between broods1. We suggest that the most likely explanation for this suite of results is that males exert choice before and after copulation in a way that favours larger females over smaller females during every phase of pre- and post-copulatory sexual selection. Gwynne et al.2 have challenged the interpretation of one facet of our results by suggesting that males do not differentially allocate resources to offspring originating from different females. Rather, they suggest that our results can be explained entirely by differences among females in fecundity, egg s! ize and egg quality2. View full text Author information * Author information * Comments Affiliations * Department of Biology, 3258 TAMU, Texas A&M University, College Station, Texas 77845, USA. kpaczolt@mail.bio.tamu.edu * Kimberly A. Paczolt & * Adam G. Jones Competing financial interests declared none. Additional data
• The evolution of eusociality
  - Nature (London) 466(7310):1057 (2010)
  Nature | Analysis The evolution of eusociality * Martin A. Nowak1 Search for this author in: * NPG journals * PubMed * Google Scholar * Corina E. Tarnita1 Search for this author in: * NPG journals * PubMed * Google Scholar * Edward O. Wilson2 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1057–1062Date published:(26 August 2010)DOI:doi:10.1038/nature09205Received10 March 2010Accepted26 May 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Eusociality, in which some individuals reduce their own lifetime reproductive potential to raise the offspring of others, underlies the most advanced forms of social organization and the ecologically dominant role of social insects and humans. For the past four decades kin selection theory, based on the concept of inclusive fitness, has been the major theoretical attempt to explain the evolution of eusociality. Here we show the limitations of this approach. We argue that standard natural selection theory in the context of precise models of population structure represents a simpler and superior approach, allows the evaluation of multiple competing hypotheses, and provides an exact framework for interpreting empirical observations. View full text Subject terms: * Evolution Figures at a glance * Figure 1: The ultimate superorganisms. The gigantic queens of the leafcutter ants, one of whom (upper panel) is shown here, attended by some of her millions of daughter workers. Differences in size and labour specialization allows the ants to cut and gather leaf fragments (middle panel), and convert the fragments into gardens to grow fungi (lower panel). The species shown are respectively, top to bottom, Atta vollenweideri, Atta sexdens and Atta cephalotes. (Photos by Bert Hölldobler.) * Figure 2: Species on either side of the eusociality threshold. , A colony of a primitively eusocial Synalpheus snapping shrimp, occupying a cavity excavated in a sponge. The large queen (reproductive member) is supported by her family of workers, one of whom guards the nest entrance (from Duffy59). , A colony of the primitively eusocial halictid bee Lasioglossum duplex, which has excavated a nest in the soil (from Sakagami and Hayashida60). , Adult erotylid beetles of the genus Pselaphacus leading their larvae to fungal food (from Costa9); this level of parental care is widespread among insects and other arthropods, but has never been known to give rise to eusociality. These three examples illustrate the principle that the origin of eusociality requires the pre-adaptation of a constructed and guarded nest site. * Figure 3: The limitation of inclusive fitness. , The standard approach of evolutionary dynamics takes into account the relevant interactions and then calculates the fitness of each individual. , The inclusive fitness of an individual is the sum of how the action of that individual affects its own fitness plus that of any other individuals multiplied by relatedness. Inclusive fitness theory is based on the very limiting assumption that the fitness of each individual can be broken down into additive components caused by individual actions. This is not possible in general. , For calculating inclusive fitness one has to keep track of all competitive interactions that occur in the population. Here A acts on B changing its payoff and fitness. If A or B compete with other individuals, then their fitness values are also affected by A's action, although no action is directed towards them. Inclusive fitness theory is not a simplification over the standard approach. It is an alternative accounting method, but one that works only ! in a very limited domain. Whenever inclusive fitness does work, the results are identical to those of the standard approach. Inclusive fitness theory is an unnecessary detour, which does not provide additional insight or information. * Figure 4: Solitary and primitively eusocial wasps. , Progressive provisioning in a solitary wasp. Cutaway view of a nest showing a female Synagris cornuta feeding her larva with a fragment of caterpillar. An ichneumonid wasp and parasite Osprynchotus violator lurks on the outside of the nest (from Cowan61) waiting for the right moment to attack the larva. , A colony of the primitively eusocial wasp Polistes crinitus. Its workers, working together are able simultaneously to guard the nest, forage for food, and attend the larvae sequestered in the nest cells. (Photo by Robert Jeanne.) Author information * Author information * Supplementary information Affiliations * Program for Evolutionary Dynamics, Department of Mathematics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA * Martin A. Nowak & * Corina E. Tarnita * Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA * Edward O. Wilson Contributions M.A.N., C.E.T. and E.O.W. collaborated on all aspects of this research project. C.E.T. led the development of the mathematical framework, presented in Part A of the Supplementary Information, which proves the foundational weakness of inclusive fitness theory. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Martin A. Nowak (martin_nowak@harvard.edu) Supplementary information * Author information * Supplementary information PDF files * Supplementary Information (649K) This file contains Supplementary Information in 3 parts comprising: Natural selection versus kin selection; Empirical tests re-examined and a Mathematical model for the origin of eusociality (see contents list for full details). Also included are Supplementary Figures 1-6 with legends and additional References. Additional data
• Lithospheric layering in the North American craton
  - Nature (London) 466(7310):1063 (2010)
  Nature | Article Lithospheric layering in the North American craton * Huaiyu Yuan1 Search for this author in: * NPG journals * PubMed * Google Scholar * Barbara Romanowicz1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1063–1068Date published:(26 August 2010)DOI:doi:10.1038/nature09332Received11 December 2009Accepted25 June 2010 Abstract * Abstract * Author information * Supplementary information * Comments Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg How cratons—extremely stable continental areas of the Earth's crust—formed and remained largely unchanged for more than 2,500 million years is much debated. Recent studies of seismic-wave receiver function data have detected a structural boundary under continental cratons at depths too shallow to be consistent with the lithosphere–asthenosphere boundary, as inferred from seismic tomography and other geophysical studies. Here we show that changes in the direction of azimuthal anisotropy with depth reveal the presence of two distinct lithospheric layers throughout the stable part of the North American continent. The top layer is thick (~150 km) under the Archaean core and tapers out on the surrounding Palaeozoic borders. Its thickness variations follow those of a highly depleted layer inferred from thermo-barometric analysis of xenoliths. The lithosphere–asthenosphere boundary is relatively flat (ranging from 180 to 240 km in depth), in agreement with the presenc! e of a thermal conductive root that subsequently formed around the depleted chemical layer. Our findings tie together seismological, geochemical and geodynamical studies of the cratonic lithosphere in North America. They also suggest that the horizon detected in receiver function studies probably corresponds to the sharp mid-lithospheric boundary rather than to the more gradual lithosphere–asthenosphere boundary. View full text Subject terms: * Geophysics * Geology * Planetary sciences * Earth sciences Figures at a glance * Figure 1: Precambrian basement age in the North American continent and seismic depth profiles at selected locations. , Precambrian basement age (after ref. 23). The white triangles are the seismic stations used in , and the blue lines are the locations of profiles AA′, BB′ and CC′, discussed in the text. Petrologic sample locations are from ref. 13. The thick dashed black line shows the approximate boundary of the stable parts of the continent, bounded by the Laramide deformation/Rocky Mountain front from the west, and the Ouachita and Appalachian fronts from the south and east1. The thick dashed grey lines indicate crustal shear zones1. GSL, the Great Slave Lake shear zone; GFT, the Great Falls tectonic zone; TH, the Trans-Hudson orogen; CB, the Cheyenne belt; NQO and Torngat, shear zones related to the New Quebec orogen and the Torngat orogen, respectively. Blue two-letter labels are Xenocryst sample site names. –, Seismic depth profiles at stations YKW3 (), ULM (), FFC () and SCHQ (). Panels show, from left to right, the direction of the fast axis of azimuthal anisotropy, isotro! pic shear-wave velocity (VS), radial anisotropy (ξ) and azimuthal anisotropy magnitude (G), respectively. The green dashed lines indicate local maxima in the fast-axis direction gradient as a function of depth, and also delimit three anisotropic layers. The gradient itself is shown as a red line in the fast-axis panels, and the vertical thin black lines denote the North American APM direction26 at the station. (In and , there are two black lines, which show the same APM directions owing to 180° periodicity.) Regions of negative gradients in VS and ξ are highlighted as thick blue rectangles. Changes in anisotropy direction at depths shallower than 50 km (, ) are probably artefacts at the edge of our inversion domain. * Figure 2: Upper-mantle layering defined by changes in the direction of the fast axis of azimuthal anisotropy. Depth cross-sections across the three profiles—AA′ (), BB′ () and CC′ ()—shown in Fig. 1a. The direction of the fast axis is colour-coded as a deviation from the North American APM (see scale)26. The thick dashed line is our inferred LAB. , Yava/Mazat/G, the Proterozoic Yavapai, Mazatzal and Grenville provinces; McR, the mid-continental rift. , The profile is truncated to the west at the Rocky Mountain front, where the lithospheric character changes abruptly. NQO, Proterozoic New Quebec orogen. , This profile follows the sites where xenocryst samples have been obtained13. Sample sites are labelled (two-letter abbreviations) at the bottom of the plot as in Fig. 1. The boundary corresponding to Mg#93 (ref. 13) is indicated by a grey line, and the black line corresponds to Mg#92. * Figure 3: Thickness and anisotropy of layer 1 and LAB thickness across the North American continent. The thick broken line indicates the borders of the stable part of the continent as in Fig. 1. , Lithospheric (LAB) thickness, determined from changes in the fast axis direction towards the APM26 beneath the Archaean and Proterozoic parts of the continent. The Rocky Mountain front represents a sharp transition to a distinct anisotropic regime, described elsewhere27. , Fast-axis direction and strength of anisotropy at a depth of 50 km in layer 1 (blue bars) and correspondence with main geological sutures. Black dashed lines are the major crustal province boundaries (from Fig. 1). Suture zones (thick red dashed lines) are inferred from figure 1b of ref. 1: the Great Slave Lake shear zone/Thelon magnetic zone (between Slave and Rae), the Snowbird shear zone (Rae and Hearne), the Great Falls tectonic zone (Hearne/Medicine Hat and Wyoming), and the Cheyenne belt (Wyoming and Proterozoic Yavapai). Thinner red dashed lines (from figure 1b of ref. 29) show approximate subprovince b! oundaries in the Superior craton. Light grey shading indicates regions outside stable North America; , Map of layer 1 thickness. Light grey shading indicates regions where no layer 1 has been detected. * Figure 4: Relative thickness of layers 1 and 2 along the depth cross-section AA' shown in Figs 1a and 2a. , Gradient of the fast-axis direction as a function of depth along the profile. Gradient extremes mark the boundaries between layers 1 and 2 (white dashed line) and the LAB (continuous white line). The red dashed line is the prediction of LAB depth from the geodynamic calculation10, according to the relation between thickness of chemical (layer 1) and thermal (layer 1 + layer 2) lithosphere (), and using as input our layer 1 thickness. This is in good agreement with the seismically inferred LAB north of 38° latitude. The black dots indicate depth of boundary detected by receiver function studies15, 16, 17. * Figure 5: Cartoon illustrating the inferred stratification of the lithosphere. Beneath the craton, three layers of anisotropy are present: two in the lithosphere (layers 1 and 2), and one in the asthenosphere. Layer 1 corresponds to the chemically distinct, depleted Archaean lithosphere, and layer 2 is the thermal root, separated from the asthenosphere by the LAB, which is at relatively constant depth beneath the stable part of the continent, but rapidly shallows between the tectonic part of the continent (in the western USA) and in the oceans. The boundary between layers 1 and 2 is seismically sharp but its fine-scale structure is likely to be complex. The depth extent of the zone of present-day flow-related anisotropy is not tightly constrained by our study. This figure was modified from ref. 3. Author information * Abstract * Author information * Supplementary information * Comments Affiliations * Berkeley Seismological Laboratory, 209 McCone Hall, Berkeley, California 94720, USA * Huaiyu Yuan & * Barbara Romanowicz Contributions B.R. developed the concept and methodology of the study. H.Y. assembled the data set, and performed the inversions and the supporting resolution tests. Both authors extensively discussed the results and jointly developed implications. Both authors contributed to writing the paper. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Barbara Romanowicz (barbara.romanowicz@gmail.com) Supplementary information * Abstract * Author information * Supplementary information * Comments PDF files * Supplementary Information (4.8M) This file contains Supplementary Information 1 - 2, References and Supplementary Figures 1 - 12 with legends. Additional data
• Ataxin-2 intermediate-length polyglutamine expansions are associated with increased risk for ALS
  - Nature (London) 466(7310):1069 (2010)
  Nature | Article Ataxin-2 intermediate-length polyglutamine expansions are associated with increased risk for ALS * Andrew C. Elden1, 8 Search for this author in: * NPG journals * PubMed * Google Scholar * Hyung-Jun Kim2, 8 Search for this author in: * NPG journals * PubMed * Google Scholar * Michael P. Hart1, 8 Search for this author in: * NPG journals * PubMed * Google Scholar * Alice S. Chen-Plotkin3, 4, 8 Search for this author in: * NPG journals * PubMed * Google Scholar * Brian S. Johnson1 Search for this author in: * NPG journals * PubMed * Google Scholar * Xiaodong Fang1 Search for this author in: * NPG journals * PubMed * Google Scholar * Maria Armakola1 Search for this author in: * NPG journals * PubMed * Google Scholar * Felix Geser3 Search for this author in: * NPG journals * PubMed * Google Scholar * Robert Greene3 Search for this author in: * NPG journals * PubMed * Google Scholar * Min Min Lu1 Search for this author in: * NPG journals * PubMed * Google Scholar * Arun Padmanabhan1 Search for this author in: * NPG journals * PubMed * Google Scholar * Dana Clay-Falcone3 Search for this author in: * NPG journals * PubMed * Google Scholar * Leo McCluskey4 Search for this author in: * NPG journals * PubMed * Google Scholar * Lauren Elman4 Search for this author in: * NPG journals * PubMed * Google Scholar * Denise Juhr5 Search for this author in: * NPG journals * PubMed * Google Scholar * Peter J. Gruber5 Search for this author in: * NPG journals * PubMed * Google Scholar * Udo Rüb6 Search for this author in: * NPG journals * PubMed * Google Scholar * Georg Auburger7 Search for this author in: * NPG journals * PubMed * Google Scholar * John Q. Trojanowski3 Search for this author in: * NPG journals * PubMed * Google Scholar * Virginia M.-Y. Lee3 Search for this author in: * NPG journals * PubMed * Google Scholar * Vivianna M. Van Deerlin3 Search for this author in: * NPG journals * PubMed * Google Scholar * Nancy M. Bonini2 Search for this author in: * NPG journals * PubMed * Google Scholar * Aaron D. Gitler1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorsJournal name:NatureVolume:466,Pages:1069–1075Date published:(26 August 2010)DOI:doi:10.1038/nature09320Received11 November 2009Accepted28 June 2010 Abstract * Abstract * Author information * Supplementary information * Comments Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg The causes of amyotrophic lateral sclerosis (ALS), a devastating human neurodegenerative disease, are poorly understood, although the protein TDP-43 has been suggested to have a critical role in disease pathogenesis. Here we show that ataxin 2 (ATXN2), a polyglutamine (polyQ) protein mutated in spinocerebellar ataxia type 2, is a potent modifier of TDP-43 toxicity in animal and cellular models. ATXN2 and TDP-43 associate in a complex that depends on RNA. In spinal cord neurons of ALS patients, ATXN2 is abnormally localized; likewise, TDP-43 shows mislocalization in spinocerebellar ataxia type 2. To assess the involvement of ATXN2 in ALS, we analysed the length of the polyQ repeat in the ATXN2 gene in 915 ALS patients. We found that intermediate-length polyQ expansions (27–33 glutamines) in ATXN2 were significantly associated with ALS. These data establish ATXN2 as a relatively common ALS susceptibility gene. Furthermore, these findings indicate that the TDP-43–ATXN2 inte! raction may be a promising target for therapeutic intervention in ALS and other TDP-43 proteinopathies. View full text Subject terms: * Genetics * Genomics Figures at a glance * Figure 1: Pbp1 is a dose-sensitive modifier of TDP-43 toxicity in yeast. , Yeast spotting assays with yeast TDP-43 showing toxicity. Fivefold serial dilutions of yeast cells spotted onto glucose (expression repressed) or galactose (expression induced). Upregulation of PBP1 enhances TDP-43 toxicity. Whereas Pbp1 has no effect on yeast viability when expressed with the control protein YFP, when co-expressed with TDP-43, it enhances toxicity. Enhancement is specific because Pbp1 does not affect the toxicity of a pathogenic huntingtin fragment (htt72Q) or α-synuclein (α-syn). , Yeast spotting assays with yeast TDP-43 showing that PBP1 deletion (pbp1Δ) suppresses TDP-43 toxicity. Whereas expression of TDP-43 from a plasmid in wild-type yeast (WT) was toxic, this was mitigated in pbp1Δ cells. The effect was specific because α-synuclein or htt72Q toxicity was not suppressed by pbp1Δ. * Figure 2: Atx2 is a dose-sensitive modifier of TDP-43 toxicity in Drosophila. , Expression of TDP-43 caused a dose-dependent disruption of retinal structure. Genotypes: gmr-GAL4(YH3)in trans to UAS–GFP (control), UAS-TDP-43(M) or UAS-TDP-43–YFP(S). (M) and (S) are moderate and strong TDP-43 expression, respectively (Methods and Supplementary Fig. 2). , TDP-43 caused motility deficits when expressed in motor neurons. TDP-43(Q331K) caused a more severe loss of motility than the wild-type protein at the same level of expression (Supplementary Fig. 2). Genotypes: D42-GAL4in trans to +, UAS-TDP-43 or UAS-TDP-43(Q331K). Error bars represent the mean ± 95% confidence interval of four climbing trials. , Atx2 modulates TDP-43 toxicity. Flies expressing TDP-43 or Atx2 alone (Atx2EP; Atx2 enhancer and promoter containing P-element (EP) insertion line Atx2EP3145) have a mild effect on retinal structure. TDP-43 toxicity is more severe with upregulation of Atx2 (TDP-43 + Atx2EP). TDP-43 toxicity is markedly mitigated on reduction of Atx2 (flies in trans to nul! l allele Atx2X1). See Methods for details of the genotypes. Atx2X1/+ has wild-type retinal structure. , Atx2 modulates the reduced lifespan conferred by TDP-43. Expression of TDP-43 in the nervous system reduces lifespan (black, compared to normal in blue). Upregulation of Atx2 causes more rapid death (red, compared to TDP-43 in black). Upregulation of Atx2 on its own has no effect (purple). Reduction of Atx2 significantly extends lifespan (green, compared to TDP-43 in black). Heterozygous loss of Atx2 on its own has no effect (not shown). Quantitative PCR with reverse transcription (RT–PCR) showed that TDP-43 expression has no effect on levels of Atx2 transcript in Atx2EP flies. See Methods for details of the genotypes. Flies raised at 25 °C, lifespan performed at 29 °C. , TDP-43 immunoblot on Atx2 modulation. Reduction of Atx2 has no effect on TDP-43 levels, whereas upregulation of Atx2 enhances TDP-43 protein levels. Atx2 has