Hot off the presses! Oct 01 Nature

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Latest Articles Include:

• Back on the map
  - Nature 461(7264):569 (2009)
  Central and eastern European nations still lag behind Western countries in science. But they are slowly catching up.
• Containing risk
  - Nature 461(7264):569 (2009)
  The US Department of Homeland Security should not be put in charge of biodefence research.
• Delimiting death
  - Nature 461(7264):570 (2009)
  Procuring organs for transplant demands a realistic definition of life's end.
• Computational biology: Protein comets
  - Nature 461(7264):572 (2009)
  
• Molecular evolution: A colourful history
  - Nature 461(7264):572 (2009)
  
• Particle physics: Top quarks measure up
  - Nature 461(7264):572 (2009)
  
• Immunology: T cells on the move
  - Nature 461(7264):572 (2009)
  
• Biology: Antennae show the way
  - Nature 461(7264):572 (2009)
  
• Geology: Killer quake
  - Nature 461(7264):572 (2009)
  
• Climate change: Looming locusts
  - Nature 461(7264):573 (2009)
  
• Neuroscience: Wake up to dementia
  - Nature 461(7264):573 (2009)
  
• Atmospheric science: Menacing methane
  - Nature 461(7264):573 (2009)
  
• Ecology: Survival tips
  - Nature 461(7264):573 (2009)
  
• Journal club
  - Nature 461(7264):573 (2009)
  
• News briefing: 1 October 2009
  - Nature 461(7264):574 (2009)
  The week in science This article is best viewed as a PDF. Policy|Events|Research|Business|The week ahead|News maker|Number crunch The on 27 September returned Chancellor Angela Merkel to power. She aims to strike a new coalition with the Free Democratic Party, which has promised a liberal approach to contentious research issues such as human embryonic stem cells and genetically modified crops (see Nature 461, 456–457; 2009). Merkel is also expected to review the country's plans to phase out its nuclear power stations over the next decade. The unanimously backed a non-binding resolution to bolster efforts aimed at slowing the spread of nuclear weapons. It endorsed strengthening the Nuclear Non-Proliferation Treaty, ratifying the Comprehensive Nuclear-Test-Ban Treaty (which would outlaw nuclear bomb tests) and improving nuclear security. The US has announced its nationwide reporting system for greenhouse-gas emissions. Large facilities will have to disclose their emissions every year, as part of a programme that the agency said should cover 85% of US emissions. Data collection begins in January 2010, with disclosure for that year happening in 2011. The has created a committee to weed out companies that offer unapproved stem-cell 'therapies'. The society's president, Irving Weissman of Stanford University in Palo Alto, California, launched the committee on 22 September at the World Stem Cell Summit in Baltimore, Maryland. The 18-member panel plans to create a of companies that don't provide documentation showing that their treatments have been reported in peer-reviewed literature, have been overseen by the institutional review board and have received regulatory approval. "That's the minimum beginning," says Weissman. Click here for a longer version of this story. A review committee assessing the safety of — a pesticide used to fumigate soils — began work on 24 September in Sacramento, California. The chemical was approved for agricultural use by the US Environmental Protection Agency in October 2007, prompting protests from activists and scientists. California, Washington and New York have yet to approve the fumigant, and a 2009 report from the California Department of Pesticide Regulation (DPR) warned of significant health risks. The DPR will wait to make a ruling until after the review committee reports its findings. Click here for a longer version of this story. Roger Beachy, the founding president of the Donald Danforth Plant Science Center in St Louis, Missouri, was last week appointed to direct the US Department of Agriculture's , a new agency that will distribute the department's external basic research funding. For more, see page 580. : Political influence led the US (FDA) to approve a device to repair damaged knees against the recommendations of its own scientists, the agency has admitted. Scientific reviewers had twice turned down applications for , made by ReGen Biologics of Hackensack, New Jersey, but FDA officials approved it last December after lobbying from four New Jersey congressmen. This was a "clear deviation from the principles of integrity", the FDA wrote in a report analysing its review process. The European Commission exceeded its authority in imposing tighter-than-requested caps for greenhouse-gas emissions on Poland and Estonia in the second period of the , a court ruled last week. The price of carbon credits fell following the news, because traders thought the commission might have to grant additional allowances to Poland, Estonia and to six other countries that are also appealing against their caps. The ruling, which is subject to appeal, is limited to 2008–12 emissions, however — and its long-term effect on European carbon emissions is unclear. R. GALBRAITH/REUTERS Thousands of students, professors and other staff at the ten University of California campuses staged mass protests on 24 September, objecting to deep budget cuts that have led to enforced periods of unpaid leave, higher fees and job losses. More than US$800 million has been sliced from $3.2 billion in state funds expected for the 2009–10 fiscal year, delaying the construction of new research facilities and halting recruitment efforts. has admitted to having a second uranium-enrichment plant. On 25 September, the US, French and British premiers held a press conference to announce their intelligence on the site. Iran had informed the International Atomic Energy Agency in Vienna about the underground facility, near the city of Qom, four days earlier. The plant, not yet in operation, is thought to be big enough to hold around 3,000 gas centrifuges, which could enrich enough uranium for one nuclear weapon in a year. Two , including Kamran Daneshjou, minister for science and education, have been accused of co-authoring plagiarized academic papers. Several of the papers in question have been retracted, and an Iranian parliamentary commission is considering an investigation. For more, see page 578. : An experimental HIV vaccine has shown at preventing infection by the virus. A US$119-million study involving more than 16,000 HIV-negative men and women from Thailand found that a combination of two older drugs, which had failed to work individually, together reduced the risk of contracting HIV by nearly a third. "It's the largest step forward that's ever occurred in the HIV-vaccine field," says Dan Barouch of the Beth Israel Deaconess Medical Center in Boston, Massachusetts. Click here for a longer version of this story. The launch of Phobos-Grunt mission to study Mars and collect soil samples from one of its moons has been postponed to 2011, together with first Mars probe, the orbiter Yinghuo-1. Both crafts were supposed to take off in October this year, carried on a Russian rocket, but Russian space agency Roscosmos said last week that Phobos testing couldn't be completed in time to meet this year's launch window. The US announced 115 new awards for high-risk research on 24 September. The grants, which total US$348 million over five years, come in three varieties: Pioneer Awards for creative researchers at any career stage; New Innovator Awards for early-stage investigators; and a new category, Transformative R01 (T-R01) Awards to support unconventional projects. Improving on previous gender disparities, women researchers made up more than a third of Pioneer and New Innovator awardees — well above the 2008 R01 average of 26%. But only 15.5% of T-R01 awardees were women. The gender ratios of applicants were not available. The drug company in Abbott Park, Illinois, is to buy 's pharmaceutical business for €4.5 billion (US$6.6 billion). The company will pay cash for the deal, which includes Solvay's vaccines business, based in Belgium. The acquisition will also see Abbott increase its annual US$2.7-billion pharmaceutical research and development investment by $500 million. of Chicago, Illinois, the largest US nuclear-power provider, has become the latest company to quit the US because of differences over climate change. In recent months the chamber, which is among the nation's most influential business groups, has opposed a government plan to regulate carbon dioxide emissions. Exelon's 28 September announcement that it would not renew its membership of the chamber came a few days after similar withdrawals by two other utilities: the Public Service Company of New Mexico and California's Pacific Gas and Electric. SOURCE: NASDAQ A university spin-off company has got battery investors buzzing. A123Systems, which makes rechargeable lithium-ion batteries, raised US$380 million at $13.50 a share at its initial public offering, before watching its share price rocket (see chart). The cash boost, together with earlier federal grants and private investments, made A123 a billion-dollar company, even though it has yet to turn a profit. It has also applied for a $1.8-billion loan from the US government to build a mass-production facility in Michigan, and has signed a deal with US car manufacturer Chrysler. The company, based in Waterford, Massachusetts, was founded in 2001 by materials scientist Yet-Ming Chiang and his colleagues from the Massachusetts Institute of Technology in Cambridge. It uses lithium iron phosphate in the cathodes, and is currently in a patent dispute with the University of Texas in Austin, where the material was developed. The compound is more stable than the lithium metal oxides used in today's laptops and mobile phones, but cannot store as much charge. The 2009 Nobel prizes for physiology or medicine, physics and chemistry are announced. → http://nobelprize.org Singapore hosts the Stem Cells and Regenerative Medicine Congress Asia. → http://www.terrapinn.com/2009/stemcellsasia The American Association for Cancer Research holds its 'Frontiers in basic cancer research' conference in Boston, Massachusetts. → http://tinyurl.com/aacrbost J. BRINON/AP The Bulgarian diplomat is the first woman to be elected director-general of the United Nations Educational, Scientific and Cultural Organization (UNESCO). The 'increasingly plausible' rise in global warming by 2060 if greenhouse-gas emissions are not curbed quickly, according to Richard Betts, presenting a UK study from the Met Office's Hadley Centre. There are currently no comments.