no effect on the transgene expression! system and 2× TDP-43 does not produce the same effect as TDP! -43+Atx2EP (Supplementary Figs 2 and 3). —, control lane. TDP-43 lanes show expression of TDP-43 alone (—) or with reduced Atx2 (Atx2X1), or with upregulated Atx2 (Atx2EP). Details of genotypes in Methods. Bottom, quantification of immunoblots from 3–5 independent experiments; normalized to tubulin. Data are presented as mean ± standard deviation of 3–5 independent immunoblots. * Figure 3: ATXN2 and TDP-43 interact in a manner dependent on RNA. , TDP-43 and ATXN2 associate in mammalian cells in a manner dependent on the RRMs. HEK293T cells were transfected with plasmids encoding YFP, TDP-43–YFP, TDP-43(ΔNLS)–YFP (NLS mutant localizes to cytoplasm), TDP-43(ΔNLS/5FL)–YFP (NLS mutant + RNA-binding mutant), or TDP-43(5FL)–YFP (RNA-binding mutant). Protein was immunoprecipitated (IP) with anti-GFP antibody and then subjected to immunoblotting with anti-ataxin-2 to detect endogenous ATXN2. Whereas TDP-43 and TDP-43(ΔNLS) both interact with ATXN2, RNA-binding mutant versions do not. , Co-immunoprecipitation in HEK293T cells as in , but now with lysates treated with RNase. The interaction between ATXN2 and TDP-43 seen normally was abolished on RNase treatment. , HEK293T cells transfected with YFP-tagged wild-type and mutant TDP-43 constructs then immunostained for endogenous ATXN2. Normally, ATXN2 is localized to the cytoplasm forming occasional cytoplasmic accumulations. TDP-43 localized to the nucleus in a dif! fuse pattern. TDP-43(ΔNLS) localized to the cytoplasm where it occasionally formed cytoplasmic aggregates; these aggregates always co-localized with ATXN2 cytoplasmic accumulations (arrow). Abolishing the ability of TDP-43 to interact with RNA (TDP-43(ΔNLS/5FL) or TDP-43(5FL)) eliminated ATXN2 co-localization (white arrowheads pointing at green TDP-43 accmulations; see high magnification merge). TDP-43(5FL)–YFP was restricted to the nucleus where it formed multiple foci. Scale bar is 2.5 μm for merge panels and 0.5 μm for high magnification merge panels (high mag. merge). , Yeast spotting assays for TDP-43 toxicity. Whereas wild-type and TDP-43(ΔNLS) constructs are toxic, mutations of TDP-43 that prevent RNA binding abolish toxicity. * Figure 4: ATXN2 localization is perturbed in ALS patient neurons. –, Immunostaining for ATXN2 in spinal cord. , , In control spinal cord neurons, ATXN2 is localized throughout the cytoplasm in a diffuse pattern (also Supplementary Fig. 11). , , In ALS spinal cord neurons, ATXN2 was present in distinct cytoplasmic accumulations (arrows). In some cases, ATXN2-positive accumulations were adjacent to clearings indicative of TDP-43 aggregates (* in ). , , Quantification of large accumulations of ATXN2 in control (normal) versus ALS spinal cord neurons. In ALS patients, 27.2 ± 12.3% of spinal cord neurons had large accumulations of ATXN2 compared to 4.7 ± 2.6% of control neurons. ALS patients with normal (ALS 1–3) and intermediate-length (ALS 4–6) ATXN2 polyQ repeats (see Fig. 5) were included and the ATXN2 pathology was not significantly different. An ALS case with both a SOD1 mutation and an ATXN2 polyQ expansion (27 glutamines) was included (case ALS 4). Data are presented as mean ± standard deviation. Scale bars, 1.25 μm for ! ; 5 μm for –. * Figure 5: Intermediate-length ATXN2 polyQ expansions linked to ALS. , The ATXN2 gene contains a trinucleotide repeat encoding polyQ. The repeat length is normally 22–23 glutamines. Expansions of >34 cause SCA212. We proposed that intermediate-length polyQ expansions (for example, 24–34) could be linked to ALS. The ATXN2 polyQ length was defined by Genescan analysis of ALS cases and neurologically normal controls (for details, see Table 1 and Methods). , Representative examples of Genescan analysis of polyQ lengths from control and ALS cases. , The distribution of ATXN2 polyQ repeat lengths in ALS and control cases. PolyQ lengths ≥27 are significantly enriched in ALS versus controls. Furthermore, polyQ lengths >31 were never observed in our controls but we found nine ALS patients above this threshold. , In a selected cohort of ALS patients (n = 65), those with ATXN2 polyQ expansions showed a significantly lower age of onset (compared by survival analysis).*, P = 0.01. Author information * Abstract * Author information * Supplementary information * Comments Primary authors * These authors contributed equally to this work. * Andrew C. Elden, * Hyung-Jun Kim, * Michael P. Hart & * Alice S. Chen-Plotkin Affiliations * Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA * Andrew C. Elden, * Michael P. Hart, * Brian S. Johnson, * Xiaodong Fang, * Maria Armakola, * Min Min Lu, * Arun Padmanabhan & * Aaron D. Gitler * Department of Biology, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA * Hyung-Jun Kim & * Nancy M. Bonini * Department of Pathology and Laboratory Medicine and Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA * Alice S. Chen-Plotkin, * Felix Geser, * Robert Greene, * Dana Clay-Falcone, * John Q. Trojanowski, * Virginia M.-Y. Lee & * Vivianna M. Van Deerlin * Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA * Alice S. Chen-Plotkin, * Leo McCluskey & * Lauren Elman * The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA * Denise Juhr & * Peter J. Gruber * Institute of Clinical Neuroanatomy, Dr Senckenberg Anatomy, Goethe University, Frankfurt am Main D-60590, Germany * Udo Rüb * Molecular Neurogenetics, Department of Neurology, Goethe University, Frankfurt am Main D-60528, Germany * Georg Auburger Contributions N.M.B. and A.D.G. are co-senior authors. M.P.H., H.-J.K., A.S.C.-P., F.G., U.R., G.A., J.Q.T., V.M.-Y.L., V.M.V.D., N.M.B. and A.D.G. designed the experiments. A.C.E., H.-J.K., M.P.H., B.S.J., X.F., M.A., R.G., M.M.L., U.R. and A.D.G. performed the research. D.J. and P.J.G. provided the reagents. D.C. and V.M.V.D. collected the clinical data. A.S.C.-P., L.E. and L.M. assessed clinical characteristics. M.P.H., H.-J.K., A.S.C.-P., F.G., A.P., L.E., L.M., U.R., G.A., J.Q.T., V.M.-Y.L., V.M.V.D., N.M.B. and A.D.G. analysed and interpreted data. N.M.B. and A.D.G. wrote the paper with contributions from all authors. Competing financial interests [Competing Interests: A.D.G. is an inventor on patents and patent applications that have been licensed to FoldRx.] Corresponding authors Correspondence to: * Aaron D. Gitler (gitler@mail.med.upenn.edu) or * Nancy M. Bonini (nbonini@sas.upenn.edu) Supplementary information * Abstract * Author information * Supplementary information * Comments Excel files * Supplementary Table 1 (35K) This file contains Ataxin-2 polyQ lengths for ALS patients and control individuals and ages for control individuals. * Supplementary Table 2 (22K) This file contains the demographic and clinical characteristics of ALS patients and control individuals. PDF files * Supplementary Information (990K) This file contains Supplementary Data, a Supplementary Discussion, additional References and Supplementary Figures 1-11 with legends. Additional data
• Heterochromatin silencing of p53 target genes by a small viral protein
  - Nature (London) 466(7310):1076 (2010)
  Nature | Article Heterochromatin silencing of p53 target genes by a small viral protein * Conrado Soria1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Fanny E. Estermann1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Kristen C. Espantman1 Search for this author in: * NPG journals * PubMed * Google Scholar * Clodagh C. O'Shea1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1076–1081Date published:(26 August 2010)DOI:doi:10.1038/nature09307Received13 May 2009Accepted23 June 2010 Abstract * Abstract * Accession codes * Author information * Supplementary information * Comments Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg The transcription factor p53 (also known as TP53) guards against tumour and virus replication and is inactivated in almost all cancers. p53-activated transcription of target genes is thought to be synonymous with the stabilization of p53 in response to oncogenes and DNA damage. During adenovirus replication, the degradation of p53 by E1B-55k is considered essential for p53 inactivation, and is the basis for p53-selective viral cancer therapies. Here we reveal a dominant epigenetic mechanism that silences p53-activated transcription, irrespective of p53 phosphorylation and stabilization. We show that another adenoviral protein, E4-ORF3, inactivates p53 independently of E1B-55k by forming a nuclear structure that induces de novo H3K9me3 heterochromatin formation at p53 target promoters, preventing p53–DNA binding. This suppressive nuclear web is highly selective in silencing p53 promoters and operates in the backdrop of global transcriptional changes that drive oncogenic rep! lication. These findings are important for understanding how high levels of wild-type p53 might also be inactivated in cancer as well as the mechanisms that induce aberrant epigenetic silencing of tumour-suppressor loci. Our study changes the longstanding definition of how p53 is inactivated in adenovirus infection and provides key insights that could enable the development of true p53-selective oncolytic viral therapies. View full text Subject terms: * Cancer * Genetics * Genomics * Virology * Molecular biology Figures at a glance * Figure 1: p53 is induced and phosphorylated in ΔE1B-55k infection but p53 activity is dominantly suppressed. , SAECs were infected and protein lysates analysed by immunoblotting. , U2OS cells with inducible ARF were infected as indicated and analysed for p53 levels and activation by immunoblotting. , RT–qPCR of p53 transcriptional targets in infected SAECs (36 h.p.i.) ±10 Gy γ irradiation (IR). Error bars represent s.d. (n = 3). , Immunoblot of p53 protein phosphorylation in infected or doxorubicin (dox)-treated SAECs (36 h.p.i.). , Immunoblot of SAECs (36 h.p.i.) infected as indicated and treated with either control (−), dox, nutlin, or TSA at 24 h.p.i. * Figure 2: E4-ORF3 inactivates p53 independently of E1B-55k and p53 degradation. , SAECs were infected with the indicated viruses (detailed description in Supplementary Fig. 8) and protein lysates (36 h.p.i.) were analysed for p53 activation by immunoblotting. , SAECs were co-infected as indicated with either a GFP control virus (Ad-GFP, +) or a virus expressing E4-ORF3 (Ad-ORF3, +). Protein lysates (36 h.p.i.) were analysed for p53 activation by immunoblotting. , SAECs were infected and harvested over a 48 h time course as indicated and analysed for p53 activation by immunoblotting. , RT–qPCR of p53 transcriptional targets in infected SAECs at 36 h.p.i. Error bars represent s.d. (n = 3). * Figure 3: E4-ORF3 induces heterochromatin formation and prevents p53–DNA binding at endogenous promoters. , U2OS cells were transfected with p53-luc (solid line) or p53-mutant (dashed line) luciferase plasmids and infected with indicated viruses. Luminescence is plotted against time. , , U2OS cells were infected as indicated or treated with doxorubicin. , p53 induction was analysed by immunoblotting and p53 transcriptional targets quantified by RT–qPCR (36 h.p.i.). Error bars represent s.d. (n = 3) , p53 ChIPs were analysed by semiquantitative PCR for p21 and MDM2 promoter sequences. , p53 (green) and H3K9me3 (red) immunofluorescence of infected U2OS cells (36 h.p.i.). , Localization of SUV39H1, SUV39H2, SETDB1 and G9a (green) with H3K9me3 (red) in Δ55k-infected U2OS cells (36 h.p.i.). * Figure 4: E4-ORF3 forms a nuclear scaffold that specifies heterochromatin assembly and H3K9 trimethylation at p53 target promoters. , Protein lysates from infected U2OS cells (36 h.p.i.) were analysed for total histone H3 or H3K9me3 levels by immunoblotting. H3K9me3 and p53 ChIPs were quantified by RT–qPCR, normalized relative to input DNA and plotted as fold-change relative to mock. Error bars represent s.d. (n = 2) , H3K9me3 (green) and E4-ORF3 (red) localization in Δ55k-infected SAECs (36 h.p.i.) was visualized by immunofluorescence. A high resolution confocal slice (0.3 µm) through the nucleus is shown with a magnified section of E4-ORF3 and associated heterochromatin domains on the far right. * Figure 5: p53 transcriptional targets are silenced selectively in the backdrop of global transcriptional changes that drive oncogenic cellular and viral replication. Affymetrix global gene expression analyses of SAECs. , Heat map of the 1,730 overlapping differentially regulated genes (log-fold change >2 or <−2 with a false discovery rate (FDR) of 0.05) between Δ55k/ΔORF3- and Δ55k- versus mock-infected SAECs (36 h.p.i.). , Unsupervised hierarchical clustering of 46 top differentially upregulated transcripts in both Δ55k/ΔORF3 infection and nutlin treatment. , Pie-chart depicting the percentage of upregulated transcripts (log-fold change >2 and FDR of 0.05) in Δ55k/ΔORF3 versus Δ55k that have predicted p53 transcription factor binding sites and/or induced by a log-fold change >1.5 in response to nutlin. , Summary and model. Accession codes * Abstract * Accession codes * Author information * Supplementary information * Comments Primary accessions Gene Expression Omnibus * GSE20607 Author information * Abstract * Accession codes * Author information * Supplementary information * Comments Primary authors * These authors contributed equally to this work. * Conrado Soria & * Fanny E. Estermann Affiliations * Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037-1099, USA * Conrado Soria, * Fanny E. Estermann, * Kristen C. Espantman & * Clodagh C. O'Shea Contributions C.S. performed the p53 activation and virus studies, including immunoblotting, RT–qPCR and microarray experiments. F.E.E. performed all chromatin immunoprecipitation and immunofluorescence studies. K.C.E. performed the luciferase assays, E4-ORF3 sufficiency and complementation, and assisted C.S. with viral mutant studies. C.C.O. analysed the array data and wrote the paper with contributions from all authors. C.C.O. was responsible for the overall conceptual design and supervision of the studies. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Clodagh C. O'Shea (oshea@salk.edu) Microarray data are deposited in NCBI's Gene Expression Omnibus (GSE20607). Supplementary information * Abstract * Accession codes * Author information * Supplementary information * Comments PDF files * Supplementary Figures (4.5M) This file contains Supplementary Figures 1-31 with legends. * Supplementary Tables (1.1M) This file contains Supplementary Tables 1-5. Additional data
• Direct formation of supermassive black holes via multi-scale gas inflows in galaxy mergers
  - Nature (London) 466(7310):1082 (2010)
  Nature | Letter Direct formation of supermassive black holes via multi-scale gas inflows in galaxy mergers * L. Mayer1 Search for this author in: * NPG journals * PubMed * Google Scholar * S. Kazantzidis2, 3 Search for this author in: * NPG journals * PubMed * Google Scholar * A. Escala4, 5 Search for this author in: * NPG journals * PubMed * Google Scholar * S. Callegari1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1082–1084Date published:(26 August 2010)DOI:doi:10.1038/nature09294Received26 April 2010Accepted21 June 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Observations of distant quasars indicate that supermassive black holes of billions of solar masses already existed less than a billion years after the Big Bang1. Models in which the 'seeds' of such black holes form by the collapse of primordial metal-free stars2, 3 cannot explain the rapid appearance of these supermassive black holes because gas accretion is not sufficiently efficient4, 5, 6. Alternatively, these black holes may form by direct collapse of gas within isolated protogalaxies7, 8, but current models require idealized conditions, such as metal-free gas, to prevent cooling and star formation from consuming the gas reservoir9, 10, 11. Here we report simulations showing that mergers between massive protogalaxies naturally produce the conditions for direct collapse into a supermassive black hole with no need to suppress cooling and star formation. Merger-driven gas inflows give rise to an unstable, massive nuclear gas disk of a few billion solar masses, which fun! nels more than 108 solar masses of gas to a sub-parsec-scale gas cloud in only 100,000 years. The cloud undergoes gravitational collapse, which eventually leads to the formation of a massive black hole. The black hole can subsequently grow to a billion solar masses on timescales of about 108 years by accreting gas from the surrounding disk. View full text Subject terms: * Astronomy * Astrophysics Figures at a glance * Figure 1: Time evolution of the nuclear gas disk from its formation until the onset of central collapse. The surface density maps of the nuclear disk are shown at large scales (, top) and small scales (, bottom). Particles are colour-coded on a logarithmic scale with brighter colours in regions of higher density. The density ranges from 2 × 104 to 108  per square parsec (upper panels) and from 2 × 106 to 2 × 1010  per square parsec (lower panels). The time of the merger is defined as the time at which the two density peaks associated with the merging galactic cores are no longer distinguishable. For reference, the disk orbital time at ~20 pc is 5 × 104 years, while at 1 pc it is ~4 × 103 years. Global spiral modes, in particular the two-armed spiral initially triggered by the final collision between the two cores, are evident at scales of tens of parsecs (top panels of and ) and cause the mass increase in the central parsec region (bottom panels) that allows the collapse into a massive central cloud (bottom panels of and ). * Figure 2: Evolution of the mass distribution of the nuclear region. , The cumulative gas mass profile at scales of tens of parsecs is shown. , The cumulative gas mass profile within the inner few parsecs is displayed. Profiles are normalized to the total gas mass within the radius of the nuclear disk (100 pc). The disk radius is determined from the sharp drop in the nuclear gas density distribution. The black, red and blue curves in each panel correspond to the mass profile at the indicated times after the merger, these being the same snapshots used in Fig. 1. Mass redistribution occurs as spiral arms (at scales of tens of parsecs) push mass inward and shed angular momentum outwards, gradually leading to an increasing mass concentration in the very central region (blue line in ) and, correspondingly, a flattening of the mass distribution at scales of tens of parsecs (blue line in ). This triggers the Jeans collapse of the central inner few parsecs into a supercloud containing ~13% of the total disk mass, which manifests as a strong flatten! ing of the profile at parsec scales as the cloud absorbs a large fraction of the mass in that region (red line in ). Author information * Author information * Supplementary information * Comments Affiliations * Institute for Theoretical Physics, University of Zürich, 190 Winterthurestrasse, Zürich 8057, Switzerland * L. Mayer & * S. Callegari * Center for Cosmology and Astro-Particle Physics, The Ohio State University, Ohio 43210, USA * S. Kazantzidis * Departments of Physics and Astronomy, The Ohio State University, Ohio 43210, USA * S. Kazantzidis * Departamento de Astronomia, Universidad de Chile, Casilla 36-D, Santiago 7550000, Chile * A. Escala * Kavli Institute for Particle Astrophysics and Cosmology (KIPAC), Stanford University, 2575 Sand Hill Road MS 29 Menlo Park, California 94025, USA * A. Escala Contributions L.M. provided the scientific leadership, led the design of the numerical experiments, wrote the paper and led the analysis and interpretation of the simulations. S.K. and A.E. contributed to the initial concept of the numerical experiments and to their analysis and interpretation. They also helped with the writing of the paper. S.C. performed some of the additional experiments described in the Supplementary Information, and carried out important parts of the analysis. S.C. also helped substantially with understanding the results of the mass dependence of the inflow process as well as with the writing of the final version of this Letter. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * L. Mayer (lmayer@physik.unizh.ch) Supplementary information * Author information * Supplementary information * Comments PDF files * Supplementary Information (1M) This file contains Supplementary Information comprising Supplementary Methods, and Data, Supplementary Figures 1-5 with legends and References. Additional data
• Formation of asteroid pairs by rotational fission
  - Nature (London) 466(7310):1085 (2010)