• Booming biosafety labs probed
  - Nature 461(7264):577 (2009)
  Researchers are pushing back against moves in the US Congress to regulate more strictly the laboratories that handle the most dangerous pathogens. The scientists argue that adding rules to those already implemented since the anthrax attacks of 2001 could hobble work on countermeasures for killer pathogens, and drive researchers from the field. There are currently no comments.
• Iranian ministers in plagiarism row
  - Nature 461(7264):578 (2009)
  Nature investigation reveals duplications in papers by science and transport chiefs. Kamran Daneshjou faces plagiarism questions.A. TAHERKENAREH/EPA/CORBIS Two Iranian government ministers have co-authored peer-reviewed papers that duplicate substantial amounts of text from previously published articles, according to an investigation by Nature. Three journals have already confirmed that they will retract papers co-authored by Iran's science and education minister Kamran Daneshjou, a professor in the school of mechanical engineering at the Iran University of Science & Technology (IUST) in Tehran. Before being appointed science minister in early September, Daneshjou was also head of the interior ministry office overseeing the disputed presidential elections in June that kept Mahmoud Ahmadinejad in power. A further publication by Iran's transport minister and his deputy has also been called into question. In an online story last week (see Nature doi:10.1038/news.2009.945; 2009), Nature revealed that substantial sections of text in a 2009 paper in the journal Engineering with Computers1 by Daneshjou and IUST colleague Majid Shahravi were identical to a 2002 paper2 by South Korean scientists in the Journal of Physics D. New York-based Springer, which publishes Engineering with Computers, has told Nature that it will retract the paper. The work also duplicates smaller amounts of material from papers given by other researchers at conferences3,4,5,6, as well as a 2006 article7 in the International Journal of Impact Engineering. Similar duplications also appear in other papers by the same co-authors in Springer's Journal of Mechanical Science and Technology (JMST)8, the Taiwanese Journal of Mechanics9 and the Iranian journal Mechanical & Aerospace Engineering Journal10 — the text of which is almost identical to that in their paper in Engineering with Computers1. "This is a bitter blow to Iranian academic society, it's a scandal." Mark de Jongh, publishing editor of the JMST, says that the journal intends to retract the second Springer article8. "I conclude that the paper in question contains about 50% identical content as the formerly published article" in the Journal of Physics D2, he says. The Journal of Mechanics intends to take similar action. "We have just finished the investigation of this serious case and the result showed that the paper by K. Daneshjou and M. Shahravi indeed plagiarized other works," says Yi-Chung Shu, executive editor of the journal and a researcher in mechanical engineering at the National Taiwan University in Taipei. "This paper will be definitely retracted." Senior Iranian scientists have called for an inquiry into the affair, and an Iranian parliamentary commission is considering an investigation. "This is a bitter blow to Iranian academic society, it's a scandal," says Ali Gorji, an Iranian neuroscientist based at the University of Münster in Germany. Transport dispute Nature's investigation has also revealed that a paper11 co-authored by Hamid Behbahani, Iran's minister of roads and transportation, also contains large amounts of text from earlier articles by other researchers. The paper was co-authored by Hassan Ziari, Behbahani's deputy minister, and president of the national rail company, the Islamic Republic of Iran Railways. Both authors hold positions at the IUST, while the third author, Mohammed Khabiri, was a PhD student at the time. Behbahani was also the supervisor of Ahmadinejad's PhD in transportation engineering and planning. Much of the text and the results of their 2006 article11, in the journal Transport, is identical to sections from three earlier publications12,13,14. "Two of my papers were copied-and-pasted by the plagiarizing paper," says Bin Jiang, a researcher at the University of Gävle in Sweden. "This is outrageous." ADVERTISEMENT "The plagiarism is obvious," concurs Jiang's co-author, Christophe Claramunt, a scientist at the Naval Academy Research Institute in Brest, France. "We look forward to appropriate action from the editor of Transport." Nature has attempted, without success, to contact each of the Iranian authors of all the disputed papers. However, two Iranian news websites have published a response attributed to Majid Shahravi (see http://www.tabnak.ir/fa/pages/?cid=65586 and http://alef.ir/1388/content/view/54040). That statement refutes any plagiarism and defends the originality of the paper in Engineering with Computers1, based on the fact that it had passed peer review and had cited the 2002 Korean paper2. * References * Daneshjou, K. & Shahravi, M. Eng. Comp.25, 191-206 (2009). | Article * Lee, W., Lee, H.-J. & Shin, H. J. Phys. D35, 2676-2686 (2002). | Article | ChemPort | * Quan, X. et al. in Fifth Asia–Pacific Conference on Shock and Impact Loads on Structures (eds Jones, N. & Brebbia, C. A) (WIT Press, 2003); available at http://hsrlab.gatech.edu/AUTODYN/papers/paper152.pdf. * Yaziv, D., Mayseless, M. & Reifen, Y. in Proc. 19th Int. Symp. Ballistics (ed. Crewther, I. R.) (Technomic Publishing Company, 2001); available at http://hsrlab.gatech.edu/AUTODYN/papers/paper111.pdf. * Sauer, S., Hiermaier, S. & Scheffer, U. Paper given at 10th International Symposium on Interaction of the Effects of Munitions with Structures, San Diego, California, 7–11 May 2001; available at http://hsrlab.gatech.edu/AUTODYN/papers/paper126.pdf. * Quan, X. & Birnbaum, N. in Proc. 18th Int. Symp. Ballistics (ed. Reinecke, W. G.) (Technomic Publishing Company, 1999); available at http://hsrlab.gatech.edu/AUTODYN/papers/paper092.pdf. * Segletes, S. B. Int. J. Impact Eng.32, 1403-1439 (2006). | Article * Daneshjou, K. & Shahravi, M. J. Mech. Sci. Tech.22, 2076-2089 (2008). | Article * Daneshjou, K. & Shahravi, M. J. Mech.25, 117-128 (2009). * Daneshjou, K. & Shahravi, M. Mech. Aerosp. Eng. J.3, 69-86 (2008). | ChemPort | * Ziari, H., Behbahani, H. & Khabiri, M. M. Transport XXI, 207-212 (2006). * Forbes, G. Transportation Research Circular Issue Number: E C019 B-6/1 (Transportation Research Board ISSN, 2000); available at http://www.urbanstreet.info/2nd_sym_proceedings/Volume 1/Ec019_b6.pdf. * Jiang, B. & Claramunt, C. Paper given at 5th AGILE Conference on Geographic Information Science, Palma, Spain, 25–27 April 2002; available at http://www2.hig.se/~bjg/s6_Jiang.pdf. * Jiang, B. & Claramunt, C. GeoInformatica8, 157-171 (2004). | Article