  Nature | Letter Formation of asteroid pairs by rotational fission * P. Pravec1 Search for this author in: * NPG journals * PubMed * Google Scholar * D. Vokrouhlický2 Search for this author in: * NPG journals * PubMed * Google Scholar * D. Polishook3 Search for this author in: * NPG journals * PubMed * Google Scholar * D. J. Scheeres4 Search for this author in: * NPG journals * PubMed * Google Scholar * A. W. Harris5 Search for this author in: * NPG journals * PubMed * Google Scholar * A. Galád1, 6 Search for this author in: * NPG journals * PubMed * Google Scholar * O. Vaduvescu7, 8 Search for this author in: * NPG journals * PubMed * Google Scholar * F. Pozo7 Search for this author in: * NPG journals * PubMed * Google Scholar * A. Barr7 Search for this author in: * NPG journals * PubMed * Google Scholar * P. Longa7 Search for this author in: * NPG journals * PubMed * Google Scholar * F. Vachier9 Search for this author in: * NPG journals * PubMed * Google Scholar * F. Colas9 Search for this author in: * NPG journals * PubMed * Google Scholar * D. P. Pray10 Search for this author in: * NPG journals * PubMed * Google Scholar * J. Pollock11 Search for this author in: * NPG journals * PubMed * Google Scholar * D. Reichart12 Search for this author in: * NPG journals * PubMed * Google Scholar * K. Ivarsen12 Search for this author in: * NPG journals * PubMed * Google Scholar * J. Haislip12 Search for this author in: * NPG journals * PubMed * Google Scholar * A. LaCluyze12 Search for this author in: * NPG journals * PubMed * Google Scholar * P. Kušnirák1 Search for this author in: * NPG journals * PubMed * Google Scholar * T. Henych1 Search for this author in: * NPG journals * PubMed * Google Scholar * F. Marchis13, 14 Search for this author in: * NPG journals * PubMed * Google Scholar * B. Macomber13, 14 Search for this author in: * NPG journals * PubMed * Google Scholar * S. A. Jacobson15 Search for this author in: * NPG journals * PubMed * Google Scholar * Yu. N. Krugly16 Search for this author in: * NPG journals * PubMed * Google Scholar * A. V. Sergeev16 Search for this author in: * NPG journals * PubMed * Google Scholar * A. Leroy17 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1085–1088Date published:(26 August 2010)DOI:doi:10.1038/nature09315Received26 April 2010Accepted22 June 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Pairs of asteroids sharing similar heliocentric orbits, but not bound together, were found recently1, 2, 3. Backward integrations of their orbits indicated that they separated gently with low relative velocities, but did not provide additional insight into their formation mechanism. A previously hypothesized rotational fission process4 may explain their formation—critical predictions are that the mass ratios are less than about 0.2 and, as the mass ratio approaches this upper limit, the spin period of the larger body becomes long. Here we report photometric observations of a sample of asteroid pairs, revealing that the primaries of pairs with mass ratios much less than 0.2 rotate rapidly, near their critical fission frequency. As the mass ratio approaches 0.2, the primary period grows long. This occurs as the total energy of the system approaches zero, requiring the asteroid pair to extract an increasing fraction of energy from the primary's spin in order to escape. We do ! not find asteroid pairs with mass ratios larger than 0.2. Rotationally fissioned systems beyond this limit have insufficient energy to disrupt. We conclude that asteroid pairs are formed by the rotational fission of a parent asteroid into a proto-binary system, which subsequently disrupts under its own internal system dynamics soon after formation. View full text Subject terms: * Planetary sciences Figures at a glance * Figure 1: Primary rotation periods P1 versus mass ratios q of asteroid pairs. The mass ratio values were estimated from the differences between the absolute magnitudes of the pair components, ΔH. The curves were generated with the model of pair separation from the post-fission transient proto-binary. Dashed curve, the set of parameters best representing the properties of the pairs: a system scaled angular momentum αL = 1.0, a primary axial ratio a1/b1 = 1.4 and an initial orbit's normalized semi-major axis Aini/b1 = 3. Red and blue curves, upper and lower limiting cases, respectively. The upper curves are for αL = 1.2, a1/b1 = 1.2, and Aini/b1 = 2 and 4. The lower curves are for αL = 0.7, a1/b1 = 1.5, and Aini/b1 = 2 and 4. The choice of a1/b1 = 1.2 for the upper limit cases is because the four primaries closest to the upper limit curve have low lightcurve amplitudes A1 = 0.1–0.2 mag. Similarly, the choice of a1/b1 = 1.5 for the lower limit cases is because the point closest to the lower limit curve has the amplitude A1 = 0.49 mag, suggest! ing that the equatorial elongation is ~1.5. Circles, data points with quality code rating U1 = 3, meaning a precise period determination; diamonds, data points with U1 = 2, which are somewhat less certain estimates (see Table 1 and Supplementary Information). Error bars, standard errors. * Figure 2: A disparity between the lightcurve amplitudes of the primary components in asteroid pairs and binary systems. The lightcurve amplitudes of primaries of asteroid pairs () are distributed relatively randomly, and achieve high values in general, whereas primaries of binary asteroids () have more subdued amplitudes. Either asteroids with shapes closer to rotational symmetry are more prone to form stable binaries, or some process occurs during the formation process of a binary asteroid to create such a shape. Author information * Author information * Supplementary information * Comments Affiliations * Astronomical Institute AS CR, Fričova 1, CZ-25165 Ondřejov, Czech Republic * P. Pravec, * A. Galád, * P. Kušnirák & * T. Henych * Institute of Astronomy, Charles University, V Holešovičkách 2, CZ-18000 Prague, Czech Republic * D. Vokrouhlický * Wise Observatory and Department of Geophysics and Planetary Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel * D. Polishook * Department of Aerospace Engineering Sciences, University of Colorado, Boulder, Colorado 80309, USA * D. J. Scheeres * Space Science Institute, 4603 Orange Knoll Avenue, La Canada, California 91011, USA * A. W. Harris * Modra Observatory, Comenius University, Bratislava SK-84248, Slovakia * A. Galád * Instituto de Astronomia, Universidad Catolica del Norte, Avenida Angamos 0610, Antofagasta, Chile * O. Vaduvescu, * F. Pozo, * A. Barr & * P. Longa * Isaac Newton Group of Telescopes, E-38700 Santa Cruz de la Palma, Canary Islands, Spain * O. Vaduvescu * IMCCE-CNRS-Observatoire de Paris, 77 avenue Denfert Rochereau, 75014 Paris, France * F. Vachier & * F. Colas * Carbuncle Hill Observatory, West Brookfield, Massachusetts 01585, USA * D. P. Pray * Physics and Astronomy Department, Appalachian State University, Boone, North Carolina 28608, USA * J. Pollock * Physics and Astronomy Department, University of North Carolina, Chapel Hill, North Carolina 27514, USA * D. Reichart, * K. Ivarsen, * J. Haislip & * A. LaCluyze * University of California at Berkeley, Berkeley, California 94720, USA * F. Marchis & * B. Macomber * SETI Institute, Mountain View, California 94043, USA * F. Marchis & * B. Macomber * Department of Astrophysical and Planetary Sciences, University of Colorado, Boulder, Colorado 80309, USA * S. A. Jacobson * Institute of Astronomy of Kharkiv National University, Sumska Str. 35, Kharkiv 61022, Ukraine * Yu. N. Krugly & * A. V. Sergeev * Observatoire Midi Pyrénées and Association T60, Pic du Midi, France * A. Leroy Contributions This work was a team effort; here we specify only the most important contributions by individual authors. P.P. led the project and worked on most of its parts, except Supplementary Information sections 1 and 4. D.V. performed the backward orbit integrations and contributed to interpretations of the results. D.P. ran the observations and data reduction, and contributed to interpretations. D.J.S. developed the fission theory and worked out its implications for the observational data. A.W.H. contributed to interpretations and implications of the data. A.G., O.V., F.P., A.B., P.L., F.V., F.C., D.P.P., J.P., D.R., K.I., J.H., A.L., P.K., T.H., F.M., B.M., Yu.N.K., A.V.S. and A.L. carried out the observations, data reduction and analyses. S.A.J. ran simulations of the satellite ejection process in a proto-binary after fission. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * P. Pravec (ppravec@asu.cas.cz) Supplementary information * Author information * Supplementary information * Comments PDF files * Supplementary Information (10M) This file contains Supplementary Figures 1- 45 with Legends, Supplementary Methods, Supplementary Data, Supplementary Discussions 1-2 with additional References and Supplementary Tables 1-2. Additional data
• Coherent measurements of high-order electronic correlations in quantum wells
  - Nature (London) 466(7310):1089 (2010)
  Nature | Letter Coherent measurements of high-order electronic correlations in quantum wells * Daniel B. Turner1 Search for this author in: * NPG journals * PubMed * Google Scholar * Keith A. Nelson1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1089–1092Date published:(26 August 2010)DOI:doi:10.1038/nature09286Received09 November 2009Accepted15 June 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Strong, long-range Coulomb interactions can lead to correlated motions of multiple charged particles, which can induce important many-body effects in semiconductors. The exciton states formed from correlated electron–hole pairs have been studied extensively1, 2, but basic properties of multiple-exciton correlations—such as coherence times, population lifetimes, binding energies and the number of particles that can be correlated—are largely unknown because they are not spectroscopically accessible from the ground state. Here we present direct observations of high-order coherences in gallium arsenide quantum wells, achieved using two-dimensional multiple-quantum spectroscopy methods in which up to seven successive light fields were used. The measurements were made possible by the combination of a reconfigurable spatial beam-shaper that formed multiple beams in specified geometries and a spatiotemporal pulse-shaper that controlled the relative optical phases and temporal ! delays among pulses in all the beams. The results reveal triexciton coherences (correlations of three excitons or six particles), whose existence was not obvious because the third exciton spin is unpaired, and the values of their coherence times and binding energies. Rephasing of biexcitons, triexcitons and unbound two-exciton coherences was demonstrated. We also determined that there are no significant unbound correlations of three excitons and no bound or unbound four-exciton (eight-particle) correlations. Thus, the limits, as well as the properties, of many-body correlations in this system were revealed. The measurement methods open a new window into high-order many-body interactions in materials and molecules3, and the present results should guide ongoing work on first-principles calculations of electronic interactions in semiconductor nanostructures4. View full text Subject terms: * Applied physics * Engineering Figures at a glance * Figure 1: GaAs exciton and multiexciton states observed or sought in this work. , Exciton ladder illustrating the ground state (|0), the two exciton states H and L (|1), the three biexciton states HH, HL and LL (|2), the four triexciton states HHH, HHL, HLL and LLL (|3), and the five quadexciton states (|4). , The spectrum of our laser field (solid line) and the emission spectrum of the two excitons (dashed line), with peaks at 1,539.98 ± 0.01 meV and 1,547.47 ± 0.02 meV for the H and L excitons, respectively. * Figure 2: Four-particle correlations. Fifth-order collinear-polarization rephasing 32 − 21 spectrum showing the three biexcitons—HH, HL and LL at two-quantum energies near 3,080, 3,090 and 3,100 meV, respectively—observed through emission at both H and L exciton energies. An interaction-induced (II) unbound HH two-exciton feature with energy equal to exactly twice the H exciton energy (dashed line) is visible near the HH biexciton peak. The Feynman pathways ((i)–(iii)) illustrate how the fields create each main feature: the three biexciton coherences are represented by |02| and the two single-exciton/ground state coherences that emit signal are represented in (i) by |10|. In pathways (ii) and (iii), the last three field interactions produce radiative biexciton–exciton (|21|) and triexciton–biexciton (|32|) coherences that appear as redshifted wings of the main peaks. * Figure 3: Six-particle correlations. , Three-quantum fifth-order collinear-polarization spectrum showing four triexciton coherences near 4,618.2 ± 0.2 meV (HHH), 4,625.6 ± 0.2 meV (HHL), 4,632.5 ± 0.3 meV (HLL) and 4,640.0 ± 0.03 meV (LLL). The HHH triexciton binding energy is determined by the location of the peak below the diagonal line drawn along E3Q = 3Eemit, and it is measured to be 1.7 ± 0.2 meV. The coherence pathway on the left (at bottom) illustrates how the main peaks are created: |30| represents the four triexciton coherences and |10| represents the two single-exciton coherences that emit the signal. As in Fig. 2, the redshifted shoulders of the main peaks are due to biexciton–exciton and triexciton–biexciton emission. , Seventh-order collinear-polarization rephasing spectrum showing HHH and perhaps HHL triexciton coherences, represented by the seventh-order pathway (bottom right), and a large exciton-continuum scattering feature. , Seventh-order co-circular-po! larization rephasing spectrum showing lack of three-quantum interaction-induced features. Only the exciton-continuum scattering feature is visible, and the redshifted shoulders are gone because neither biexciton–exciton emission nor triexciton–biexciton emission is possible. * Figure 4: Four-quantum spectroscopy. A four-quantum seventh-order collinear-polarization measurement indicates the absence of eight-particle correlations. If HHHH quadexciton coherences were produced by the first four (2) field interactions, then three interactions with the variably delayed (−1) field would project them onto single-quantum coherences and a peak would appear below the diagonal line drawn along E4Q = 4Eemit, as illustrated by the pathway shown. The large vertical features are due to exciton-continuum scattering. Author information * Author information * Supplementary information * Comments Affiliations * Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA * Daniel B. Turner & * Keith A. Nelson Contributions D.B.T. designed the apparatus, collected and analysed the data, and wrote the manuscript. K.A.N. provided guidance throughout the experiments and helped write the manuscript. Competing financial interests [COMPETING INTERESTS: A patent application similar to the optical set-up used here is presently being filed.] Corresponding author Correspondence to: * Keith A. Nelson (kanelson@mit.edu) Supplementary information * Author information * Supplementary information * Comments PDF files * Supplementary Information (2.1M) This file contains a Supplementary Discussion, References and Supplementary Figures 1-3 with legends. Additional data
• Upper-ocean-to-atmosphere radiocarbon offsets imply fast deglacial carbon dioxide release
  - Nature (London) 466(7310):1093 (2010)
  Nature | Letter Upper-ocean-to-atmosphere radiocarbon offsets imply fast deglacial carbon dioxide release * Kathryn A. Rose1, 7, 8 Search for this author in: * NPG journals * PubMed * Google Scholar * Elisabeth L. Sikes2, 8 Search for this author in: * NPG journals * PubMed * Google Scholar * Thomas P. Guilderson3, 4 Search for this author in: * NPG journals * PubMed * Google Scholar * Phil Shane5 Search for this author in: * NPG journals * PubMed * Google Scholar * Tessa M. Hill1 Search for this author in: * NPG journals * PubMed * Google Scholar * Rainer Zahn6 Search for this author in: * NPG journals * PubMed * Google Scholar * Howard J. Spero1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1093–1097Date published:(26 August 2010)DOI:doi:10.1038/nature09288Received19 October 2009Accepted14 June 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Radiocarbon in the atmosphere is regulated largely by ocean circulation, which controls the sequestration of carbon dioxide (CO2) in the deep sea through atmosphere–ocean carbon exchange. During the last glaciation, lower atmospheric CO2 levels were accompanied by increased atmospheric radiocarbon concentrations that have been attributed to greater storage of CO2 in a poorly ventilated abyssal ocean1, 2. The end of the ice age was marked by a rapid increase in atmospheric CO2 concentrations2 that coincided with reduced 14C/12C ratios (Δ14C) in the atmosphere3, suggesting the release of very 'old' (14C-depleted) CO2 from the deep ocean to the atmosphere3. Here we present radiocarbon records of surface and intermediate-depth waters from two sediment cores in the southwest Pacific and Southern oceans. We find a steady 170 per mil decrease in Δ14C that precedes and roughly equals in magnitude the decrease in the atmospheric radiocarbon signal during the early stages of t! he glacial–interglacial climatic transition. The atmospheric decrease in the radiocarbon signal coincides with regionally intensified upwelling and marine biological productivity4, suggesting that CO2 released by means of deep water upwelling in the Southern Ocean lost most of its original depleted-14C imprint as a result of exchange and isotopic equilibration with the atmosphere. Our data imply that the deglacial 14C depletion previously identified in the eastern tropical North Pacific5 must have involved contributions from sources other than the previously suggested carbon release by way of a deep Southern Ocean pathway5, and may reflect the expanded influence of the 14C-depleted North Pacific carbon reservoir across this interval. Accordingly, shallow water masses advecting north across the South Pacific in the early deglaciation had little or no residual 14C-depleted signals owing to degassing of CO2 and biological uptake in the Southern Ocean. View full text Subject terms: * Climate science * Earth sciences * Geology * Geophysics Figures at a glance * Figure 1: Ocean circulation in the South Pacific and Southern Ocean and ambient water-mass patterns at the location of the sediment cores used in this study. , Schematic presentation of major currents. The bold solid line marks the approximate location of the sub-Antarctic front (SAF), which separates cold and fresher polar surface waters, to the south, from the warmer and saltier surface waters in the sub-Antarctic zone (SAZ), to the north. SAMW forms in the SAZ (grey shaded area) and becomes entrained in the South Pacific subtropical gyre circulation (solid red line). At the equator, its chemical signal can be identified in STMW (~100–300-m water depth) in the western basin. Denser AAIW (~800–1,400-m water depth) forms south of the SAF, in the polar frontal zone (PFZ, blue shaded area), and flows northwards below SAMW. The triangles mark the core sites used in this study: RR0503-JPC64 (37° 25.34′ S, 177° 00.41′ E; 651 m; turquoise triangle) and MD97-2120 (43° 32.06′ S, 174° 55.85′ E; 1,210 m; green triangle). , Wind-driven upwelling in the Southern Ocean causes shallow, mid-depth and deep-water masses to shoal! . Cores RR0503-JPC64 and MD97-2120 are proximal to the formation zones of SAMW and AAIW and are positioned within the flow paths of both water masses as they are advected to the north and ventilate the South Pacific thermocline. In the Pacific, circumpolar deep water (CPDW) resides below SAMW and AAIW, providing a source for upwelled waters in the Southern Ocean. In the modern ocean, CPDW carries a strong contribution from North Atlantic Deep Water (NADW) flowing out of the Atlantic Ocean at abyssal depths. Inset, ship's track/sampling transect for the salinity vertical profile shown in the main panel. p.s.u., practical salinity units. * Figure 2: Records of radiocarbon activities, Antarctic temperatures and Southern Ocean upwelling across the last deglaciation. , Antarctic ice-core δ18O ([(18O/16O)sample/(18O/16O)standard − 1] × 1,000) from EDML (green13) and the hydrogen isotope deuterium (δD) from EPICA Dome C (light blue2), each of which is a temperature proxy, placed on the Greenland GISP2 timescale5. , Atmospheric radiocarbon activities from the Cariaco basin (black), placed on the Hulu cave timescale7, and south Chatham Rise marine Δ14C from planktonic and benthic foraminifera (blue): Globigerina bulloides (planktonic; up-triangles show new data (this study); down-triangles show data from ref. 17), Globorotalia inflata (planktonic; squares), Neogloboquadrina pachyderma (s) (planktonic; diamonds), mixed G. bulloides and N. pachyderma (planktonic; half-open square), and mixed benthics (filled circles). , Atmospheric radiocarbon activities from the Cariaco basin (black), placed on the Hulu cave timescale, and Bay of Plenty Δ14C from core RR0503-JPC64 (red): G. inflata (planktonic; open squares) and mixed benthic f! oraminifera (closed circles). , Opal fluxes, a proxy for upwelling south of the Antarctic polar front, from sediment core TN057-13-4PC (53.2° S, 5.1° E) in the Southern Ocean4 (SO). The vertical dashed lines denote climatic intervals of the deglaciation as indicated at top: Heinrich event 1 (H1; timing as determined by reduced deep-water flux in the North Atlantic24), the Bølling–Allerød/Antarctic cold reversal (BA/ACR) and the Younger Dryas (YD). The shaded area corresponds to the period of enhanced upwelling in the Southern Ocean and the rapid drop in atmospheric Δ14C. * Figure 3: Records of atmospheric CO2, radiocarbon activities, and surface δ13C and productivity across the last deglaciation. The initial deglacial rise in atmospheric CO2 shown in the Southern Hemisphere ice-core records, the decrease in surface ocean δ13C and the increase in alkenone productivity all coincide with the initial decrease in intermediate-water Δ14C. , Atmospheric Δ14C from the Cariaco basin (black7) and IntCal04 (grey20), and atmospheric CO2 concentration from Antarctic ice core EPICA Dome C (purple2), placed on the GISP2 timescale5. , Intermediate-water Δ14C from south Chatham Rise core MD97-2120 (mixed benthics; blue circles), Bay of Plenty core RR0503-JPC64 (mixed benthics; red circles) and the Baja California ETNP site (mixed benthics; open circles5), and North Pacific deep-water Δ14C (mixed benthics; green circles10). Although the three shallow sites show a decrease in Δ14C beginning at ~17.8 kyr bp, only the tropical North Pacific site shows an extreme decrease in Δ14C, starting at the beginning of Heinrich event 1. , MD97-2120 G.bulloidesδ13C (blue triangles17) and a! lkenone concentrations (grey triangles32) tuned to EDML. The alkenone concentrations are a measure of haptophyte productivity. The vertical dashed lines and the shaded area are as in Fig. 2. Author information * Author information * Supplementary information * Comments Primary authors * These authors contributed equally to this work. * Kathryn A. Rose & * Elisabeth L. Sikes Affiliations * Department of Geology, University of California, Davis, California 95616, USA * Kathryn A. Rose, * Tessa M. Hill & * Howard J. Spero * Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, New Jersey 08901, USA * Elisabeth L. Sikes * Lawrence Livermore National Laboratory, Livermore, California 94550, USA * Thomas P. Guilderson * Institute of Marine Sciences, University of California, Santa Cruz, California 95064, USA * Thomas P. Guilderson * School of Environment, University of Auckland, Auckland 1142, New Zealand * Phil Shane * Institució Catalana de Recerca i Estudis Avançats, ICREA, Universitat Autònoma de Barcelona, Institut de Ciència i Tecnologia Ambientals, Departmento de Geologia, 08193 Bellaterra, Spain * Rainer Zahn * Present address: Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02540, USA. * Kathryn A. Rose Contributions K.A.R. participated in the RR0503 cruise, sampled cores, prepared sediments, speciated foraminifera for isotopic and radiocarbon analyses, performed all stable isotopic analyses and prepared figures. E.L.S. led the RR0503 cruise, sampled cores, speciated foraminifera for isotopic and radiocarbon analyses, prepared figures and wrote the paper. T.P.G. participated in the RR0503 cruise and performed all radiocarbon analyses. P.S. participated in the RR0503 cruise and identified all tephras. H.J.S. designed the study and, with T.M.H., supervised KAR during her MSc. R.Z. provided the MD core samples and supplementary data for that core. All authors contributed to the interpretation of the results and provided input on the manuscript. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Elisabeth L. Sikes (sikes@marine.rutgers.edu) Supplementary information * Author information * Supplementary information * Comments PDF files * Supplementary Information (485K) This file contains Supplementary Methods and Data, Supplementary Figures 1 - 3 with legends, References and Supplementary Tables 1 - 4. Additional data