• Experts draw up ocean-drilling wish list
  - Nature 461(7264):578 (2009)
  Researchers seek deeper understanding of crust formation. The United States' research vessel the JOIDES Resolution is equipped to drill down 2 kilometres into the seabed.J. Beck/IODP Earth scientists have laid the groundwork for the future of ocean drilling. More than 500 scientists — almost twice as many as organizers had initially expected — gathered last week in Bremen, Germany, to discuss priorities and research goals for the second phase of the Integrated Ocean Drilling Program (IODP), which is expected to begin in late 2013. Since ocean drilling began in the 1960s, sediment and rock cores retrieved from the seabed have provided information about everything from plate tectonics to Earth's climate history. Much more remains to be discovered, scientists said at the meeting. "We're not done," says Alan Mix, a marine geologist at Oregon State University in Corvallis. "Actually, we ain't seen nothing yet." Researchers have generated a detailed wish list for new ocean-drilling projects, which will be boiled down into a science plan for the 2013–23 period by a group yet to be appointed. The finalized science plan will then be forwarded to funding agencies in Japan, Europe and North America, which currently support the IODP to the tune of around US$200 million per year. Mix says that targets might include the role of greenhouse gases in transitions between cold and warm climates, and the magnitude, speed and locations of resulting sea-level changes. A more ambitious project would be to relaunch the effort to drill through Earth's crust and into its mantle. A 1960s attempt to drill through the sea floor into this boundary, known as the Mohorovičić discontinuity, or 'Moho', failed. The Japanese IODP vessel, the Chikyu, is already outfitted with technology to drill down some 7,000 metres into the crust, and there are plans to refit the vessel over the next three years with drilling and core-recovery technology to allow it to drill even deeper. "Japan will lead the Moho project," says Asahiko Taira, the Yokohama-based executive director of the Japan Agency for Marine–Earth Science and Technology, which oversees Japan's ocean-drilling operations. "It's a classic geological quest, and definitely one of our prime targets." "The journey down is equally important to the things we may find at the bottom," adds Benoît Ildefonse, a geologist at France's National Centre for Scientific Research (CNRS) based in Montpellier, France. "Recovering rocks from near Moho will, for the first time, allow us to test our ideas and models about how the crust forms." The deepest sea-floor holes drilled so far include a 2,111-metre-deep hole drilled during the 1970s and 1980s off Nicaragua, and a 1,500-metre-deep hole drilled in 2005 in the Cocos plate in the eastern Pacific Ocean. The latter, performed by the US vessel JOIDES Resolution, was the first continuous retrieval of core from Earth's upper crust. Following a $130-million refurbishment, the 30-year-old ship is now capable of drilling 2,000 metres into the sea floor in waters as deep as 7,000 metres. IODP leaders say they are increasingly aware of the need to explain the societal relevance of their work. "We need to explain very well why what we are doing matters," says Catherine Mével, director of the European Consortium for Ocean Research Drilling, which coordinates the activities of 16 European IODP members and Canada. "We haven't always been able to make this clear enough in the past." Meanwhile, China — an associate IODP member alongside South Korea, Taiwan, India, Australia and New Zealand — has announced plans to build a deep-sea drilling vessel of its own. "The small Chinese deep-sea research community is rapidly growing in numbers, and our formerly reluctant government is increasingly convinced about the significance of ocean drilling," says Wang Pinxian, a marine geologist at Tongji University in Shanghai and vice-chair of the Chinese IODP science committee. As an associate member with limited ship time and managerial rights, China pays the reduced IODP membership of US$1 million. The Chinese government and the Chinese Academy of Sciences are currently discussing whether China should apply for full membership beyond 2013, for which it would need to pay around $6 million per year, says Wang. ADVERTISEMENT IODP rules and overall programme architecture are unlikely to undergo any substantial changes after 2013, says Rodey Batiza, section head of marine geosciences at the US National Science Foundation in Arlington, Virgina. New members will be welcome to join, but membership will not be linked to specific national drilling preferences, he says. "We'd like to seamlessly continue drilling after 2013 with a programme designed to deliver the best science at the lowest cost," he says. "We do already have some very exciting questions that we can ask, and perhaps answer, in the next ten years." There are currently no comments.
• US agriculture research gets priority plan
  - Nature 461(7264):580 (2009)
  US agricultural research is getting a makeover. The National Institute of Food and Agriculture (NIFA) opens its doors on 1 October, with plant biotechnologist Roger Beachy at its helm. There are currently no comments.
• Instant climate model gears up
  - Nature 461(7264):581 (2009)
  Simulation tool gives rapid feedback on implications of policy changes. A climate simulator that started life in a doctoral dissertation is being adopted by negotiators to assess their national greenhouse-gas commitments ahead of December's climate summit in Copenhagen. Dubbed C-ROADS — for Climate Rapid Overview and Decision-support Simulator — the tool translates complex climate modelling into readily digestible predictions. Using data on greenhouse-gas emissions input by country or region over a given period, the simulator projects temperatures, sea level and atmospheric carbon dioxide concentrations to 2100. Online collection The tool hit the headlines last week when Robert Corell, chairman of the Washington-based Climate Action Initiative, made a dire assessment: even with all the international pledges to reduce greenhouse-gas emissions, including a yet-to-be-enacted commitment by the United States, by the end of this century global average temperature will still outpace the 2 °C increase targeted by the G8 countries and others. "We're headed to a 4-degree world," Corell told reporters at a press conference in Washington DC. "We don't want to go there." C-ROADS has its origins in 1997 doctoral work by Thomas Fiddaman, now a modeller with Ventana Systems in Harvard, Massachusetts. The current version represents a collaboration between Ventana, researchers at the Massachusetts Institute of Technology (MIT) in Cambridge and the Sustainability Institute in Hartland, Vermont. The tool made its debut in the policy world last year during a global-warming war game in Washington DC, and has since been picked up by climate negotiators in the United States and Europe. Earlier this month, modellers on the C-ROADS team travelled to Beijing to train Chinese negotiators on the software. The goal is to distribute C-ROADS to all parties so that everybody is working off of the same baseline in evaluating proposals, says Andrew Jones, who co-leads the initiative at the Sustainability Institute. "We want to get a lot of the bickering over the different numbers out of the way," he says. The team has calibrated C-ROADS against global climate models used by the Intergovernmental Panel on Climate Change (IPCC). Unlike those, it can be run on a laptop and produces instant results. Users can adjust dates and emissions from all of the major emitters and groups of developing countries, providing immediate feedback on the likely effects of any given policy commitments. An independent team led by climatologist Robert Watson of the University of East Anglia in Norwich, UK, reviewed the model and recommended in March that the United Nations consider adopting it as a formal tool to support the climate negotiations. That hasn't happened yet, but modellers with the C-ROADS team are attending UN climate meetings to help negotiators assess policy proposals. C-ROADS tracks historical data well and generally performs in line with average IPCC modelling results, says John Sterman, an MIT management professor who works on the project. Sterman says a key problem with global-warming policy is the time lag between today's emissions and the problems they cause, which can be decades down the road. The model attempts to get around that by allowing policy-makers — and the public, through a simplified version on the Climate Interactive website — to see the likely consequences of their decisions immediately. "It's not that the other models are flawed," Sterman says. "They are opaque to the policy-makers." ADVERTISEMENT Jones says that the model produces warming of 4.5 °C by 2100 for business as usual and 3.8 °C based on the targets announced in March. Taking into account all the latest pledges by countries, including a commitment from Russia this summer, the model's current reading is 3.5 °C. "The doom and gloom story is getting 90% of the attention," he says, "but now we're at 3.5 °C. The global climate deal is getting better over time." Still, global leaders made little headway on climate last week, at both a UN summit in New York and a meeting of the G20 in Pittsburgh, Pennsylvania. Leaders of the G20 did, however, agree to phase out fossil-fuel subsidies while providing "targeted support for the poorest". nature.com/roadtocopenhagen. Corrected: An earlier version of this story said that Andrew Jones heads up the initiative at the Sustainability Institute. He co-leads it with Elizabeth Sawin. There are currently no comments.
• Cellulosic ethanol hits roadblocks
  - Nature 461(7264):582 (2009)
  The business of biofuels This year was supposed to be a big year for BlueFire Ethanol. The company, based in Irvine, California, had planned to start operating its first commercial cellulosic biofuel plant by the end of the year, converting waste from a neighbouring landfill into ethanol. There are currently no comments.
• Innovation strategy
  - Nature 461(7264):585 (2009)
  US President Barack Obama travelled to a struggling city in upper New York state last week to unveil a 22-page "Strategy for American Innovation". The Obama administration is genuinely interested in developing policies to foster innovation, but a close reading of the strategy indicates that it is just beginning to figure out how to do that. There are currently no comments.
• Eastern Europe: Scaling the wall
  - Nature 461(7264):586 (2009)
  The collapse of communism opened up the world to scientists from eastern Europe. Quirin Schiermeier talks to researchers about what changed. Download a PDF of this article On the 9 November 1989, the lights were out early for Pavel Jungwirth. Jungwirth had recently graduated from Charles University in Prague, Czechoslovakia, and he was hoping eventually to pursue a PhD in physics. But his plans had been interrupted when he was drafted into the army, and for now he was quartered in barracks outside the city. With a 10 p.m. curfew, Jungwirth had little opportunity to watch the historic spectacle that was captivating audiences around the world, as an ecstatic crowd breached the Berlin wall. That year, Soviet-controlled communist governments throughout central and eastern Europe had been stumbling in a historic chain reaction. In May, Hungary had begun to dismantle the Iron Curtain. In June, the Polish anti-communist Solidarity party led by shipyard worker Lech Wałęsa had won by a landslide in free elections. But for many, the most powerful symbol of communism's collapse was on the November day when East Germany's rulers surrendered to weeks of peaceful rebellion by its citizens and announced that people from East Berlin could pass through the formidable barrier that had divided the city since 1961. One of those watching the events on her family television was Alicja Józkowicz, a 22-year old then studying zoology at the Jagiellonian University in Kraków, Poland. "It was a very emotional moment," she says. Like Jungwirth, Józkowicz was set on becoming a scientist. The drama unfolding on the screen made her realize, she says, "it would change my professional opportunities". Neither Jungwirth nor Józkowicz could anticipate how dramatically their professions would change. The region's political transformation meant that universities and research institutes that had been isolated from international science were now expected to take part in it. Some researchers found this a formidable challenge, grappling for the first time with having to publish their work and compete for funding. But many others, such as Jungwirth, Józkowicz and a generation of eastern European students who in 1989 were embarking on a career in science, saw it as an opportunity. These researchers soon became a common sight at labs in western Europe and North America, and many of them have gone on to establish competitive laboratories. "I consider it a small miracle that within the past 20 years sprouts of excellence have grown in my country," says Jungwirth, who now runs a chemistry laboratory in Prague. "Compared with 1989, our academic community is profoundly different — inspiring, self-confident and international." Józkowicz, now a group leader in the Department of Medical Biotechnology at Jagiellonian University, agrees: "Personally I have a feeling I am a rightful member of an international society of scientists." Lost tradition Yet something could have been lost in the internationalization of eastern Europe, says Wolf Lepenies, a sociologist and former director of the Institute of Advanced Study in Berlin. When he and others used to visit the