• Global patterns and predictors of marine biodiversity across taxa
  Tittensor DP Mora C Jetz W Lotze HK Ricard D Berghe EV Worm B - Nature (London) 466(7310):1098 (2010)
  Nature | Letter Global patterns and predictors of marine biodiversity across taxa * Derek P. Tittensor1 Search for this author in: * NPG journals * PubMed * Google Scholar * Camilo Mora1 Search for this author in: * NPG journals * PubMed * Google Scholar * Walter Jetz2 Search for this author in: * NPG journals * PubMed * Google Scholar * Heike K. Lotze1 Search for this author in: * NPG journals * PubMed * Google Scholar * Daniel Ricard1 Search for this author in: * NPG journals * PubMed * Google Scholar * Edward Vanden Berghe3 Search for this author in: * NPG journals * PubMed * Google Scholar * Boris Worm1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1098–1101Date published:(26 August 2010)DOI:doi:10.1038/nature09329Received11 March 2010Accepted08 July 2010Published online28 July 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Global patterns of species richness and their structuring forces have fascinated biologists since Darwin1, 2 and provide critical context for contemporary studies in ecology, evolution and conservation. Anthropogenic impacts and the need for systematic conservation planning have further motivated the analysis of diversity patterns and processes at regional to global scales3. Whereas land diversity patterns and their predictors are known for numerous taxa4, 5, our understanding of global marine diversity has been more limited, with recent findings revealing some striking contrasts to widely held terrestrial paradigms6, 7, 8. Here we examine global patterns and predictors of species richness across 13 major species groups ranging from zooplankton to marine mammals. Two major patterns emerged: coastal species showed maximum diversity in the Western Pacific, whereas oceanic groups consistently peaked across broad mid-latitudinal bands in all oceans. Spatial regression analyses r! evealed sea surface temperature as the only environmental predictor highly related to diversity across all 13 taxa. Habitat availability and historical factors were also important for coastal species, whereas other predictors had less significance. Areas of high species richness were disproportionately concentrated in regions with medium or higher human impacts. Our findings indicate a fundamental role of temperature or kinetic energy in structuring cross-taxon marine biodiversity, and indicate that changes in ocean temperature, in conjunction with other human impacts, may ultimately rearrange the global distribution of life in the ocean. View full text Subject terms: * Environmental science Figures at a glance * Figure 1: Patterns of species richness for individual taxa. –, Species groups that primarily occur in coastal (–) or oceanic habitats (–) are shown. Empirically gathered point data (coastal fishes, foraminifera) were co-kriged using GLM predictions as the co-variable30 to extrapolate to undersampled regions for display purposes. Horizontal tick marks on colour-bars indicate richness quartiles; colour-scaling is adjusted by taxon to optimize contrast. * Figure 2: Global species richness and hotspots across taxa. () Global marine species richness for all taxa from Table 1 combined. Richness values for each taxon were then normalized by rescaling from zero to one, and averaged across taxa by cell for all taxa (), primarily coastal taxa () and primarily oceanic taxa (). Cells with a bold outline are hotspots (defined as the 10% of cells with highest mean richness). Horizontal tick marks on colour-bars indicate quartiles. * Figure 3: Diversity, SST and human impact overlap. –, Relationship between mean normalized diversity and SST for () all taxa, () coastal taxa without pinnipeds (solid line and black points) and coastal taxa with pinnipeds (dashed line and grey points) and () oceanic taxa. Trends (red lines with grey 95% confidence limits) indicated by generalized additive model fit with basis dimension 3. Taxon-specific plots provided in Supplementary Fig. 3. , Histogram of diversity hotspots (10% of cells with highest mean richness from Fig. 2c, d) by human impact. For each cell, average human impact score calculated from ref. 10. The distribution of human impacts across all marine cells (black line) is provided for reference. Author information * Author information * Supplementary information * Comments Affiliations * Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax B3H 4J1, Canada * Derek P. Tittensor, * Camilo Mora, * Heike K. Lotze, * Daniel Ricard & * Boris Worm * Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, Connecticut 06520-8106, USA * Walter Jetz * Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey 08901-8521, USA * Edward Vanden Berghe Contributions B.W., H.K.L., D.P.T., W.J. and C.M. conceived the study, D.P.T, C.M., E.V.B., D.R., B.W. and H.K.L. compiled the data, D.P.T., W.J. and C.M. conducted the analyses, and all authors contributed to the writing of the manuscript. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Derek P. Tittensor (derekt@mathstat.dal.ca) Supplementary information * Author information * Supplementary information * Comments PDF files * Supplementary Information (2M) This file contains Supplementary Figures S1-S6 with legends, Supplementary Tables S1-S8 and References. Additional data
• Statistical inference for noisy nonlinear ecological dynamic systems
  Wood SN - Nature (London) 466(7310):1102 (2010)
  Nature | Letter Statistical inference for noisy nonlinear ecological dynamic systems * Simon N. Wood1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:NatureVolume:466,Pages:1102–1104Date published:(26 August 2010)DOI:doi:10.1038/nature09319Received04 May 2010Accepted28 June 2010Published online11 August 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Chaotic ecological dynamic systems defy conventional statistical analysis. Systems with near-chaotic dynamics are little better. Such systems are almost invariably driven by endogenous dynamic processes plus demographic and environmental process noise, and are only observable with error. Their sensitivity to history means that minute changes in the driving noise realization, or the system parameters, will cause drastic changes in the system trajectory1. This sensitivity is inherited and amplified by the joint probability density of the observable data and the process noise, rendering it useless as the basis for obtaining measures of statistical fit. Because the joint density is the basis for the fit measures used by all conventional statistical methods2, this is a major theoretical shortcoming. The inability to make well-founded statistical inferences about biological dynamic models in the chaotic and near-chaotic regimes, other than on an ad hoc basis, leaves dynamic theory! without the methods of quantitative validation that are essential tools in the rest of biological science. Here I show that this impasse can be resolved in a simple and general manner, using a method that requires only the ability to simulate the observed data on a system from the dynamic model about which inferences are required. The raw data series are reduced to phase-insensitive summary statistics, quantifying local dynamic structure and the distribution of observations. Simulation is used to obtain the mean and the covariance matrix of the statistics, given model parameters, allowing the construction of a 'synthetic likelihood' that assesses model fit. This likelihood can be explored using a straightforward Markov chain Monte Carlo sampler, but one further post-processing step returns pure likelihood-based inference. I apply the method to establish the dynamic nature of the fluctuations in Nicholson's classic blowfly experiments3, 4, 5. View full text Subject terms: * Environmental science * Zoology * Mathematics * Statistics Figures at a glance * Figure 1: Measuring fit of the Ricker model. , Population data simulated from the Ricker model in the text, observed under Poisson sampling (log(r) = 3.8, σ = 0.3, ϕ = 10). , The log joint probability density, log(fθ(, )), of data, , and random process noise terms, , plotted against the value of the first process noise deviate, e1, with the rest of and held fixed. , Log(fθ(, )) plotted against model parameter r, again with and held fixed. , The log synthetic likelihood, ls, plotted against log(r) for the Ricker model and the data given in (Nr = 500). * Figure 2: Synthetic likelihood evaluation. Starting at the top, we wish to evaluate the fit of the model with parameter vector to the raw data vector . Replicate data vectors are simulated from the model, given the value of . Each replicate, and the raw data, is converted into a vector of statistics, or , in the same way. The are used to estimate the mean vector, , and covariance matrix, , of , according to the model with parameters . We use , and respectively as the mean vector, the covariance matrix and the argument of the log multivariate normal (MVN) probability density function, to evaluate the log synthetic likelihood, ls. * Figure 3: Blowfly data and model runs. , , Two laboratory adult populations of sheep blowfly maintained under adult food limitation4, 5. , , As in and but maintained under moderate and more severe juvenile food limitation4. –, Two replicates (one solid, one dashed) from the full model (equation (4)) fitted separately to the data shown in each of panels –, immediately above. –, As in – for the model with demographic stochasticity only. The observations are made every second day. The simulation phase is arbitrary. Notice the qualitatively good match of the dynamics (–) of the full model (equation (4)) to the data, relative to the insufficiently variable dynamics of the model with demographic stochasticity only (–). * Figure 4: Blowfly model stability diagram3, 14. The coloured points are samples from the stability-controlling parameter combinations δτ and Pτ, plotted (with matching colour coding) for each experimental run shown in Fig. 3. The open and filled circles show stability properties for alternative chain starting conditions: they give indistinguishable results, although the conditions marked by the filled circle lie in the plausible range for external noise-driven dynamics14. The dynamics comprise limit cycles perturbed by noise but not driven by noise. The fluctuations are driven by the intrinsic population-dynamic processes, not by random variation exciting a resonance in otherwise stable dynamics. Author information * Author information * Supplementary information * Comments Affiliations * Mathematical Sciences, University of Bath, Bath BA2 7AY, UK * Simon N. Wood Competing financial interests The author declares no competing financial interests. Corresponding author Correspondence to: * Simon N. Wood (s.wood@bath.ac.uk) Supplementary information * Author information * Supplementary information * Comments Zip files * Supplementary Data 1 (42K) This file is an R source package (suitable for use with R on unix like operating systems), implementing the examples in the paper and supplementary material, as well as the providing some routines for rapid computation of summary statistics, and robust evaluation. R is a free statistical language and environment available from cran.r-project.org. * Supplementary Data 2 (105K) This file contains the same R package as in the Supplementary Data 1 file, but for the Windows version of R. PDF files * Supplementary Information (2.7M) This file contains Supplementary Information comprising: 1 Method Implementation and MCMC output; 2 Further examples; 3 Software: the sl package for R and References. Additional data
• A novel pathway regulates memory and plasticity via SIRT1 and miR-134
  Gao J Wang WY Mao YW Gräff J Guan JS Pan L Mak G Kim D Su SC Tsai LH - Nature (London) 466(7310):1105 (2010)
  Nature | Letter A novel pathway regulates memory and plasticity via SIRT1 and miR-134 * Jun Gao1, 2, 3, 5 Search for this author in: * NPG journals * PubMed * Google Scholar * Wen-Yuan Wang1, 2, 5 Search for this author in: * NPG journals * PubMed * Google Scholar * Ying-Wei Mao1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Johannes Gräff1, 4 Search for this author in: * NPG journals * PubMed * Google Scholar * Ji-Song Guan1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Ling Pan1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Gloria Mak1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Dohoon Kim1, 2, 6 Search for this author in: * NPG journals * PubMed * Google Scholar * Susan C. Su1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Li-Huei Tsai1, 2, 4 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1105–1109Date published:(26 August 2010)DOI:doi:10.1038/nature09271Received28 April 2010Accepted23 June 2010Published online11 July 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg The NAD-dependent deacetylase Sir2 was initially identified as a mediator of replicative lifespan in budding yeast and was subsequently shown to modulate longevity in worms and flies1, 2. Its mammalian homologue, SIRT1, seems to have evolved complex systemic roles in cardiac function, DNA repair and genomic stability. Recent studies suggest a functional relevance of SIRT1 in normal brain physiology and neurological disorders. However, it is unknown if SIRT1 has a role in higher-order brain functions. We report that SIRT1 modulates synaptic plasticity and memory formation via a microRNA-mediated mechanism. Activation of SIRT1 enhances, whereas its loss-of-function impairs, synaptic plasticity. Surprisingly, these effects were mediated via post-transcriptional regulation of cAMP response binding protein (CREB) expression by a brain-specific microRNA, miR-134. SIRT1 normally functions to limit expression of miR-134 via a repressor complex containing the transcription factor YY1! , and unchecked miR-134 expression following SIRT1 deficiency results in the downregulated expression of CREB and brain-derived neurotrophic factor (BDNF), thereby impairing synaptic plasticity. These findings demonstrate a new role for SIRT1 in cognition and a previously unknown microRNA-based mechanism by which SIRT1 regulates these processes. Furthermore, these results describe a separate branch of SIRT1 signalling, in which SIRT1 has a direct role in regulating normal brain function in a manner that is disparate from its cell survival functions, demonstrating its value as a potential therapeutic target for the treatment of central nervous system disorders. View full text Subject terms: * Neuroscience Figures at a glance * Figure 1: SIRT1 loss-of-function impairs memory and synaptic plasticity. , Freezing time of SIRT1Δ mice and littermate controls (Cont) 24 h after contextual fear conditioning training. , Shock sensitivities did not differ between control and SIRT1Δ mice. ES, electrical stimulation. , SIRT1Δ and control mice were tested for novel object discrimination 24 h after training. , Pre-test exploration times were equal for each object. , Escape latencies of SIRT1Δ and control mice were examined with the Morris water maze hidden platform test. , Left panel, swimming time spent in each quadrant in the probe trial on day 5 (T, target; L, left; O, opposite; R, right). Right panel, representative path tracings of the probe test. , LTP measurements were performed in the CA1 region of acute slices from SIRT1Δ mice and controls. fEPSP, field excitatory postsynaptic potentials. , SVP immunoreactivity in SIRT1Δ and control hippocampi. , Western blots from hippocampal lysates examined SVP in SIRT1Δ and control mice. , Density of Golgi-impregnated hippocam! pal neuronal dendritic spines was measured in SIRT1Δ and control mice. TBS, theta-burst stimulation; SVP, synaptophysin; SVP/DAPI ratio, ratio of SVP (rhodamine, A548) over DAPI (A490). *P < 0.05, **P < 0.01, ***P < 0.001. All histograms represent average ± s.e.m. * Figure 2: BDNF and CREB are downregulated, whereas miRNA-134 is upregulated, in SIRT1Δ mice. , BDNF in the SIRT1Δ and control mouse hippocampus. Left, mRNA levels; right, western blot. , Chromatin immunoprecipitation (ChIP) with an anti-CREB antibody was followed by qPCR for BDNF promoters 1, 2 and 4. , CREB in the SIRT1Δ and control mouse hippocampus. Left: mRNA levels; right, western blot. , qPCR of selected miRNAs from hippocampi of SIRT1Δ and control mice. , CAD cells were transfected with the plasmids or LNA indicated together with CRE-Luc. , Luciferase reporter constructs containing either a wild-type (WT-CREB) or a mutated (mut-CREB) CREB 3′UTR region, were cotransfected with miR-134 or control. , CREB protein expression in CAD cells after transfection with the indicated constructs or LNAs. Scr, scrambled; mut, mutant; LNA, locked-nucleic-acid (LNA); CRE-Luc, CREB activity reporter construct. **P < 0.01; ***P < 0.001; NS, not significant. * Figure 3: SIRT1 regulates CREB through miR-134. , From SIRT1 ChIP, two genomic regions, R3 and R7, corresponding to base pairs 1418–830 and 3427–2901 upstream of miR-134, respectively, were amplified from the wild type, but not the SIRT1 total knockout (SIRT1KO), brain tissue. HA, haemagglutinin. , miR-134 promoter regions R3 and R7 were quantified from SIRT1 ChIP with qPCR. , Reporter constructs containing R3, R5 or R7 regions upstream of a minimal promoter in a luciferase reporter were co-transfected with SIRT1, SIRT1 shRNA, or empty vector. , qPCR for miR-134 in CAD cells after transfection with the indicated plasmids. , CRE-luciferase reporter assay in CAD cells. , ChIP was performed on extracts from CAD cells with anti-YY1 and anti-SIRT1 antibodies. , Anti-YY1 ChIP followed by qPCR for regions R3 and R7. , Luciferase reporter constructs containing R3, R5 or R7 regions were co-transfected with the indicated plasmids. , miR-134 levels were measured in CAD cells with qPCR after transfection with the indicated plasmi! ds. , Western blotting measured CREB protein levels in CAD cells after transfections with the indicated plasmids. shRNA Cont, scrambled shRNA control. *P < 0.05; **P < 0.01; ***P < 0.001; NS, not significant. All histograms represent average ± s.e.m. * Figure 4: miR-134 knockdown rescues the LTP and memory impairments caused by SIRT1 deficiency. , LTP was measured in acute hippocampal slices of mice 6 weeks after injection with Lv-miR-134 or Lv-Scr-miR. , Lv-miR-134- and Lv-Scr-miR-injected mice were tested with a contextual fear conditioning task. , Following hippocampal injections with LNA-miR-134 or LNA-scr-miR, LTP was measured in SIRT1Δ and control mouse acute hippocampal slices. , Freezing behaviour in the contextual fear conditioning task was examined in SIRT1Δ and control mice after hippocampal injections of LNA-miR-134 or LNA-scr-miR. , Western blot for CREB and BDNF in brain lysate after in vivo miR-134 knockdown. Lv-Scr-miR, control scrambled miR lentivirus. **P < 0.01; NS, not significant. Accession codes * Accession codes * Author information * Supplementary information * Comments Primary accessions Gene Expression Omnibus * GSE22530 Author information * Accession codes * Author information * Supplementary information * Comments Primary authors * These authors contributed equally to this work. * Jun Gao & * Wen-Yuan Wang Affiliations * Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA * Jun Gao, * Wen-Yuan Wang, * Ying-Wei Mao, * Johannes Gräff, * Ji-Song Guan, * Ling Pan, * Gloria Mak, * Dohoon Kim, * Susan C. Su & * Li-Huei Tsai * Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA * Jun Gao, * Wen-Yuan Wang, * Ying-Wei Mao, * Ji-Song Guan, * Ling Pan, * Gloria Mak, * Dohoon Kim, * Susan C. Su & * Li-Huei Tsai * Model Animal Research Center, MOE Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China * Jun Gao * Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02142, USA * Johannes Gräff & * Li-Huei Tsai * Present address: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA. * Dohoon Kim Contributions L.-H.T. designed, directed and coordinated the project. J.Gao designed and performed electrophysiological recordings, behaviour tests, biochemical assays and morphological analyses; W.-Y.W. contributed to the design and generation of microRNA constructs, and performed viral injections, behaviour tests and biochemical analyses; Y.-W.M., J.Gao and L.P. performed luciferase assays and biochemical analyses; J.Gr. and G.M. performed behaviour tests; S.C.S. contributed to viral injection; D.K. contributed to SIRT1 plasmid construction. The manuscript was written by J.Gao, D.K., S.C.S., W.-Y.W. and L.-H.T. and commented on by all the authors. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Li-Huei Tsai (lhtsai@mit.edu) The GEO accession number for our microRNA array data is GSE22530. Supplementary information * Accession codes * Author information * Supplementary information * Comments PDF files * Supplementary Figures (1.2M) This file contains Supplementary Figures S1-S8 with legends. Additional data