East, "institutions were poor, instruments were lacking, but intellectual traditions had prevailed that we had barely taken notice of", he says. "Debates were conducted with an earnestness and a responsibility that were largely unfamiliar to us." Lepenies says that the 'we will help you' approach that western Europe has often used in its interactions with the East carries a whiff of condescension. "Eastern Europe is a good place to shake the complacency of the West," he says. "'We need each other!' would have been a more appropriate guideline." From army to lab: Pavel Jungwirth now runs a chemistry group in Prague.P. KRALIK; COURTESY OF P. JUNGWIRTH Jungwirth's family expected him to study science. His father, a physicist himself, went frequently to Novosibirsk, a strong centre of Soviet physics and chemistry, and he would years later become a vice-president of the Academy of Sciences of the Czech Republic in Prague. But in 1970, Jungwirth's father was kicked out of the Communist Party because of his open disagreement with the 1968 Soviet occupation. This stance affected his son's plans. Jungwirth had hoped to study medicine, but according to an unwritten rule, children of politically unreliable citizens should not enrol in subjects through which they might exert an undue influence on people. Medicine was one such discipline. Jungwirth instead opted for physics, which was considered socially neutral. As a student, he followed the 1989 political events with eager anticipation. When writing his diploma thesis he had access to a computer and a printer — a rarity in a country where the few functioning photocopiers were rigidly controlled for fear of dissident activity. Some like-minded friends asked him to print copies of a letter they had written in support of Václav Havel, the playwright and essayist who had become the political figurehead of the anti-communist movement and had been taken into custody. Jungwirth helped them out, but a copy of the letter fell into the wrong hands and he was summoned to the dean. "I thought 'that's it, I'm out'," he says. He faced the dean over a massive rosewood desk surrounded by insignia of communism and the portrait of the Czech party leader Gustáv Husák. Then something unexpected happened. After lecturing him for a minute or two, the dean crumpled up the il! l-fated letter and flung it into a corner of his study. Perestroika, Jungwirth thought, had definitely arrived in Prague. By November, huge momentum was building for Havel's 'Velvet Revolution' and a student rebellion had expanded into a nationwide general strike. On 25 November, Jungwirth slipped out of the barracks to join the millions shouting for freedom on the streets of Prague. Husák resigned on 10 December, paving the way for democracy, and on 29 December Havel was installed as the new President of Czechoslovakia. Jungwirth switched from military to civil duty as soon as this option was made possible in 1990 and resumed his studies a year later. He was interested in atmospheric chemistry and, at the J. Heyrovský Institute of Physical Chemistry in Prague, started putting together molecular simulations of hydrophobic molecules such as methane. Soon he was embarking on his long-awaited PhD. Shades of grey During Józkowicz's school years in Kraków in the 1980s, the Western world and Western science seemed unimaginably far away. "I never even dreamed of going there," she says. "I remember my childhood and youth as a time when everything was grey, and each year things just seemed to get worse," she says. "The stores were empty all the time." Józkowicz was curious about the natural world and she remembers her science teachers — and textbooks — as being excellent. "Much better actually than the science education my son is getting now," she says. The high standard of science education was true of many eastern European countries. 1980s to 2000s: Alicja Józkowicz took postdocs abroad to pursue biomedical research.M. JÓZKOWICZ Józkowicz was aware early on of the Solidarity movement that began in the early 1980s and that was to become the nucleus for political changes in Poland. Solidarity, led by Wałęsa and the first independent trade union in the Soviet-controlled Eastern bloc, quickly turned into an openly anti-communist political and social movement supported by millions of Poles. For Józkowicz, the most significant time was when Solidarity was elected and Tadeusz Mazowiecki became prime minister. "We really felt that a new era was about to begin," she says. But when capitalism eventually arrived in Poland it also brought problems, as it did in other countries. The political and intellectual freedom was invigorating but, at least in the early days, disillusionment was never far behind. "The stores filled up," she says. "But salaries dropped just as quickly." Scientists found the transition particularly harsh. Until that time their research money had been guaranteed by the government. With the collapse of communism, many countries were close to bankrupt and science funding dropped abruptly to almost zero. It was impossible in the early years for most scientists to make a living without getting second jobs, and many gave up altogether. Those who managed to hold onto their labs could travel freely to other countries for the first time, meet their counterparts there and begin to integrate with the international scientific community. But this came with tough international competition and new codes of conduct. Conferences were rare, peer review was unknown, and few researchers spoke English. Many developed something of an inferiority complex. The national science academies, which operate hundreds of basic-research institutes throughout central and eastern Europe, today have a disproportionate number of members close to or above the age of retirement who have continued to pursue their research and have domestic influence but have never really entered the international science arena. Jungwirth and other young scientists, though, had little to lose. Pitifully low salaries, poorly equipped labs and a lack of grant money quickly led to thousands of mainly young scientists leaving for the West. Jungwirth was lucky: his PhD supervisor, chemist Rudolf Zahradník, had good contacts and used them to send Jungwirth to Switzerland in 1992. He spent a year there working with Thomas Bally at the University of Fribourg, where his 3,000 Swiss-franc (US$2,290) monthly salary made him feel "rich beyond measure". (During his PhD Jungwirth also became casual acquaintances with another former PhD student of Zahradník's, Angela Merkel). "I saw that scientists abroad acquired positions because they knew something, not because they knew somebody." Pavel Jungwirth Later, Jungwirth worked as a postdoc for a few months at the Hebrew University of Jerusalem in Israel and at the University of California, Irvine, with the same supervisor, Benny Gerber. He became interested in computational modelling of atmospheric chemistry. "In Switzerland, and later in the United States, I saw that scientists acquired positions because they knew something, not because they knew somebody," says Jungwirth. He was impressed by how his supervisor "developed new methods in amazing outbursts of creativity. I felt on top of the world." Józkowicz was also learning about science abroad. Her first international meeting — the 1991 world immunology congress in Budapest — was a shock. Not only did she realize that she could hardly understand the English-language talks, she also found that her group's science was hopelessly behind. She had recently started a PhD comparing the amphibian immune system to those of mammalian species in the department of evolutionary immunology at Jagiellonian University. "Our research was completely outside the mainstream," she says. "Worse, the methods we used were just totally outdated." Her lab had no cell sorters and only the most basic molecular-biology apparatus and microscopes. Józkowicz realized that she needed to change direction. She started to learn English intensively and decided that as soon as she had completed her PhD she would switch from zoology to medicine. She did this in 1996, moving to the Department of Clinical Biochemistry in the medical school at Jagiellonian University. She studied the control of blood-vessel growth — angiogenesis — by the gas nitric oxide. But she was still not happy with the pace at which things were improving. In Poland, as in other countries, grant systems for science were being established and foreign aid and philanthropic aid were providing