• Rb regulates fate choice and lineage commitment in vivo
  Calo E Quintero-Estades JA Danielian PS Nedelcu S Berman SD Lees JA - Nature (London) 466(7310):1110 (2010)
  Nature | Letter Rb regulates fate choice and lineage commitment in vivo * Eliezer Calo1 Search for this author in: * NPG journals * PubMed * Google Scholar * Jose A. Quintero-Estades1 Search for this author in: * NPG journals * PubMed * Google Scholar * Paul S. Danielian1 Search for this author in: * NPG journals * PubMed * Google Scholar * Simona Nedelcu1 Search for this author in: * NPG journals * PubMed * Google Scholar * Seth D. Berman1 Search for this author in: * NPG journals * PubMed * Google Scholar * Jacqueline A. Lees1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1110–1114Date published:(26 August 2010)DOI:doi:10.1038/nature09264Received08 January 2010Accepted07 June 2010Published online04 August 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Mutation of the retinoblastoma gene (RB1) tumour suppressor occurs in one-third of all human tumours and is particularly associated with retinoblastoma and osteosarcoma1. Numerous functions have been ascribed to the product of the human RB1 gene, the retinoblastoma protein (pRb). The best known is pRb's ability to promote cell-cycle exit through inhibition of the E2F transcription factors and the transcriptional repression of genes encoding cell-cycle regulators1. In addition, pRb has been shown in vitro to regulate several transcription factors that are master differentiation inducers2. Depending on the differentiation factor and cellular context, pRb can either suppress or promote their transcriptional activity. For example, pRb binds to Runx2 and potentiates its ability to promote osteogenic differentiation in vitro3. In contrast, pRb acts with E2F to suppress peroxisome proliferator-activated receptor γ subunit (PPAR-γ), the master activator of adipogenesis4, 5. Beca! use osteoblasts and adipocytes can both arise from mesenchymal stem cells, these observations suggest that pRb might play a role in the choice between these two fates. However, so far, there is no evidence for this in vivo. Here we use mouse models to address this hypothesis in mesenchymal tissue development and tumorigenesis. Our data show that Rb status plays a key role in establishing fate choice between bone and brown adipose tissue in vivo. View full text Subject terms: * Stem cells * Cancer * Cell biology * Developmental biology Figures at a glance * Figure 1: Rb cooperates with p53 and modulates mesenchymal tumour fate in a dose-dependent manner. , Haematoxylin and eosin staining of representative sarcomas (×20 magnification). HIB, hibernoma; OS, osteosarcoma; RMS, rhabdomyosarcoma; SAR, undifferentiated sarcoma. , PCR genotyping to detect Rb wild type (WT) and non-recombined conditional mutant (loxp) alleles in control Rbfl/+;p53fl/+ tissues (lane 1) or cell lines derived from Prx1-Cre;Rbfl/fl;p53fl/fl (DKO) or Prx1-Cre;Rbfl/+;p53fl/fl osteosarcomas. Cell lines were cultured for at least 20 passages before genotyping to eliminate stromal cell contribution. * Figure 2: Rb regulates osteosarcoma cell-lineage plasticity in vitro and in vivo. The differentiation potential of three different Osx-Cre;Rbfl/fl:p53fl/fl (DKO) and Osx-Cre:p53fl/fl (p53KO) osteosarcoma cell lines was assessed 0, 7, 14 or 21 days after addition of differentiation media. , Representative staining for (left lane) alkaline phosphatase before differentiation induction, (middle lane) Alizarin red to detect bone mineralization 14 days after culture in osteogenic-induction media and (right lane) Oil red O to detect lipid droplets 14 days after culture in adipogenic-induction media. Expression of bone (Runx2, Alp, Coll1a and Bsp) and fat (Ap2, Pparγ, C/ebpα and Pgc1α) markers was assessed by qPCR of uninduced DKO (orange) and p53KO (black) osteosarcoma cells. Bars represent the mean of three independent experiments (± SD). NS, not significantly expressed. RLU, relative light units. , Rb or control (Luc) shRNAs were expressed in the p53KO cell lines. Rb knockdown was confirmed by immunoprecipitation and qPCR showed that this caused do! wnregulation of bone markers Bsp (also Coll1a and Alp, data not shown), and upregulation of fat markers Pparγ (also Ap2 and C/ebpα, data not shown) without culture in differentiating media. Bars represent the mean of three independent experiments (± SD). , The osteogenic and adipogenic potential of shLuc- and shRb-p53KO cell lines was assessed 0, 7, 14 and 21 days after differentiation induction by Alizarin red and Oil red O staining. A representative time point (14 days) is shown. , Haematoxylin and eosin staining of representative tumours derived from shLuc- and shRb-p53KO cell lines injected subcutaneously into immunocompromised mice. shRb-p53KO osteosarcoma cells consistently (ten out of ten injections) yielded tumours that arose faster, and were more aggressive, than those arising from the parental p53KO osteosarcoma controls (ten injections). Moreover, the shRb-p53KO osteosarcoma-derived tumours were frequently (six out of ten injections) mixed lineage (top i! nset shows fat neoplasm; bottom inset shows bone/undifferentia! ted sarcoma), whereas the control shLuc-p53KO tumours were uniformly (ten out of ten injections) osteosarcomas. Additional analysis of these tumours (haematoxylin and eosin, Sirius red staining and Runx2 immunohistochemistry) is shown in Supplementary Fig. 4. * Figure 3: pRb modulates the activity and the expression of the master lineage regulators Runx2 and Ppar-γ. , The stable DKO-RbDox-ON osteosarcoma cells were generated by drug selection of pools of DKO cells transfected with the doxocyline-inducible construct pCW22-Rb. These were cultured for 2 days in the absence (Rb off) or presence (Rb on) of doxocycline and then analysed. Results are representative of three independent experiments. Promoter occupancy was assessed by chromatin immunoprecipitation. Sequence analysis identified two potential E2f binding sites (−278 and −160) within the Pparγ promoter. pRb induction caused a dramatic upregulation of both pRb and E2F4 binding to the proximal site. (No binding was observed at the distal element.) Similarly, pRb induction allowed pRb to bind to the known Runx2 response element of Col1α20 and increased the binding of Runx2. These changes correlated with the downregulation of Pparγ mRNA and upregulation of Col1α mRNA, as judged by qPCR. Bars, the mean of three independent experiments (± SD). ChIP, chromatin immunoprecipita! tion , Western blotting detected Runx2 in pRb-immunoprecipitates from p53KO osteosarcoma cell lines (left, top panel). Western blotting of whole-cell extracts confirmed that Runx2 was expressed in both DKO and p53KO osteosarcoma cell lines (left, bottom panel). Mesenchymal stem cells and osteoblasts were used as a positive control. Right panel: Runx2 transcriptional activity was shown to be higher in the p53KO- versus the DKO osteosarcoma cell lines as judged by activation of the artificial Runx2-responsive reporter p6OSE2-Luc. Results are the average of six independent samples. Error bars, s.e.m. * Figure 4: Rb maintains the osteoblastic fate commitment in normal osteoblasts and regulates fate choice during normal development in vivo. , Calvarial osteoblasts were prepared from Rbfl/fl or p53fl/fl embryos at embryonic day 18.5 and infected with Ad-GFP or Ad-Cre at P1. Five days later, the cells were induced with differentiation media and assayed for osteogenesis and adipogenesis at 0, 14 and 25 days by staining with Alizarin red and Oil red O. A representative time point (25 days) is shown. , qPCR was also used to assess osteogenic and adipogenic markers in the uninduced Rbfl/fl (WT) versus Rbfl/fl + Ad-Cre (Rb−/−) osteoblasts. Bars, the mean of three independent experiments (± SD). , Alizarin red (bone mineralization) and Alcian blue (cartilage) staining of skeletons at embryonic day 15.5 (e15.5) (top panel), calvaria at embryonic day 18.5 (e18.5) (middle panel) and limbs at embryonic day 18.5 (bottom panel) from Meox2-Cre;Rb+/+ and Meox2-Cre;Rbfl/fl littermate embryos. Arrows, visible skeletal defects. qPCR was used to assess osteogenic (Runx2, Alp and Bsp) and adipogenic (Ap2 and C/ebpα)! markers in mRNA extracted from the calvarial bones of Meox2-Cre;Rb+/+ and Meox2-Cre;Rbfl/fl embryos at embryonic day 18.5. Bars, the mean of three embryos arising in two independent crosses (± SD). , Brown adipose tissue was dissected from the backs of Meox2-Cre;Rbfl/fl embryos (n = 10) and their Meox2-Cre;Rb+/+ littermate controls. All ten showed a dramatic expansion of the brown fat compartment. A representative example is shown (upper two panels). Introduction of the LSL-LacZ reporter into this model, and LacZ staining, confirmed equal, widespread expression of Cre in the control and Rb mutant brown adipose tissue (third panel). Haematoxylin and eosin staining of brown adipose tissue (bottom panel). Author information * Author information * Supplementary information * Comments Affiliations * David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA * Eliezer Calo, * Jose A. Quintero-Estades, * Paul S. Danielian, * Simona Nedelcu, * Seth D. Berman & * Jacqueline A. Lees Contributions E.C. conducted all the experiments with assistance from J.A.Q.-E. in the Rb re-introduction study, P.S.D. and S.D.B. in the generation and analysis of compound mutant mouse strains and S.N. for the LSL-LacZ;Prx1-Cre embryo analysis. E.C. and J.A.L. were responsible for conceiving this study, interpreting the data and manuscript preparation. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Jacqueline A. Lees (jalees@mit.edu) Supplementary information * Author information * Supplementary information * Comments PDF files * Supplementary Information (4.3M) This file contains Supplementary Figures 1-6 with legends. Additional data
• IκBβ acts to inhibit and activate gene expression during the inflammatory response
  - Nature (London) 466(7310):1115 (2010)
  Nature | Letter IκBβ acts to inhibit and activate gene expression during the inflammatory response * Ping Rao1, 5 Search for this author in: * NPG journals * PubMed * Google Scholar * Mathew S. Hayden1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Meixiao Long1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Martin L. Scott3, 5 Search for this author in: * NPG journals * PubMed * Google Scholar * A. Philip West1 Search for this author in: * NPG journals * PubMed * Google Scholar * Dekai Zhang1, 5 Search for this author in: * NPG journals * PubMed * Google Scholar * Andrea Oeckinghaus1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Candace Lynch4 Search for this author in: * NPG journals * PubMed * Google Scholar * Alexander Hoffmann4 Search for this author in: * NPG journals * PubMed * Google Scholar * David Baltimore3 Search for this author in: * NPG journals * PubMed * Google Scholar * Sankar Ghosh1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1115–1119Date published:(26 August 2010)DOI:doi:10.1038/nature09283Received05 August 2009Accepted11 June 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg The activation of pro-inflammatory gene programs by nuclear factor-κB (NF-κB) is primarily regulated through cytoplasmic sequestration of NF-κB by the inhibitor of κB (IκB) family of proteins1. IκBβ, a major isoform of IκB, can sequester NF-κB in the cytoplasm2, although its biological role remains unclear. Although cells lacking IκBβ have been reported3, 4, in vivo studies have been limited and suggested redundancy between IκBα and IκBβ5. Like IκBα, IκBβ is also inducibly degraded; however, upon stimulation by lipopolysaccharide (LPS), it is degraded slowly and re-synthesized as a hypophosphorylated form that can be detected in the nucleus6, 7, 8, 9, 10, 11. The crystal structure of IκBβ bound to p65 suggested this complex might bind DNA12. In vitro, hypophosphorylated IκBβ can bind DNA with p65 and c-Rel, and the DNA-bound NF-κB:IκBβ complexes are resistant to IκBα, suggesting hypophosphorylated, nuclear IκBβ may prolong the expression of cert! ain genes9, 10, 11. Here we report that in vivo IκBβ serves both to inhibit and facilitate the inflammatory response. IκBβ degradation releases NF-κB dimers which upregulate pro-inflammatory target genes such as tumour necrosis factor-α (TNF-α). Surprisingly, absence of IκBβ results in a dramatic reduction of TNF-α in response to LPS even though activation of NF-κB is normal. The inhibition of TNF-α messenger RNA (mRNA) expression correlates with the absence of nuclear, hypophosphorylated-IκBβ bound to p65:c-Rel heterodimers at a specific κB site on the TNF-α promoter. Therefore IκBβ acts through p65:c-Rel dimers to maintain prolonged expression of TNF-α. As a result, IκBβ−/− mice are resistant to LPS-induced septic shock and collagen-induced arthritis. Blocking IκBβ might be a promising new strategy for selectively inhibiting the chronic phase of TNF-α production during the inflammatory response. View full text Subject terms: * Immunology * Molecular biology * Physiology * Genetics * Genomics Figures at a glance * Figure 1: Mice lacking IκBβ are resistant to LPS-induced endotoxin shock. , Wild-type and IκBβ−/− MEF cells transfected with pBIIx-luc reporter and Renilla luciferase vectors were treated with TNF-α, IL-1β or LPS for 4 h and analysed for luciferase activity. Results are expressed as relative luciferase units (RLU) normalized by Renilla luciferase activity; error bars, s.d. (n = 3). , Age- and sex-matched mice received intra-peritoneal injection of LPS and survival rates were scored every 8 h for 3 days (n = 7). , Serum TNF-α, IL-6 and IL-1β 1 h and/or 2 h after intraperitoneal injection of LPS was examined by ELISA; error bars, s.d. (n = 5). , TEPMs from littermate mice were treated for 20 h with LPS as indicated, and TNF-α and IL-6 in the media were determined by ELISA; error bars, s.d. (n = 3). * Figure 2: Deficient TNF-α transcription in IκBβ−/− macrophages. , TEPMs from littermate wild-type and IκBβ−/− mice were treated with LPS and secreted TNF-α and IL-6 were determined by ELISA; error bars, s.d. (n = 3). , TEPMs from littermate mice were treated as in in the presence of brefeldin A, and intracellular pro-TNF-α was examined with flow cytometry. , Intracellular pro-TNF-α production was examined as in with macrophages isolated from three pairs of littermate mice; error bars, s.d. , TEPMs were stimulated with LPS as in and relative TNF-α mRNA level was determined by qRT–PCR; error bars, s.d. (n = 3). * Figure 3: IκBβ is recruited to the promoter of TNF-α with p65 and c-Rel. , , Raw264.7 were stimulated with LPS and immunoprecipitated (IP) with anti-IκBβ (), anti-p65 () or anti-c-Rel () antibodies and immunoblotted as indicated. , LPS-stimulated Raw264.7 lysates were immunoprecipitated with anti-IκBβ, eluted with IκBβ peptide, immunoprecipitated with anti-c-Rel antibody and immunoblotted as indicated. , Raw264.7 lysates were subjected to chromatin immunoprecipitation as indicated and analysed by qPCR targeting TNF-α and IL-6 promoter κB sites; error bars, s.d. (n = 3). , Chromatin immunoprecipitation was performed as in on wild-type and IκBβ−/− BMDMs treated with LPS for 2 h; error bars, s.d. (n = 3). , BMDMs treated as in were immunoprecipitated with anti-p65 antibody. , RAW264.7 were treated with LPS and nuclear extracts were subjected to EMSA with TNF-α κB3 or κB2 probes. Super shifts were performed using cells stimulated for 1 h. , BMDMs were treated with LPS and EMSA and supershifts with the κB2 probe were performed as! in . * Figure 4: IκBβ knockout selectively affects only certain LPS-responsive genes and attenuates collagen-induced arthritis. , LPS-responsive genes whose expression is either downregulated, upregulated or unchanged in IκBβ−/− BMDMs. , Host–pathogen interaction genes that are IκBβ dependent, LPS-responsive and whose expression pattern resembles TNF-α. , RNase protection assay using wild-type and IκBβ−/− MEF stimulated with LPS. , IL-12b relative mRNA level in TEMP determined by qRT–PCR; error bars, s.d. (n = 3). , ELISA for IL-12p40 secreted from wild-type and IκBβ−/− TEPMs stimulated with LPS for 20 h; error bars, s.d. , Arthritis clinical scoring in wild-type (n = 10) or IκBβ−/− (n = 8) DBA/1J mice; error bars, s.e.m. , Serum TNF-α, IL-1β and IL-6 levels in wild-type or IκBβ−/− DBA/1J mice in ; error bars, s.e.m. Accession codes * Accession codes * Author information * Supplementary information * Comments Primary accessions Gene Expression Omnibus * GSE22223 Author information * Accession codes * Author information * Supplementary information * Comments Affiliations * Department of Immunobiology and Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA * Ping Rao, * Mathew S. Hayden, * Meixiao Long, * A. Philip West, * Dekai Zhang, * Andrea Oeckinghaus & * Sankar Ghosh * Department of Microbiology & Immunology, College of Physicians & Surgeons, Columbia University, New York, New York 10032, USA * Mathew S. Hayden, * Meixiao Long, * Andrea Oeckinghaus & * Sankar Ghosh * Department of Biology, California Institute of Technology, Pasadena, California 91125, USA * Martin L. Scott & * David Baltimore * Signaling Systems Laboratory, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA * Candace Lynch & * Alexander Hoffmann * Present addresses: Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, California 90033, USA (P.R.); Merck Research Laboratories, Boston, Massachusetts 02115, USA (M.L.S.); Center for Extracellular Matrix Biology, Texas A & M University Institute of Biosciences and Technology, Houston, Texas 77030, USA (D.Z.). * Ping Rao, * Martin L. Scott & * Dekai Zhang Contributions P.R. characterized the mice and performed most of the experiments, M.S.H. performed the immunoprecipitation experiments and helped in writing the paper, M.L. performed collagen-induced arthritis experiments, D.Z. and A.P.W. performed generation of BMDM cells, A.O. performed some experiments, M.L.S. and D.B. generated the knockout mice, C.L. and A.H. performed the RNAse protection assays, and S.G. conceived the study and wrote the paper. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Sankar Ghosh (sg2715@columbia.edu) The microarray data are deposited in National Center for Biotechnology Information Gene Expression Omnibus under accession number GSE22223. Supplementary information * Accession codes * Author information * Supplementary information * Comments PDF files * Supplementary Information (2.6M) This file contains Supplementary Figures 1-10 with legends. Additional data
• A ribosome-associating factor chaperones tail-anchored membrane proteins
  Mariappan M Li X Stefanovic S Sharma A Mateja A Keenan RJ Hegde RS - Nature (London) 466(7310):1120 (2010)