some relief. In 1992, for example, Hungarian-born billionaire George Soros founded the International Science Foundation, which provided emergency grants to more than 20,000 researchers across eastern Europe. In Poland, grants were provided by the Warsaw-based Ministry of Science and Higher Education and Foundation for Polish Science. But individual grants were still small, modern equipment remained mostly unaffordable and Józkowicz felt that Polish science generally lacked international flair and recognition. An opportunity presented itself in 1997 when a poster of hers on in vitro gene therapy was shown at a congress in Germany. Diabetes researcher Lawrence Chan of the Baylor College of Medicine in Houston, Texas, noticed it and invited her to join his group for a year. Four weeks later she landed in Houston, leaving behind her husband and six-year-old son. She threw herself into her work. "I felt painfully lonely," she says. Culture shock Texas was quite an experience for the then 30-year-old, now officially a postdoc (a job term that at the time hadn't been much used in eastern Europe). Józkowicz found the style with which Chan ran his 40-strong research team inspiring. "Each postdoc got a gene, human, mouse or monkey, to work on, and within one week of their arrival everybody was busy doing experiments and producing results," she says. Józkowicz got mice, and her experiments with them identified a way to perform gene therapy that protected against atherosclerosis for the animal's lifetime. It was to become her most cited paper1. "The year with Chan taught me what real teamwork can achieve — it was really the first crucial step in my development." She later signed up for three years of postdoctoral research at the Medical University of Vienna. "Compared with 1989, our academic community is profoundly different — inspiring, self-confident and international." Alicja Jólzkowicz Just as Józkowicz was leaving home, Jungwirth was returning. Like many young scientists who had taken the opportunity to leave eastern Europe, he decided to go back there (see 'Heading home'). In 1995 he took up a group-leader position in his native country — by this time the Czech Republic after its split with Slovakia — at the Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic in Prague. With the help of a 200,000-Deutschmark (US$143,000) grant from the German Volkswagen Foundation, Jungwirth was able to quickly establish a reasonably competitive group. He also secured grants from the US National Science Foundation in Arlington, Virginia, and the North Atlantic Treaty Organization (NATO) Science Programme in Brussels. "Buying serious equipment was still out of the question," Jungwirth says. "But the students were excellent and the computers were just fine." As a theorist, computers were the main thing he needed and Jungwirth started to establish a reputation with his molecular models2. Over time Jungwirth started to feel that things were getting better. The Czech government invested relatively generously in science, and the Academy of Sciences was less resistant to reform than its counterparts in some other countries. Jungwirth expanded his research interests. By the late 1990s he was exploring atmospheric chemistry, simulating ions such as chloride at aqueous surfaces to try to work out how they could react with ozone and other pollutants3. He also ventured into biology, studying how salt ions influence the properties of proteins4. "I had a lot of luck," he says. "The timing was just right. I see many people 5–10 years older than me who are now in a much worse situation." In 2003, Józkowicz returned home too — to Kraków, where her son had just celebrated his twelfth birthday. She had maintained a formal affiliation with Jagiellonian University, and was eager to teach a group of her own the new methods and styles she had learned abroad. But although the world had been changing, Polish academic circles had not. For 18 months all her applications for independent funding came to nothing. The academic establishment was still very hierarchical, with advancement based on favouritism rather than merit. Changing labs was — and sometimes still is — considered an act of disloyalty. Józkowicz found that the years spent abroad pretty much debarred her from the national funding system. Her break came in 2004 when she won a prestigious Central European Senior Research Fellowship worth some £350,000 (US$570,000) awarded by the British Wellcome Trust, which is open to researchers in Estonia, Poland, the Czech Republic and Hungary. The money supported projects aimed, among other things, at studying blood vessels in tumours and during cardiovascular disease. Home for good The grant seemed to make it easier for her to convince Polish grant-givers of the quality of her research and since 2007 she has won funding totalling €330,000 (US$488,000) from the Polish Science Ministry, the Wellcome Trust and from Adamed, a Warsaw-based pharmaceutical company. Her small group — now with access to modern fluorescent microscopes and other equipment — has become the nucleus for Jagiellonian's Department of Medical Biotechnology, created in 2005, where she hopes to receive tenure soon. "My plans?" she says. "Make the most of the new money, produce papers in leading journals — and live in Kraków with my family for the rest of my life." Some of the region's catch-up has been aided by the expansion of the European Union (EU), which was joined in May 2004 by ten countries, including Poland and the Czech Republic, followed by Bulgaria and Romania in 2007. Józkowicz's department this year received around €6,000,000 from EU structural funding, which is aimed at generating equal living conditions across the EU and can be used to fund research infrastructure and equipment. The university received an extra 45 million zloty (US$16 million) to establish a new Jagiellonian Center for Experimental Therapeutics, due to open later this year. The European Research Council has also begun to make generous grants available to young investigators across Europe. Both Jungwirth and Józkowicz believe that the East–West gap will narrow further as old cultural habits die away and scientific borders dissolve. "Don't forget we started from empty walls," says Józkowicz. "But we now have a young and energetic environment for science, with excellent students who are eager to work. I do believe that at least some labs in Poland and elsewhere will very soon become attractive to foreign scientists." Some of that change is palpable in the attitudes of the scientists that Jungwirth now meets. "Until the turn of the decade or so I could still play the game of coming from a poor country," says Jungwirth. "People had been eager to see us, and keen to help. The feeling of being welcomed with open arms made things a lot easier for us when times were not so good." Not so now, he says, as the history starts to fade from memory: scientists who are starting their PhDs today were born after the Berlin Wall fell. "We cannot say now that we do not publish well," says Józkowicz, "or we do not make valuable research because of 'them' or 'circumstances beyond our control'. I remember that, when I was a teenager, the often repeated sentence was 'in the West it would be obvious or easy but here — forget about it. Never-ever would it be possible in Poland'. And it is possible." ADVERTISEMENT If any further evidence was needed of what is possible for scientists in the Eastern bloc, it was apparent at a party last year in Prague. Jungwirth was attending the 80th birthday of his former supervisor, Zahradník, who served as president of the Czech Academy of Sciences between 1993 and 2001. Late in the evening a black limo with a German licence plate pulled up. Merkel, now the German Chancellor, had spontaneously decided to come down from Berlin to congratulate her aged PhD supervisor. Free from rules of protocol, she chatted the hours away, in fluent Russian, with her science colleagues of old. The word is that it was a good party. * References * Kim, I. H., Józkowicz, A., Piedra, P. A., Oka, K. & Chan L. Proc. Natl Acad. Sci. USA98, 13282-13287 (2001). | Article | PubMed | ChemPort | * Jungwirth, P. & Tobias, D. J. J. Phys. Chem. B106, 6361-6373 (2002). | Article | ChemPort | * Knipping, E. M. et al. Science288, 301-306 (2000). | Article | PubMed | ChemPort | * Vrbka, L., Vondrášek, J., Jagoda-Cwiklik, B., Vácha, R. & Jungwirth, P. Proc. Natl Acad. Sci. USA103, 15440-15444 (2006). | Article | PubMed | ChemPort | There are currently no comments.