  Nature | Letter A ribosome-associating factor chaperones tail-anchored membrane proteins * Malaiyalam Mariappan1 Search for this author in: * NPG journals * PubMed * Google Scholar * Xingzhe Li1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Sandra Stefanovic1 Search for this author in: * NPG journals * PubMed * Google Scholar * Ajay Sharma1 Search for this author in: * NPG journals * PubMed * Google Scholar * Agnieszka Mateja3 Search for this author in: * NPG journals * PubMed * Google Scholar * Robert J. Keenan3 Search for this author in: * NPG journals * PubMed * Google Scholar * Ramanujan S. Hegde1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1120–1124Date published:(26 August 2010)DOI:doi:10.1038/nature09296Received31 January 2010Accepted18 June 2010Published online01 August 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Hundreds of proteins are inserted post-translationally into the endoplasmic reticulum (ER) membrane by a single carboxy-terminal transmembrane domain (TMD)1. During targeting through the cytosol, the hydrophobic TMD of these tail-anchored (TA) proteins requires constant chaperoning to prevent aggregation or inappropriate interactions. A central component of this targeting system is TRC40, a conserved cytosolic factor that recognizes the TMD of TA proteins and delivers them to the ER for insertion2, 3, 4. The mechanism that permits TRC40 to find and capture its TA protein cargos effectively in a highly crowded cytosol is unknown. Here we identify a conserved three-protein complex composed of Bat3, TRC35 and Ubl4A that facilitates TA protein capture by TRC40. This Bat3 complex is recruited to ribosomes synthesizing membrane proteins, interacts with the TMDs of newly released TA proteins, and transfers them to TRC40 for targeting. Depletion of the Bat3 complex allows non-TRC40 ! factors to compete for TA proteins, explaining their mislocalization in the analogous yeast deletion strains5, 6, 7. Thus, the Bat3 complex acts as a TMD-selective chaperone that effectively channels TA proteins to the TRC40 insertion pathway. View full text Subject terms: * Cell biology * Biochemistry Figures at a glance * Figure 1: Identification of a TMD-interacting protein complex. , Cytosolic proteins bound and eluted from anti-Bat3 or anti-green fluorescent protein (control) affinity columns are shown. HC and LC are IgG heavy and light chain. , Sec61β (wild type; WT), a deletion construct lacking its TMD (ΔTMD) or the insertion-deficient 3R mutant were translated in reticulocyte lysate, affinity-purified on an anti-Sec61β column and immunoblotted for the indicated products. Total lysate was included for comparison. An autoradiograph of the blot revealed equal recovery of the three translated substrates. IPs, immunoprecipitations. , Crosslinking products of Sec61β (from pooled sucrose-gradient fractions 6–9 in Supplementary Fig. 4) were immunoprecipitated under denaturing or native conditions. Non-immune serum (N.I.S.) was included as a control. , Versions of Sec61β containing the TMD from the indicated proteins were analysed for interaction with Bat3 and TRC40 by in vitro translation, crosslinking and immunoprecipitation. An aliquot of the tot! al translation reaction is shown for each substrate, as well as the immunoprecipitation products of the crosslinking reactions. The Sec61β crosslinked adducts are indicated by 'βx'. , The TMD of Sec61β was mutated as indicated to change its hydrophobicity. , Each construct was analysed for its interactions with the Bat3 complex and TRC40 as in . An aliquot of the total translation product was analysed by autoradiography to reveal the substrates. * Figure 2: The Bat3 complex mediates substrate capture by TRC40. , Translation extracts were passed over anti-green fluorescent protein (anti-GFP; control), anti-Bat3 or anti-TRC40 affinity resins and different amounts of each depleted lysate were analysed by immunoblotting. , Substrate capture assay using either total cytosol, or cytosol immunodepleted (Δ) with the indicated affinity resins. In this assay (see Supplementary Fig. 1), radiolabelled Sec61β RNCs were released with puromycin, and capture by TRC40 was assessed by crosslinking. The portion of gel showing the TRC40–Sec61β crosslink is shown. Failure of TRC40 to capture substrate typically results in capture by a 38-kDa protein (p38). The 'addback' lanes are Bat3-depleted cytosol replenished with affinity-purified Bat3 complex (prepared with an anti-TRC35 resin; Supplementary Fig. 8) at three concentrations spanning that present in the original cytosol. The 'mock' addback sample was prepared in parallel but employed an irrelevant affinity resin (anti-GFP) in place of! TRC35 affinity resin (Supplementary Fig. 8). A reaction lacking crosslinker (XL) is shown in the left-hand lane. Aliquots of each reaction (before crosslinking) were also analysed by immunoblotting against Bat3 and TRC40 to document their relative amounts in the reactions. * Figure 3: The Bat3 complex captures substrates on ribosomes for transfer to TRC40. , Ribosomes were purified under native conditions from reticulocyte lysate and analysed for TRC40, Bat3, Ubl4A and SRP54 by immunoblotting. About 30–50% of SRP, 2–5% of Bat3 complex, and undetectable (less than 1%) amounts of TRC40 are ribosome-bound. , Affinity-purifed and size-purified RNCs (from 60-μl translation reactions) of Sec61β, a TMD-lacking version (ΔTMD) and the 3R mutant were analysed by immunoblotting for the indicated antigens. For comparison, 0.5 μl of translation lysate was analysed. L9 is a ribosomal protein. Autoradiography confirmed equal recovery of each substrate. , The amounts of ribosomes, Ubl4A and SRP54 were quantified in total lysate, purified empty ribosomes and purified RNC preparations. Shown are the amounts of SRP54 and Ubl4A, normalized to 100 ribosomes, averaged from multiple independent purifications (n = 3 for empty ribosomes, n = 7 for Sec61β-RNCs, and n = 6 for β(3R)-RNCs). , Translations of Sec61β in TRC40-depleted lysates l! acking or replenished with recombinant zebrafish TRC40 were rapidly diluted, crosslinked and separated by centrifugation into soluble and ribosome fractions. Sec61β, Bat3 crosslinks (immunopreciptiated with anti-Bat3) and TRC40 crosslinks are shown in the total (T), soluble (S) and ribosome (P) fractions. , Cytosolic fractions from HT1080 cells lacking or stably overexpressing haemagglutinin (HA)-tagged human TRC40 were bound to anti-HA resin and selectively eluted with tobacco etch virus (TEV) protease (which cleaves between the HA tag and TRC40). The eluted products, along with starting lysates, were analysed by immunoblotting for Bat3, TRC40 or small glutamine-rich tetratricopeptide repeat-containing protein α (SGTA; a control protein). Note that endogenous TRC40 is present but not visible at this exposure of the blot. Identical results were obtained when elution of the affinity column was with HA peptide instead of TEV protease (data not shown). * Figure 4: Translation termination is delayed for a TA protein. , Schematic diagram of Sec61β synthesis, illustrating that nascent chains competent for recruitment of the Bat3 complex would be almost full-length and contain a covalently associated tRNA (red star). Such recruitment-competent polypeptides should migrate on gels close to the full-length size but should be precipitated by CTAB, which selectively precipitates tRNA-associated proteins. , Time course of Sec61β and Sec61β(ΔTMD) (both tagged at the C terminus with the same 12-residue epitope tag) synthesized at 25 °C in reticulocyte lysate. At each time point, samples were analysed directly or after CTAB precipitation. The proportion of total full-length polypeptide that was precipitated by CTAB is plotted. The dashed lines indicate theoretical expectations (Supplementary Fig. 15) for a t1/2 of translational termination of 15 and 60 s. , Model for shuttling of TA proteins from the ribosome to TRC40 by means of a pre-targeting intermediate involving recruitment of the Bat! 3 complex to the ribosome. Author information * Author information * Supplementary information * Comments Affiliations * Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA * Malaiyalam Mariappan, * Xingzhe Li, * Sandra Stefanovic, * Ajay Sharma & * Ramanujan S. Hegde * School of Basic Medical Sciences, Peking University, 100191 Beijing, China * Xingzhe Li * Department of Biochemistry and Molecular Biology, 929 East 57th Street, University of Chicago, Chicago, Illinois 60637, USA * Agnieszka Mateja & * Robert J. Keenan Contributions M.M. performed most of the functional analyses of the Bat3 complex, with significant contributions from X.L. during the initial phase of this study. S.S. and R.S.H. developed and characterized the RNC release assay, S.S. initially identified Bat3, and A.S. performed the tRNA-association experiments. A.M. and R.J.K. produced and functionally characterized recombinant proteins, and provided experimental ideas. M.M., X.L., S.S. and R.S.H. analysed data. R.S.H. conceived the project, guided experiments and wrote the paper with input from all authors. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Ramanujan S. Hegde (hegder@mail.nih.gov) Supplementary information * Author information * Supplementary information * Comments PDF files * Supplementary Figures (5.9M) This file contains Supplementary Figures S1-S15 with legends Additional data
• NRMT is an α-N-methyltransferase that methylates RCC1 and retinoblastoma protein
  Schaner Tooley CE Petkowski JJ Muratore-Schroeder TL Balsbaugh JL Shabanowitz J Sabat M Minor W Hunt DF Macara IG - Nature (London) 466(7310):1125 (2010)
  Nature | Letter NRMT is an α-N-methyltransferase that methylates RCC1 and retinoblastoma protein * Christine E. Schaner Tooley1 Search for this author in: * NPG journals * PubMed * Google Scholar * Janusz J. Petkowski1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Tara L. Muratore-Schroeder3 Search for this author in: * NPG journals * PubMed * Google Scholar * Jeremy L. Balsbaugh3 Search for this author in: * NPG journals * PubMed * Google Scholar * Jeffrey Shabanowitz3 Search for this author in: * NPG journals * PubMed * Google Scholar * Michal Sabat3 Search for this author in: * NPG journals * PubMed * Google Scholar * Wladek Minor2 Search for this author in: * NPG journals * PubMed * Google Scholar * Donald F. Hunt3, 4 Search for this author in: * NPG journals * PubMed * Google Scholar * Ian G. Macara1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1125–1128Date published:(26 August 2010)DOI:doi:10.1038/nature09343Received04 February 2010Accepted08 July 2010Published online28 July 2010Corrected online26 August 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg The post-translational methylation of α-amino groups was first discovered over 30 years ago on the bacterial ribosomal proteins L16 and L33 (refs 1, 2), but almost nothing is known about the function or enzymology of this modification. Several other bacterial and eukaryotic proteins have since been shown to be α-N-methylated3, 4, 5, 6, 7, 8, 9, 10. However, the Ran guanine nucleotide-exchange factor, RCC1, is the only protein for which any biological function of α-N-methylation has been identified3, 11. Methylation-defective mutants of RCC1 have reduced affinity for DNA and cause mitotic defects3, 11, but further characterization of this modification has been hindered by ignorance of the responsible methyltransferase. All fungal and animal N-terminally methylated proteins contain a unique N-terminal motif, Met-(Ala/Pro/Ser)-Pro-Lys, indicating that they may be targets of the same, unknown enzyme3, 12. The initiating Met is cleaved, and the exposed α-amino group is mono-,! di- or trimethylated. Here we report the discovery of the first α-N-methyltransferase, which we named N-terminal RCC1 methyltransferase (NRMT). Substrate docking and mutational analysis of RCC1 defined the NRMT recognition sequence and enabled the identification of numerous new methylation targets, including SET (also known as TAF-I or PHAPII) and the retinoblastoma protein, RB. Knockdown of NRMT recapitulates the multi-spindle phenotype seen with methylation-defective RCC1 mutants3, demonstrating the importance of α-N-methylation for normal bipolar spindle formation and chromosome segregation. View full text Subject terms: * Biochemistry * Cancer * Molecular biology * Cell biology Figures at a glance * Figure 1: Mettl11a is the α-N-RCC1 methyltransferase (NRMT). , Purification scheme for RCC1 N-terminal methyltransferase. , In vitro methylation assay (NE, nuclear extract; D, dialysed nuclear extract; FT, flow through, W, wash) showing activity elutes in the 40 and 60 mM NaP fractions. , ELISA assay showing NRMT overexpression increases RCC1 α-N methylation. Data were analysed by two-tailed independent t tests. n = 3–5 independent reactions per condition. Error bars represent ± 1 s.d. , Lentiviral knockdown of NRMT in 293LT cells significantly decreases NRMT (arrowhead), di- and trimethylated RCC1, and levels of another methylated protein, later shown to be SET(*), as compared to control cells. β-catenin was the loading control. , Expression of murine NRMT–Flag rescues RCC1 methylation levels in NRMT knockdown (KD) cells. , In vitro methylation assays showing that immunoprecipitated Flag–NRMT methylates RCC1–His6 (1, IP input; 2, substrate only; 3, Flag–NRMT elution; 4, Flag–NRMT elution without substrate; 5, con! trol IP elution). , His6–NRMT di- and trimethylates SPK-RCC1–His6 and dimethylates PPK-RCC1–His6. , Immunofluorescence of endogenous NRMT in HeLa cells with or without NRMT siRNA. * Figure 2: Substrate recognition motif of NRMT. , NRMT structure with distribution of electrostatic potential. Electrostatic potential was calculated using APBS Tools plug-in23 with default settings, visualized with PyMol program (DeLano Scientific LLC) and coloured from red (−1 kT) to blue (+1 kT). SPK-RCC1 hexapeptide (SPKRIA) is modelled into the active site. , Schematic view of the interactions between the RCC1 substrate peptide (light blue) and the conserved residues of NRMT. Interactions between Lys 4 of the RCC1 peptide and Asp 178, Asp 181 and Ser 183 of NRMT are shown. All distances are in Å. , Modelling of RCC1 mutant hexapeptide (yellow), in which Lys 4 was replaced by Gln, into NRMT active site. , Mutational analysis of NRMT residues predicted to be involved in SPK-RCC1 recognition. , The affinity of the enzyme was measured using isothermal titration calorimetry. Wild-type 12-residue RCC1 N-terminal peptide showed exothermic binding to NRMT (ΔH = −9.8 kcal mol−1) with a Kd = 70 μM ! (left panel). A mutant peptide in which Gln replaced Lys 4 showed no detectable binding (right panel). * Figure 3: NRMT methylates many targets, including SETα and RB. , His6–NRMT can methylate RCC1–His6 with any amino acid in the second position except Leu, Ile, Trp, Asp and Glu. Data were compared to the unmethylatable SPQ mutant by two-tailed independent t tests. * P < 0.01. n = 3 independent reactions per mutant. Error bars ± 1 s.d. , Coomassie stain of ~40 kDa protein immunoprecipitated by anti-me3-SPK (*). , SETα–GFP is recognized by the anti-me3-SPK antibody. , MS analysis showing SETα–Flag is stoichiometrically N-terminally trimethylated in HeLa cells. Mutation of SETα Lys 4 to Gln abolishes methylation. , Immunoprecipitations with anti-me3-SPK from mouse spleen (shown) and heart lysate produce at least three specific bands visible by Coomassie staining (*). These bands (*), and one additional (+), are recognized by immunoblotting with anti-me3-SPK and correspond to the sizes of the identified mouse proteins (kelch-like 31 = 70 kDa, RCC1 = 45 kDa, SET = 33 kDa, and myosin light chain or ribosomal prote! in L23a ~20 kDa). , Table of N-terminal sequence and methylation status of identified targets. , NRMT–His6 can methylate in vitro the N termini of SET and RB fused to GFP. , Endogenous RB from HCT116 cells, but not HeLa cells, is recognized by the anti-me2-PPK antibody (left panel) and depletion of NRMT in HCT116 cells substantially reduces RB α-N methylation (right panel). * Figure 4: Silencing NRMT reduces RCC1 association with chromatin, and increases frequency of mitotic defects. , Lentiviral silencing of NRMT decreases RCC1 association with chromatin in mitotic (arrowheads) 293LT cells. Chromatin to cytoplasmic ratio of endogenous RCC1 is twice higher in control compared to NRMT-depleted mitotic cells. Data analysed by two-tailed independent t tests. n = 50 mitotic cells for each condition. Error bars, ± 1 s.e.m. , Lentiviral silencing of NRMT decreases the association of RCC1–RFP with chromatin in live 293LT cells. Data were analysed by two-tailed independent t tests. n = 50 mitotic cells for each condition. Error bars, ± 1 s.e.m. , Lentiviral silencing of NRMT increases the frequency of supernumerary spindles to three times higher than that of control cells. Data were analysed by a χ2 test. n = 109 mitotic cells for each condition. Error bars, ± 1 s.d. Change history * Change history * Author information * Supplementary information * CommentsCorrected online 26 August 2010A note was added in proof. Author information * Change history * Author information * Supplementary information * Comments Affiliations * Department of Microbiology, Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA * Christine E. Schaner Tooley, * Janusz J. Petkowski & * Ian G. Macara * Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA * Janusz J. Petkowski & * Wladek Minor * Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA * Tara L. Muratore-Schroeder, * Jeremy L. Balsbaugh, * Jeffrey Shabanowitz, * Michal Sabat & * Donald F. Hunt * Department of Pathology, University of Virginia, Charlottesville, Virginia 22908, USA * Donald F. Hunt Contributions C.E.S.T. purified NRMT and performed the experiments characterizing its function and targets and wrote the paper with I.G.M.; J.J.P. performed the ITC experiments and the RCC1 mutagenesis, and the docking experiments with the aid of M.S.; T.L.M.-S. and J.L.B. performed the mass spectrometry with J.S.; D.F.H. directed the mass spectrometry. W.M. coordinated the experiments of J.J.P.; I.G.M directed the biochemical and cell biological studies. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Christine E. Schaner Tooley (ces5g@virginia.edu) Supplementary information * Change history * Author information * Supplementary information * Comments PDF files * Supplementary Information (5.1M) This file contains Supplementary Table 1 and Supplementary Figures 1-9 with legends. Additional data
• Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification
  Ito S D'Alessio AC Taranova OV Hong K Sowers LC Zhang Y - Nature (London) 466(7310):1129 (2010)
  Nature | Letter Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification * Shinsuke Ito1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Ana C. D'Alessio1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Olena V. Taranova1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Kwonho Hong1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Lawrence C. Sowers3 Search for this author in: * NPG journals * PubMed * Google Scholar * Yi Zhang1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:NatureVolume:466,Pages:1129–1133Date published:(26 August 2010)DOI:doi:10.1038/nature09303Received15 March 2010Accepted28 June 2010Published online18 July 2010Corrected online26 August 2010 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg DNA methylation is one of the best-characterized epigenetic modifications1, 2, 3, 4. Although the enzymes that catalyse DNA methylation have been characterized, enzymes responsible for demethylation have been elusive5. A recent study indicates that the human TET1 protein could catalyse the conversion of 5-methylcytosine (5mC) of DNA to 5-hydroxymethylcytosine (5hmC), raising the possibility that DNA demethylation may be a Tet1-mediated process6. Here we extend this study by demonstrating that all three mouse Tet proteins (Tet1, Tet2 and Tet3) can also catalyse a similar reaction. Tet1 has an important role in mouse embryonic stem (ES) cell maintenance through maintaining the expression of Nanog in ES cells. Downregulation of Nanog via Tet1 knockdown correlates with methylation of the Nanog promoter, supporting a role for Tet1 in regulating DNA methylation status. Furthermore, knockdown of Tet1 in pre-implantation embryos results in a bias towards trophectoderm differentiatio! n. Thus, our studies not only uncover the enzymatic activity of the Tet proteins, but also demonstrate a role for Tet1 in ES cell maintenance and inner cell mass cell specification. View full text Subject terms: * Biochemistry * Cell biology * Molecular biology * Stem cells Figures at a glance * Figure 1: The Tet protein family converts 5mC of DNA to 5hmC. , Expression of wild-type Tet proteins, but not Fe(ii)-binding mutants of Tet1 or Tet2, in U2OS cells results in the generation of 5hmC. Forty-eight hours after transfection, the cells were co-stained with Flag and 5hmC antibodies. Nuclei are counterstained by DAPI. , Recombinant catalytic domains of Tet proteins, but not their catalytic mutants, convert 5mC in DNA oligonucleotides to 5hmC in vitro. Double-stranded DNA oligonucleotides containing a fully methylated MspI site were incubated with wild-type and catalytic mutant forms of Flag–Tet1(1367–2039), Flag–Tet2(916–1921), or Flag–Tet3(697–1668) proteins (1:10 enzyme to substrate ratio) in the presence of Fe(ii) and α-KG. Recovered oligonucleotides were digested with MspI, end labelled with T4 DNA kinase, digested with DNaseI and phosphodiesterase, and analysed by TLC. Unmethylated or 5hmC oligonucleotides containing the same sequences were used as a control for marking the migration of dCMP and hmC on TLC pl! ates. * Figure 2: Knockdown of Tet1, but not Tet2 or Tet3, impairs ES cell self-renewal and maintenance. , Tet1 knockdown impairs ES cell proliferation. Growth curves were determined for control and Tet1 knockdown (KD1 and KD2) cells by counting the cell numbers every day. The average cell numbers, with s.d. from three independent experiments, are shown. , Tet1 knockdown impairs ES cell self-renewal. A single control or knockdown cell was plated in each well and its ability to form colonies was evaluated at day 6 after plating. There is no obvious difference between the colony size, but the colony number is greatly reduced in Tet1 knockdown cells when compared to that from control cells. Error bars represent s.d. of three independent experiments. , RT–qPCR analysis of expression levels of Tet1 and selected stem cell factors in control and knockdown cells. The expression levels in control cells are set as 1. Error bars represent s.d. of three independent experiments. , Western blot analysis of Tet1 and selected stem cell factors in control and knockdown cells. Actin is used as! a loading control. , RT–qPCR analysis of the expression of various cell lineage marker genes in control and Tet1 knockdown ES cells. The expression level in control knockdown cells is set as 1. Error bars represent s.d. of three independent experiments. * Figure 3: Nanog is a direct Tet1 target and Tet1 knockdown phenotypes can be partially rescued by expression of exogenous Nanog. , ChIP analysis demonstrates that Nanog is a direct target of Tet1. The top panel is a diagram of the Nanog gene with the four amplicons indicated. The proximal and distal T-DMR as well as regions I and II are defined as in ref. 8. The numbers in the diagram refer to the gene coordinates. The bottom left panel shows Tet1 enrichment in control and Tet1 knockdown cells relative to IgG controls. The bottom right panel is 5mC enrichment in Tet1 knockdown relative to control knockdown. Results presented are the average of three independent experiments with s.d. , Bisulphite sequencing results indicate that Tet1 knockdown in ES cells results in an increase in DNA methylation at the proximal T-DMR (Fig. 3a) of the Nanog promoter. Open circles indicate unmethylated CpG dinucleotides; filled circles indicate methylated CpGs. , RT–qPCR analysis demonstrates that knockdown of Tet1 in wild-type J1 ES cells, but not in the DNMT triple knockout (TKO) J1 ES cells, results in Nanog downre! gulation. Error bars represent s.d. of two independent experiments. , Alkaline phosphatase staining of mouse ES cells after puromycin selection of cells infected with lentiviruses expressing control and Tet1 knockdown shRNAs with or without co-expression of Nanog. , The self-renewal defects associated with Tet1 knockdown can be partially rescued by expression of exogenous Nanog. Self-renewal assay was performed as that described in Fig. 2b. , RT–qPCR analysis demonstrates that expression of exogenous Nanog suppressed upregulation of differentiation genes (Cdx2, Gata6) caused by Tet1 knockdown. Data shown are the average of three independent experiments with error bars (s.e.m). * Figure 4: Tet1 is required for ICM cell specification in blastocysts. , Tet1 protein is present in the nuclei of pre-implantation mouse embryos. Mouse embryos at different developmental stages (one-cell to blastocyst) were stained with Tet1 antibody. Note that Tet1 is relatively enriched in the ICM when compared to that in the trophectodermal cells at the blastocyst stage. , RT–qPCR demonstrates that ICM-derived ES cells expressed higher levels of Tet1 when compared with trophoblast stem cells (TS cells). Error bars represent s.d. of three independent experiments. , Knockdown of Tet1 at the two-cell stage promotes trophectoderm cell specification. Representative Z-stack image of a control and a knockdown blastocyst are shown. Trophectoderm lineage cells are Cdx2 positive (green). Control knockdown and Tet1 knockdown cells are marked in red. Cells with yellow colour in the merge panels are trophectoderm lineage cells that were derived from the injected blastomere. , Ratio of Cdx2+RFP+ cells over RFP+ cells from control knockdown and Tet1 knoc! kdown. Eight control-injected embryos and nine Tet1 siRNA injected embryos were used for the quantification analysis (P < 0.001). Error bars represent s.e.m. , Knockdown of Tet1 prevents cells from contributing to the ICM. Representative Z-stack images with Oct4 staining (green) in control and Tet1 knockdown cells (red). Cells with yellow colour in the merge panels are the cells derived from the injected blastomere that contributed to the ICM. , Ratio of Oct4+RFP+ cells over RFP+ cells from control knockdown and Tet1 knockdown. Seven control-injected embryos and seven Tet1 siRNA injected embryos were used for the quantification analysis (P = 0.004). Error bars represent s.e.m. Change history * Change history * Author information * Supplementary information * CommentsCorrected online 26 August 2010A change was made to Acknowledgments Author information * Change history * Author information * Supplementary information * Comments Affiliations * Howard Hughes Medical Institute, * Shinsuke Ito, * Ana C. D'Alessio, * Olena V. Taranova, * Kwonho Hong & * Yi Zhang * Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295, USA * Shinsuke Ito, * Ana C. D'Alessio, * Olena V. Taranova, * Kwonho Hong & * Yi Zhang * Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350, USA * Lawrence C. Sowers Contributions Y.Z. conceived the project and wrote the manuscript. S.I., A.C.D., O.V.T. and K.H. designed and performed the experiments. L.C.S. provided the oligonucleotide substrates. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Yi Zhang (yi_zhang@med.unc.edu) Supplementary information * Change history * Author information * Supplementary information * Comments PDF files * Supplementary Information (12M) This file contains Supplementary Figures S1-S13 with legends and Supplementary Tables 1-5. Additional data
• The giant bite of a new raptorial sperm whale from the Miocene epoch of Peru
  - Nature (London) 466(7310):1134 (2010)
  Nature | Corrigendum The giant bite of a new raptorial sperm whale from the Miocene epoch of Peru * Olivier Lambert Search for this author in: * NPG journals * PubMed * Google Scholar * Giovanni Bianucci Search for this author in: * NPG journals * PubMed * Google Scholar * Klaas Post Search for this author in: * NPG journals * PubMed * Google Scholar * Christian de Muizon Search for this author in: * NPG journals * PubMed * Google Scholar * Rodolfo Salas-Gismondi Search for this author in: * NPG journals * PubMed * Google Scholar * Mario Urbina Search for this author in: * NPG journals * PubMed * Google Scholar * Jelle Reumer Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:NatureVolume:466,Page:1134Date published:(26 August 2010)DOI:doi:10.1038/nature09381 Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Nature466, 105–108 (2010) The genus name Leviathan, proposed in this Letter for a new fossil physeteroid from the Miocene of Peru, is preoccupied by Leviathan Koch, 1841 (ref. 1), a junior subjective synonym of Mammut Blumenbach, 1799 (ref. 2). We propose here a replacement name Livyatan gen. nov. The type species is placed in this genus to form the binomial Livyatan melvillei. The diagnosis and content of the new genus follow our Letter. 'Livyatan' is a Hebrew name applied to large marine monsters in popular and mythological stories. We thank M. P. Taylor and D. Yanega for bringing this to our attention. References * Koch, A.Description of the Missourium, or Missouri Leviathan 2nd edn (Prentice & Weissinger, 1841) * Blumenbach, J. F.Handbuch der Naturgeschichte, 6. Auflage (Göttingen, 1799) Download references Additional data
• Fighting the monster
  - Nature (London) 466(7310):1134 (2010)
  Nature | Corrigendum Fighting the monster * Amy Maxmen Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:NatureVolume:466,Page:1134Date published:(26 August 2010)DOI:doi:10.1038/nature09382 Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Nature466 (suppl.), S18–S19 (2010) This Outlook article incorrectly stated that David McMurray is not affiliated with Aeras; in fact he is on the board of Aeras, but he is not directly working on the AERAS-402 vaccine. Additional data
• Temperature-controlled organic carbon mineralization in lake sediments
  - Nature (London) 466(7310):1134 (2010)
  Nature | Corrigendum Temperature-controlled organic carbon mineralization in lake sediments * Cristian Gudasz Search for this author in: * NPG journals * PubMed * Google Scholar * David Bastviken Search for this author in: * NPG journals * PubMed * Google Scholar * Kristin Steger Search for this author in: * NPG journals * PubMed * Google Scholar * Katrin Premke Search for this author in: * NPG journals * PubMed * Google Scholar * Sebastian Sobek Search for this author in: * NPG journals * PubMed * Google Scholar * Lars J. Tranvik Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:NatureVolume:466,Page:1134Date published:(26 August 2010)DOI:doi:10.1038/nature09383 Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Nature466, 478–481 (2010) In Figure 1a and b of this Letter, the sign in the regression equations should have been a plus symbol, not a minus symbol. This does not affect the reported results or conclusions of the paper. Additional data
• Detection of functional haematopoietic stem cell niche using real-time imaging
  - Nature (London) 466(7310):1134 (2010)
  Nature | Corrigendum Detection of functional haematopoietic stem cell niche using real-time imaging * Yucai Xie1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Tong Yin2 Search for this author in: * NPG journals * PubMed * Google Scholar * Winfried Wiegraebe2 Search for this author in: * NPG journals * PubMed * Google Scholar * Xi C. He2 Search for this author in: * NPG journals * PubMed * Google Scholar * Diana Miller3 Search for this author in: * NPG journals * PubMed * Google Scholar * Danny Stark2 Search for this author in: * NPG journals * PubMed * Google Scholar * Katherine Perko2 Search for this author in: * NPG journals * PubMed * Google Scholar * Richard Alexander2 Search for this author in: * NPG journals * PubMed * Google Scholar * Joel Schwartz2 Search for this author in: * NPG journals * PubMed * Google Scholar * Justin Grindley2 Search for this author in: * NPG journals * PubMed * Google Scholar * Jungeun Park2 Search for this author in: * NPG journals * PubMed * Google Scholar * Jeff Haug2 Search for this author in: * NPG journals * PubMed * Google Scholar * Joshua Wunderlich2 Search for this author in: * NPG journals * PubMed * Google Scholar * Hua Li2 Search for this author in: * NPG journals * PubMed * Google Scholar * Simon Zhang2 Search for this author in: * NPG journals * PubMed * Google Scholar * Teri Johnson2 Search for this author in: * NPG journals * PubMed * Google Scholar * Ricardo A. Feldman3 Search for this author in: * NPG journals * PubMed * Google Scholar * Linheng Li2, 4 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:NatureVolume:466,Page:1134Date published:(26 August 2010)DOI:doi:10.1038/nature09384 Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Nature457, 97–101 (2009) In this Letter, affiliations 1 and 2 were in the wrong order. The correct affiliations are as shown here. Additional data Affiliations * Department of Cardiology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin 2 Road, Shanghai 200025, China * Yucai Xie * Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, Missouri 64110, USA * Yucai Xie, * Tong Yin, * Winfried Wiegraebe, * Xi C. He, * Danny Stark, * Katherine Perko, * Richard Alexander, * Joel Schwartz, * Justin Grindley, * Jungeun Park, * Jeff Haug, * Joshua Wunderlich, * Hua Li, * Simon Zhang, * Teri Johnson & * Linheng Li * Department of Microbiology and Immunology, and Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA * Diana Miller & * Ricardo A. Feldman * Department of Pathology and Laboratory Medicine, Kansas University Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA * Linheng Li
• Cellular imaging: Taking a long, hard look
  - Nature (London) 466(7310):1137 (2010)
  Nature | Technology Feature Cellular imaging: Taking a long, hard look * Monya Baker1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:NatureVolume:466,Pages:1137–1140Date published:(26 August 2010)DOI:doi:10.1038/4661137aPublished online25 August 2010 Long-term, live-cell imaging helps to settle long-running debates. Monya Baker investigates how the huge investment and time commitment is finally paying off. Subject terms: * Biotechnology * Cell biology * Developmental biology * Stem cells Introduction * Introduction * References * Author information * Comments Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg In the late 1980s, Sally Temple was studying neural development in mice at the University of Miami in Florida and needed a way to observe neural progenitor cells for days on end. At the time, no one had observed mammalian cells for more than a few hours, because the conditions that could be maintained under a microscope were too dry, cold and oxygen-rich to keep cells alive for long. Undeterred by the lack of precedent, Temple decided to build her own device that could monitor cells around the clock. S. GODERIE/TEMPLE LAB Neural stem cells and their descendants showing neurons (green) and neural epithelial cells (red). Temple, a developmental neuroscientist now at the Neural Stem Cell Institute in Rensselaer, New York, credits her husband Jeffrey Stern with the inspiration for her apparatus. "He said, 'if the cells are living well in the incubator, you have to put the microscope in the incubator'," she recalls. Although the idea was obvious to Stern — a vision researcher and co-founder (with Temple) of the Neural Stem Cell Institute — it seemed ludicrous to most cell biologists, who had long held the view that the humidity inside an incubator would ruin microscope optics. Temple was also sceptical. But she found an abandoned microscope and decided it was worth a try. She outfitted the ageing microscope with a red filter (a piece of broken glass taped onto a Petri dish) to minimize the cells' exposure to more damaging, higher-energy light during her extended experiment. She then attached a camera and drilled a hole through the incubator to connect the camera to a Panasonic tape deck, which could record image data several times an hour for up to seven days. Remarkably, the makeshift contraption worked. "We got some really neat data that showed to our surprise — I think to everyone's surprise — that the vertebrate brain had lineage trees that were similar to Caenorhabditis elegans and other invertebrates," says Temple1. But the discovery required as much luck as it did innovation. Temple's cobbled-together set-up could only keep track of what was under the microscope at a particular time, and the slide couldn't be moved around to find the most photogenic cells. If the few cells that were in the microscope's field of view had died or grown poorly, the whole project would never have panned out. TEMPLE LAB Sally Temple (inset) now uses a fully automated incubation system, but her first time-lapse set-ups relied on microscopes inside incubators. All the major microscope manufacturers now offer a new generation of devices built for live-cell imaging, complete with computerized incubation chambers and microscope stages. Jochen Tham, global marketing and communications director at Carl Zeiss MicroImaging in Thornwood, New York, tracks what he describes as some of the major developments at his company: multilayered incubation, cooling and heating, computer control of environmental parameters, integration of microscope-controlling software and image-acquisition software, incubators for super-resolution and total internal reflection, and control over oxygen levels to mimic physiological conditions, to name just a few. Such systems are helping researchers come to a more complete understanding of how functional cells and tissues develop. "Unless you can actually watch everything that is happening from the first cell up to the developing progeny, you have no idea how [cell development] actually plays out," says Michel Cayouette, a developmental neurobiologist at the Clinical Research Institute of Montréal, Canada, whose work has revealed a way to predict how retinal progenitor cells divide2, information that could help to produce cells for treating blindness. Cayouette compares studying cell differentiation to watching ice hockey: how much could he learn about the game if all he knew was the final score? Scientists have valid reasons for avoiding long-term imaging experiments. They require expensive equipment that gets tied up for days or weeks at a time and are prone to time-consuming false starts. As an experiment runs its course, all aspects of keeping cells alive and in focus get harder: cells move, routine handling becomes disruptive and computer hard drives fill up. Any one of these unpredictable events can derail an experiment, says Cayouette. "You can't say, 'I'll try this and at the end of the week, I'll figure out what to do.'" So researchers are planning ahead, and devising new systems for tracking cells in real time. T. SCHLAEGER/CHILDREN'S HOSPITAL BOSTON Human embryonic stem cells on mouse embryonic fibroblasts. Getting answers Beyond offering a lens onto new biology, long-term imaging studies are also beginning to resolve long-standing debates in developmental and cell biology. For example, Timm Schroeder, a stem-cell biologist at the Helmholtz Centre in Munich, Germany, led a team that used continuous imaging to distinguish between two competing hypotheses about the role of cytokines in blood development. One view held by some immunologists is that cytokines — regulatory proteins found in the immune system — cause cells to take on new fates; another theory is that cytokines help certain cell types but not others to survive. Both ideas would ultimately result in the same blood cells, but the path by which the cells got there would be radically different. As such, the two hypotheses would hold vastly different implications for treating diseases or generating blood in the laboratory. To tease apart the actual mechanism, Schroeder's group took pictures of mouse blood cells every two to three minutes for several days. Because the researchers did not observe extensive cell death, their time-lapse film firmly supported the active instruction over the passive-survival hypothesis3. Long-term images make "a big, big difference", says Schroeder. "You can say, 'this is how it was', not 'this is how it probably was'." HELMHOLTZ CENTRE MUNICH Timm Schroeder observes cells to disinguish between competing hypotheses. Researchers working in the fast-paced field of stem-cell reprogramming have also been keen to track how cells take on desired fates. Under most experimental set-ups, the early events are the hardest to follow. But a team led by George Daley and Thorsten Schlaeger, stem-cell biologists at the Children's Hospital Boston in Massachusetts, used long-term imaging to reveal the history of rare, reprogrammed cells. To identify the presence of expected molecules on cell surfaces, the researchers added fluorescently tagged antibodies to the culture media as the cells grew into the colonies characteristic of induced pluripotent stem (iPS) cells. Meanwhile, they set their microscope to scan the cells constantly, making a complete survey of the 4-square-centimetre area every two or three days for about two weeks. After assessing which colonies produced high-quality iPS cells, the team could go back to the images to identify the cell clusters that gave rise to fully reprogrammed cells, even though each group of iPS cells took up as little as 0.0003% of the scanned area4. Learning the hallmarks of iPS cells as they undergo reprogramming could not only yield better methods for growing patient-specific stem cells, but also prevent weeks of wasted effort (and costs) in animal experiments, says Schlaeger. Come to light These types of study are starting to shed light on hitherto unsolvable biological problems, such as why some patterns of cell division contribute to cancer and which progenitor cells give rise to blood, sperm, neurons or other tissue types. But researchers using live-cell imaging have to be careful not to shed too much light — quite literally — because illuminating cells for long durations can damage cells or alter their behaviour. Schroeder's advice to biologists is to take the worst image possible to get the necessary data. "If you're pushing the envelope, you should aim for having healthy cells rather than the best images," he says. Beautiful images, he notes, often make for unhealthy cells. So instead of continuous snapshots, researchers often rely on taking pictures at less frequent intervals. Many factors contribute to the imaging method used — the types of cell and how robust they are, what features need to be followed, even the size of the image files that will be collected (see 'A long-term live-cell commitment'). The most important decision is usually what type of light to use. Fluorescent tags can be linked to the expression of particular proteins to indicate specific biological activity or the production of an oncogene, for example. But too much fluorescence-activating light can trigger damage that prevents cells from growing — a phenomenon known as phototoxicity. Even with cells that resist phototoxicity, there are image-processing considerations. If viewed too often, fluorescent proteins can fade and become invisible. Overcoming such photobleaching requires the subtraction of background fluorescence and correcting for the fact that because the sample is not perfectly flat, levels of illumination vary across the field of view. CAYOUETTE LAB (LEFT); H. LAMBIN (RIGHT)/IRCM Michel Cayouette (right) uses long-term imaging to predict which retinal progenitors will produce neurons. Unlike fluorescence microscopy, phase-contrast imaging produces black and white pictures using less damaging wavelengths of light. But the technique reveals only the general cell shape, rather than the presence of a particular protein. Researchers often combine the two methods by, for example, taking a fluorescent image every hour and a phase-contrast image every ten minutes, but even that compromise must be planned carefully. Some instruments that are great for fluorescence microscopy perform less effectively at bright-field microscopy, explains Schlaeger. Keeping watch Keeping cells alive requires a much more delicate balancing act than finding the right mix or amount of photons. Even if cells aren't perturbed by the imaging set-up, they still need fresh culture media and the removal of waste products. Plus, any continuous imaging study that lasts for more than an hour will probably require a system with built-in environmental controls for temperature, humidity and gas concentration — and maintaining the right conditions for cells often requires special care for microscopes. For example, to avoid creating air currents that could blur an image when cells are kept at standard 37 °C, microscopes for studying live cells have to maintain the lens at the same temperature as the culture. Environmental chambers are available for all high-end microscopes, either from the microscope manufacturer or from third parties, but none works as well as an incubator, say researchers. Temple and her graduate students nicknamed an early model 'the Sahara' because it caused cells to dry out so quickly. The commercially available products have improved, says Jin-Wu Tsai, who studies cultured brain slices in Arnold Kriegstein's lab at the University of California, San Francisco. "A few years ago, we built our own incubator on top of the microscope. Now you have lots of options," he says. With these newer commercial tools, "we can just keep the culture dish on the stage of the microscope, and the software allows us to take images every ten or fifteen minutes". Although he doesn't have to transfer samples, Tsai is still tethered to his microscope, keeping watch on its confocal image. The brain slices he studies flatten over time, making the image go out of focus, and it doesn't matter how healthy the cells are if the data collected from them aren't usable. Prototype microscopes with autofocus have been introduced. They might be reliable for flat culture, Tsai says, but he doesn't trust them to work in thick brain slices yet. In addition to keeping tabs on the brain slices themselves, Tsai has to monitor every facet of the experiment. If the conditions are just slightly off — say, a shift in pH, or a slight increase in carbon dioxide — the neurons stop growing. And there is still no way to change media under the microscope and maintain sterile conditions, he says. Nonetheless, Tsai and his colleagues have been able to keep brain slices alive for more than a week, after which time bacteria have started to grow. Conditions also need to be tightly controlled to minimize artefacts and experiment-ruining variability. Over the run of a protracted experiment, subtle differences in culture conditions can start to look like cell behaviour, notes Alfred Bahnson, a biologist at Kairos Instruments in Pittsburgh, Pennsylvania, which manufactures optically accessible environmental chambers and other long-term imaging products. Movement that appears to be cell migration, says Bahnson, might instead be cells moving downhill or following slight temperature gradients. Coordinating accessories Those imaging issues are typical, says Keith Bogdon, an adviser with consulting company Coalesce Corporation in Larkspur, California, who has researched live-cell imaging products. Often features to control temperature or pH conflict with features for positioning or focusing cells in the microscope, particularly if researchers want to compare several experimental conditions. "There are a lot of wires and tubes coming out of the plates," says Bogdon, and it is difficult to design a chamber so that cells can be both monitored and unperturbed. S. GODERIE/TEMPLE LAB Stills from a film of an individual cell dividing into dozens of neurons (left), and many neural cells produced from a single neural stem cell (right). Even after the microscope, environmental chamber, and other equipment are brought together so that cells stay alive, the length of experiments can still be a problem. Most labs and core facilities aren't designed to accommodate experiments that tie up equipment for weeks at a time. If a researcher works out too late that some parameters need to be tweaked, it could take months to book the necessary time with the microscope again. And long-term imaging is costly in money as well as time. Renting equipment from a core facility at, say, US$20 an hour, 24 hours a day for a week or more could make even a single experiment pricey. "If you do this for half a year," says Schroeder, "you've paid more for renting than for buying." But buying equipment with a six-figure price tag is not always easy. "It's a classic chicken and egg scenario," says Bogdon. "How can researchers get into the area if they don't have the clout to justify funding?" NIKON Nikon BioStation CT has software and robotics to allow several scientists to conduct experiments. Still, researchers report that commercial offerings in software, cell incubation, and visual systems have expanded greatly. Microscope systems used for live-cell imaging for time periods of more than 24 hours are produced by companies including BD Biosciences in San Jose, California; Essen BioSciences in Ann Arbor, Michgian; GE Healthcare in Waukesha, Wisconsin; Leica in Wetzlar, Germany; Molecular Devices in Sunnyvale, California; Nikon in Melville, New York; Olympus in Center Valley, Pennsylvania; PerkinElmer in Waltham, Massachussetts; and Zeiss. Each system comes with its own proprietary software and storage options, and additional software is available, all of which tends to require considerable expertise (see 'A software spot'). Molecular Devices offers MetaMorph imaging analysis software; the imaging-processing software MatLab from MathWorks in Natick, Massachusetts, can be purchased with add-on image analysis tools. Volocity from PerkinElmer is popular. ImageJ from the US National Institutes of Health and Cell Profiler from the Broad Institute in Cambridge, Massachusetts, are both freely available and widely used. Several companies, such as Oko Lab in Ottaviano, Italy, Tokai Hit in Shizuoka-ken, Japan, and WaferGen Biosystems in Fremont, California, sell environmentally controlled microscope slides or other equipment to control conditions on the microscope stage. Still, a microscope accessory that solves one problem often creates another, says Schroeder. An incubator that fits to the stage of one microscope may not provide the kind of surface that a particular cell type grows on, or tubing that fits an incubator may not attach to a media pump. A computer program names files with a four-digit code, limiting experiments to less than ten-thousand images. And so on. Each problem is trivial individually, says Schroeder, but collectively they sap researchers' motivation and take up time that could be spent on experiments. Anyone who wants to conduct long-term live-cell experiments needs to be ready to spend a long time tinkering with equipment, he says. But the benefits are repeatedly proving worth the hassle, says Cayouette. "The technique is becoming increasingly user-friendly. More and more people are trying to do these long-term imaging studies." Temple predicts that the results of such studies will be profound. "We've just forgotten the fourth dimension in so many of these analyses," she says. "Now that we've got time, we can finally start to understand." References * Introduction * References * Author information * Comments * Qian, X., Goderie, S. K., Shen, Q., Stern, J. H. & Temple, S.Development125, 3143–3152 (1998). * ChemPort * ISI * PubMed * Cohen, A. R., Gomes, F. L. A. F., Roysam, B. & Cayouette, M.Nature Methods7, 213–218 (2010). * ChemPort * PubMed * Article * Rieger, M. A., Hoppe, P. S., Smejkal, B. M., Eitelhuber, A. C. & Schroeder, T.Science325, 217–218 (2009). * ChemPort * PubMed * Article * Chan, E. M.et al. Nature Biotechnol.27, 1033–1037 (2009). * Article * Carlton, P. M.et al. Proc. Natl Acad. Sci. USA advanced online publication doi:10.1073/pnas.1004037107 (2010) * Huth, J.et al. BMC Cell Biol.11, 24 (2010). * PubMed * Article Download references Author information * Introduction * References * Author information * Comments Affiliations * Monya Baker is technology editor for Nature and Nature Methods. Additional data
• Cellular imaging: A long-term live-cell commitment
  - Nature (London) 466(7310):1138 (2010)
  Nature | Technology Feature Cellular imaging: A long-term live-cell commitment Journal name:NatureVolume:466,Page:1138Date published:(26 August 2010)DOI:doi:10.1038/4661138aPublished online25 August 2010 Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg The decision to undertake a long-term imaging project is not trivial. Experts suggest questions that researchers should ask themselves before starting out. Tracking individual cells often requires taking an image every few minutes. The more dense and mobile the cells are, the less time can elapse between images. For example, Michel Cayouette at the Clinical Research Institute of Montréal, Canada, takes images of retinal progenitor cells every seven minutes until they develop into neurons, at which stage he slows the rate of image acquisition to roughly once an hour. Repeated imaging can harm cells, especially when the imaging requires high-energy light. But the tolerance of different cells for fluorescence varies widely. Blood-forming stem cells are generally more robust than neural stem cells, for example, and thus can be imaged more frequently without affecting cell behaviour, notes Tannishtha Reya, a stem-cell biologist at Duke University in Durham, North Carolina. Inexperienced researchers sometimes set up their long-term microscope systems in the middle of a heavily trafficked work station or worse, under ventilation systems. Such disturbances can easily overwhelm a system's ability to maintain stable conditions and can cause obfuscating artefacts, cautions Cayouette. Following cells in culture gets complicated once cells start crawling under and over each other. To track individual cells at low densities, labelling nuclei with Hoeschst often works well, says Thorsten Schlaeger at the Children's Hospital Boston in Massachusetts, although he cautions that some cells stain poorly, and non-toxic genetic labels can work better. If cells must be grown at high density, consider mixing in a few labelled cells and tracking just these. Crunching through large data sets can easily go beyond the capacity of standard lab computers, and a single experiment can completely fill a computer's hard drive. Researchers need appropriate servers and back-up systems. A dedicated informatics set-up and the help of a programmer are "highly desirable", says Schlaeger. See Also: Cellular imaging: Taking a long, hard look Additional data
• Cellular imaging: A software spot
  - Nature (London) 466(7310):1139 (2010)
  Nature | Technology Feature Cellular imaging: A software spot Journal name:NatureVolume:466,Page:1139Date published:(26 August 2010)DOI:doi:10.1038/4661139aPublished online25 August 2010 Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Computerized robotics are already easing lab-based wet tasks such as feeding cells and changing media. Several vendors now sell programs that can track cells in flat culture, keeping them in focus and in the field of view. The latest version of the Nikon BioStation CT can 'memorize' the positions of non-motile cells before a plate is removed for media exchange, and can then continue tracking them when the plate is replaced, avoiding the 'image jiggle' that would disrupt statistical analysis, says Ned Jastromb, a senior application manager at Nikon Instruments in Melville, New York. It also integrates a calendar function with a robotic system that slides culture plates in and out of an imaging area on schedule, allowing one instrument to run several long-term experiments. But software is poised to solve a wider range of problems. By combining a fast image-acquisition program with a noise-reducing algorithm that compares consecutive images, John Sedat at the University of California, San Francisco, and his colleagues decreased the amount of light needed to image yeast cell division by several orders of magnitude 5. Advances in fully automated cell identification and tracking, and modern continuous cell-imaging techniques can outperform traditional manual methods6. Historically, software advances have spread slowly because programs designed to follow a particular cell type tend not to recognize other types, says Andrew Cohen, a computer engineer at the University of Wisconsin–Milwaukee. More broadly, Cohen says he may be on the cusp of solving a problem that plagues many live-cell imaging experiments. Many software programs work only when cells are sparse. That limits the technology because some cells can grow only in dense cultures, and some cells divide many times before producing the desired cell types, in which case a single cell produces hundreds of daughters. By the time the most interesting cells appears, it is impossible to tell which cells they came from. Recently, Cohen found that an algorithm he originally wrote to follow hundreds of organelles within a single cell can be applied to trace neural stem-cell fate. "Our ability to track very high-density image sequences is going to improve very rapidly," he says. Larger advances, however, may come less from improvement in technology than from biologists' awareness of what software can do, says Cohen. "Sometimes the biologists start out just wanting to characterize data, and they don't think about the big questions they can ask." References * References * Comments * Carlton, P. M.et al. Proc. Natl Acad. Sci. USAadvanced online publication doi:10.1073/pnas.1004037107 (2010) * Huth, J.et al. BMC Cell Biol.11, 24 (2010). * PubMed * Article Download references See Also: Cellular imaging: Taking a long, hard look Additional data
• Correction
  - Nature (London) 466(7310):1140 (2010)
  Nature | Correction Correction Journal name:NatureVolume:466,Page:1140Date published:(26 August 2010)DOI:doi:10.1038/4661140aPublished online25 August 2010 Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg The Technology Feature 'The gatekeepers revealed' (Nature465, 823–826; 2010) stated that the crystal structure for the A2A adenosine receptor and similar receptors had been solved using an unmodified protein, but referenced the structure of a protein stabilized with T4 lysozyme. Structures for the unmodified receptors have not been published. Additional data
• Cellular imaging: Table of suppliers
  - Nature (London) 466(7310):1141 (2010)
  Nature | Technology Feature Cellular imaging: Table of suppliers Journal name:NatureVolume:466,Pages:1141–1142Date published:(26 August 2010)DOI:doi:10.1038/4661141aPublished online25 August 2010 Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Table 1 Table 1 Full table Additional data
• Me am Petri
  - Nature (London) 466(7310):1148 (2010)
  Nature | Futures Me am Petri * Martin Hayes1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:NatureVolume:466,Page:1148Date published:(26 August 2010)DOI:doi:10.1038/4661148aPublished online25 August 2010 Information overload. Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Dr Richard Finch left the lab on the Friday afternoon of the long weekend. He was looking forward to a few days R&R. Stress wasn't even the word for it. It was only two days since an asteroid the size of a microwave oven had smashed into the park just across the road. Things were still pretty crazy. It had taken three hours just for the clouds of dust to abate. The Fire Chief had been on the national news explaining how it was a miracle that no one had been killed. The lab was a write-off. The impact had emptied shelves and uprooted benches, but it could have been worse. They had been winding this facility down even before the asteroid hit, which meant that the viable embryos had already been moved to the new building across town. Finch was the only person working in the lab that week, tidying things away while his colleagues got the new facility up and running. All that the lab contained now was a selection of old and obsolete equipment and a freezer full of unviable embryos awaiting destruction. And that was just as well — because the impact had upturned the cryo-freezer and spilled its contents all over the floor. Finch had swept up and safely disposed of the vast majority of the detritus, but as he left the lab with a spring in his step he did not notice the dustpan full of broken test tubes and Petri dishes that he had left on the bench. Nor did he notice that the blast had cracked one of the lab's large windows, and that a light breeze was wafting in as he pulled the door shut. Me ... Me ... light ... Me sense light ... Me sense light on photosensitive cells amassing on back of mass that is me. Me grow pit in back. Me feel cells drift into pit in back. Me feel opening of pit get smaller. Me focus light now. Me see shapes. Me think about shapes me sees. Me begin to think more and more. Me am Petri. Me spread tendrils over lip of glass shell that houses Petri. Me outgrow shell. Me spread across flat plane that supports shell. Me sense heat from distant star. Me try to remember stars from long time gone. Me was part of something bigger. Something much bigger than what Me am now. Me's tendrils sense tickly air near faint source of heat on plane that supports shell. JACEY Me grows tendrils towards tickles. Me feels heat and new wind. Me's tendrils stroke shape that Me sees inside Me's mass. Me slips tendrils deeper in. Me touches something strange. Me frightened. Me get too much information. Me stung by surge of information. Me pull tendrils away. But Me like tickles. Me put tendrils back in deep. Me learn about history of plane on which plane that supports shell stands. Me unhappy. Me scared. Me know that locals will not like Me. Me flickers tendrils. Me accesses new information. Me learn local name of source of heat in sky. Me 'reads'. Me know that locals call it 'reads'. Me reads information to do with probable imminent demise of locals. Me reads locals know it and do not care. But for some. Who do care. Who are called liars. Me feel sad. Me feel sad for silly locals. Me flicker tendrils again. Me cannot stop surge of information. Me learn how to cook perfect duck confit. Me learn name of big star footballer's lover ... "She didn't mean to be a home-wrecker." Me see man sit on glass jar and glass jar breaks. Man sad. Me sad. Me see woman crash car. Me now know "Stupid Blondes Can't Drive!" Me see many strange protrusions being slipped in and out of many openings. Me see incredible, jaw-dropping feats of local's ingenuity and imagination. Me see these feats are "FAKE!!!" Me see locals complain that local in charge wants them to be healthy. Locals hate local chief for it. Locals must want to be sick. Locals are stupid. Me learn "FAIL" and "EPIC" and "EPIC WIN!" Me wants cheezburger. Me sees cat do funny thing. Me ROFL. Me now think that every local should have his say. No matter how ill-informed or obviously stupid local is. Me can't help but absorb stupid local's unsustainable reactionary opinions. Me think all paediatricians should be killed. Me on social networking site trying to form angry mob to kill all paediatricians. Me overwhelmed with anger and stupidity. Me PWNED by Sword of Gondor in debate over local gun law. Me want gun now. Me wish me never came here to this plane. Me want to leave here. Me miss quiet. Me bored of LATINACHICKBOYS. Me have rudimentary arm now. Me can feel me's form and shape. Me does not like what me feels. Too thick. Me want to be slim. Me hate Me now. Me hate everything now. Everything stupid. Everything EPIC FAIL!!! Dr Finch returned to the lab on the wet Tuesday morning following the long weekend. He dropped his morning coffee as he stared in horror at the primitive, misshapen and strangely humanoid life form that lay dead across his desk. It had one stumpy arm and a large rudimentary eye in the centre of its semi-transparent back. Long, moss-like tendrils had spread from the edges of the creature's mass and inched their way into his computer. He took a step closer, his mouth hanging open, and nudged the mass of tissue with the point of his umbrella. It did not move. It had slit its own throat with his letter opener. Author information * Author information * Comments Affiliations * Martin Hayes is an Irishman abroad in his own country. He potters about and tends to drink a lot of Guinness in the afternoon. You can visit him at http://www.paroneiria.com. Additional data