• Eastern Europe: Beyond the bloc
  - Nature 461(7264):590 (2009)
  This article is best viewed as a pdf. From the 1950s, science has been a priority in the Soviet-controlled Eastern bloc. Space science and nuclear physics, in particular, received generous support, and achievements such as the Soviet space missions served as proof of the alleged superiority of the communist system. Then in the late 1980s, collapse of communist regimes and their replacement by democracy and market economies led to a dramatic drop in science expenditure across the region. Reliable data for the early 1990s — the period of worst hardship — are unavailable because national statistical services were not yet up and running or had no reported science figures. Between 2003 and 2004 the European Commission included the ten countries in central and eastern Europe that have since joined the European Union (see map) in its regular reports on science and technology indicators. Figures from the 2008–09 report show that research intensity — the percentage of gross domestic product spent on research and development (R&D) — is below the European average of around 1.8% in all ten countries (see graphs). Click to enlarge.INTERNATIONAL MONETARY FUND 2007 But there are strong differences within the region. Although the Czech government has in recent years invested substantially in science, the research bases of countries such as Bulgaria and Romania are still underdeveloped. Notable improvements, mainly driven by the business sector, have been made in Estonia and Hungary — although the recent economic crisis has hit Hungary harder than it has hit others, threatening the upward trend. Poland, the largest country in the region, has in recent years fallen further behind in reaching EU and national goals for R&D intensity, as have Slovakia and Bulgaria. There is a general lack of highly qualified scientists and technical workers, whose share of the overall workforce ranges between 9.8% in Romania and 16.8% in Estonia. ADVERTISEMENT The region also still fails to attract much foreign scientific talent. Only 1% or so of participants in the EU's Marie Curie Actions programme — which promotes and facilitates the mobility of young scientists in Europe — choose a university, research institute or industry lab in the new member states as their host institution, possibly due to the resources and reputations of other member states.
• Call from China for joint nanotech toxicity-testing effort
  - Nature 461(7264):593 (2009)
  In response to your News story 'Nanoparticle safety in doubt' about lung damage in Chinese factory workers (Nature 460, 937; 2009), we would like to stress that China has been paying close attention to research into and documentation of the risks of working with nanomaterials.As in most Western countries, industrial use of nanoscale products has been proliferating in China over the past decade.
• Consent: criteria should be drawn up for tissue donors
  - Nature 461(7264):593 (2009)
  The drive to develop new human pluripotent stem-cell lines has attracted a new, exuberant cohort of researchers who may not be familiar with the regulations and standards governing donation of human tissue. Scientists should ask donors to agree to some basic rules for research involving induced pluripotent stem (iPS) cell lines derived from their tissue.
• Consent: a need for guidelines to reflect local considerations
  - Nature 461(7264):593 (2009)
  As you point out in your Editorial (Nature 460, 933; 2009) on the distribution of human cell lines, withholding scientific material from the broader research community contravenes the basic norms of science.
• Science and the Stasi
  - Nature 461(7264):594 (2009)
  The acquisition of scientific and technological secrets was at the heart of East Germany's foreign espionage operations before the fall of the Berlin Wall, reveals Kristie Macrakis.
• Showcasing the evidence for evolution
  - Nature 461(7264):596 (2009)
  Laurence D. Hurst compares two seasoned authors' strategies for explaining the difference between evolution fact and fantasy — Richard Dawkins's thunder and Carl Zimmer's poise.
• Taxonomy comes of age
  - Nature 461(7264):597 (2009)
  Faced with the bewildering diversity of nature, humans have long attempted to classify it. In her personal and readable perspective on taxonomy, Carol Yoon argues that the basic instinct to recognize natural groups has gradually been replaced by an increased rationality.
• Q&A: Gustav Metzger on destruction
  - Nature 461(7264):598 (2009)
  Gustav Metzger's monumental and technical artworks comment on the capacity of human society to obliterate itself. From displays that eat themselves with acid to liquid-crystal patterns projected onto performing bands such as The Who in the 1960s, he questions environmental degradation, nuclear war and capitalism. As a major retrospective of his work opens, Metzger argues that scientists should be more active in counteracting society's tendency to seek oblivion.
• Drug discovery: Propping up a destructive regime
  - Nature 461(7264):599 (2009)
  The Wnt signalling pathway balances the opposing activities of two proteins to transmit signals within cells. An inhibitor that stabilizes one of these proteins reveals a new target for anticancer drug development.
• Optics: Droplets set light in a spin
  - Nature 461(7264):600 (2009)
  Fusilli pasta is made by extruding dough through an appropriately shaped hole. A new method for making similar shapes in the optical field of light involves passing laser beams through droplets of liquid crystals.
• Palaeontology: Feathered dinosaurs in a tangle
  - Nature 461(7264):601 (2009)
  A dramatic feathered dinosaur fossil from the Jurassic of China resolves a 'temporal paradox'. But it adds intriguing complications to the debates on the evolution of feathers and flight in birds.
• Supramolecular chemistry: Molecular crystal balls
  - Nature 461(7264):602 (2009)
  Sorcerers have long gazed into crystal balls to conjure up information. Chemists are also getting in on the act, using porous crystals to trap unstable reaction intermediates and to reveal their structures.
• Behavioural ecology: Winged warnings
  - Nature 461(7264):603 (2009)
  Alarm signals emitted by animals may not be all that they seem. But a good example has been identified in the whistling sound of a crested pigeon's wings when it takes flight in response to a predator.
• 50 & 100 years ago
  - Nature 461(7264):604 (2009)
  A critical review of the methods of determination of the temperatures of ancient seas by the measurement of the oxygen isotopes ratio in fossil calcareous organisms is given by Y. A.
• Applied physics: Lasers go nano
  - Nature 461(7264):604 (2009)
  Two experiments that produce laser light by exploiting the collective wave-like motion of free electrons on a metal surface bring the science and technology of lasers into the nanoland.
• Correction
  - Nature 461(7264):605 (2009)
  In "Gamma-ray bursts: Maybe not so old after all" by Enrico Ramirez-Ruiz and William Lee (Nature 460, 1091–1092; 2009), an editorial error introduced the statement that GRB 070714B is "slightly more than 8 billion parsecs away". The correct units are light years, not parsecs.
• Untangling aerosol effects on clouds and precipitation in a buffered system
  - Nature 461(7264):607 (2009)
  It is thought that changes in the concentration of cloud-active aerosol can alter the precipitation efficiency of clouds, thereby changing cloud amount and, hence, the radiative forcing of the climate system. Despite decades of research, it has proved frustratingly difficult to establish climatically meaningful relationships among the aerosol, clouds and precipitation. As a result, the climatic effect of the aerosol remains controversial. We propose that the difficulty in untangling relationships among the aerosol, clouds and precipitation reflects the inadequacy of existing tools and methodologies and a failure to account for processes that buffer cloud and precipitation responses to aerosol perturbations.
• Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling
  - Nature 461(7264):614 (2009)
  The stability of the Wnt pathway transcription factor -catenin is tightly regulated by the multi-subunit destruction complex. Deregulated Wnt pathway activity has been implicated in many cancers, making this pathway an attractive target for anticancer therapies. However, the development of targeted Wnt pathway inhibitors has been hampered by the limited number of pathway components that are amenable to small molecule inhibition. Here, we used a chemical genetic screen to identify a small molecule, XAV939, which selectively inhibits -catenin-mediated transcription. XAV939 stimulates -catenin degradation by stabilizing axin, the concentration-limiting component of the destruction complex. Using a quantitative chemical proteomic approach, we discovered that XAV939 stabilizes axin by inhibiting the poly-ADP-ribosylating enzymes tankyrase 1 and tankyrase 2. Both tankyrase isoforms interact with a highly conserved domain of axin and stimulate its degradation through the ubiq! uitin-proteasome pathway. Thus, our study provides new mechanistic insights into the regulation of axin protein homeostasis and presents new avenues for targeted Wnt pathway therapies.
• Inhibitors selective for mycobacterial versus human proteasomes
  - Nature 461(7264):621 (2009)
  Many anti-infectives inhibit the synthesis of bacterial proteins, but none selectively inhibits their degradation. Most anti-infectives kill replicating pathogens, but few preferentially kill pathogens that have been forced into a non-replicating state by conditions in the host. To explore these alternative approaches we sought selective inhibitors of the proteasome of Mycobacterium tuberculosis. Given that the proteasome structure is extensively conserved, it is not surprising that inhibitors of all chemical classes tested have blocked both eukaryotic and prokaryotic proteasomes, and no inhibitor has proved substantially more potent on proteasomes of pathogens than of their hosts. Here we show that certain oxathiazol-2-one compounds kill non-replicating M. tuberculosis and act as selective suicide-substrate inhibitors of the M. tuberculosis proteasome by cyclocarbonylating its active site threonine. Major conformational changes protect the inhibitor-enzyme intermediat! e from hydrolysis, allowing formation of an oxazolidin-2-one and preventing regeneration of active protease. Residues outside the active site whose hydrogen bonds stabilize the critical loop before and after it moves are extensively non-conserved. This may account for the ability of oxathiazol-2-one compounds to inhibit the mycobacterial proteasome potently and irreversibly while largely sparing the human homologue.
• Universality of galactic surface densities within one dark halo scale-length
  - Nature 461(7264):627 (2009)
  It was recently discovered that the mean dark matter surface density within one dark halo scale-length (the radius within which the volume density profile of dark matter remains approximately flat) is constant across a wide range of galaxies1. This scaling relation holds for galaxies spanning a luminosity range of 14 magnitudes and the whole Hubble sequence1, 2, 3. Here we report that the luminous matter surface density is also constant within one scale-length of the dark halo. This means that the gravitational acceleration generated by the luminous component in galaxies is always the same at this radius. Although the total luminous-to-dark matter ratio is not constant, within one halo scale-length it is constant. Our finding can be interpreted as a close correlation between the enclosed surface densities of luminous and dark matter in galaxies4.
• Plasmon lasers at deep subwavelength scale
  - Nature 461(7264):629 (2009)
  Laser science has been successful in producing increasingly high-powered, faster and smaller coherent light sources1, 2, 3, 4, 5, 6, 7, 8, 9. Examples of recent advances are microscopic lasers that can reach the diffraction limit, based on photonic crystals3, metal-clad cavities4 and nanowires5, 6, 7. However, such lasers are restricted, both in optical mode size and physical device dimension, to being larger than half the wavelength of the optical field, and it remains a key fundamental challenge to realize ultracompact lasers that can directly generate coherent optical fields at the nanometre scale, far beyond the diffraction limit10, 11. A way of addressing this issue is to make use of surface plasmons12, 13, which are capable of tightly localizing light, but so far ohmic losses at optical frequencies have inhibited the realization of truly nanometre-scale lasers based on such approaches14, 15. A recent theoretical work predicted that such losses could be significan! tly reduced while maintaining ultrasmall modes in a hybrid plasmonic waveguide16. Here we report the experimental demonstration of nanometre-scale plasmonic lasers, generating optical modes a hundred times smaller than the diffraction limit. We realize such lasers using a hybrid plasmonic waveguide consisting of a high-gain cadmium sulphide semiconductor nanowire, separated from a silver surface by a 5-nm-thick insulating gap. Direct measurements of the emission lifetime reveal a broad-band enhancement of the nanowire's exciton spontaneous emission rate by up to six times owing to the strong mode confinement17 and the signature of apparently threshold-less lasing. Because plasmonic modes have no cutoff, we are able to demonstrate downscaling of the lateral dimensions of both the device and the optical mode. Plasmonic lasers thus offer the possibility of exploring extreme interactions between light and matter, opening up new avenues in the fields of active photonic circuits1! 8, bio-sensing19 and quantum information technology20.
• X-ray observation of a transient hemiaminal trapped in a porous network
  - Nature 461(7264):633 (2009)
  X-ray crystallography is the method of choice for the direct structural analysis of crystalline compounds1. Extending its use to the in situ mapping of chemical transformations could provide valuable insights, as illustrated by time-resolved X-ray crystallography studies2, 3; however, the transient nature of unstable reaction intermediates often poses a significant challenge. It has recently been demonstrated that standard chemical reactions can occur within the pores of porous coordination networks4, 5, 6 and that the robust crystallinity of these networks facilitates in situ X-ray analysis of the adducts and products7, 8, 9, 10, 11. Here we show that such systems even enable X-ray observations of reaction intermediates that are usually transient and non-isolable. Our proof-of-concept demonstration examines the simple and ubiquitous reaction between an amine and an aldehyde, which normally form a very short-lived hemiaminal that then yields the Schiff-base product. Th! e mechanism of this reaction has been exhaustively examined, but the hemiaminal intermediate has only rarely been observed12, 13, 14, 15, 16. We first determine the structure of a porous network with an aromatic amine embedded in it, then diffuse an aldehyde substrate into the material to transform the amine into a hemiaminal intermediate that is kinetically trapped and thus amenable to X-ray analysis, and finally raise the temperature of the system to obtain the imine product and determine its structure. These results establish that porous network materials provide a means of obtaining sequential X-ray-based snapshots of the structural transformations that occur during chemical reactions.
• Remote triggering of fault-strength changes on the San Andreas fault at Parkfield
  - Nature 461(7264):636 (2009)
  Fault strength is a fundamental property of seismogenic zones, and its temporal changes can increase or decrease the likelihood of failure and the ultimate triggering of seismic events. Although changes in fault strength have been suggested to explain various phenomena, such as the remote triggering of seismicity1, there has been no means of actually monitoring this important property in situ. Here we argue that 20 years of observation (1987–2008) of the Parkfield area at the San Andreas fault have revealed a means of monitoring fault strength. We have identified two occasions where long-term changes in fault strength have been most probably induced remotely by large seismic events, namely the 2004 magnitude (M) 9.1 Sumatra–Andaman earthquake and the earlier 1992 M = 7.3 Landers earthquake. In both cases, the change possessed two manifestations: temporal variations in the properties of seismic scatterers—probably reflecting the stress-induced migration of fluids�! ��and systematic temporal variations in the characteristics of repeating-earthquake sequences that are most consistent with changes in fault strength. In the case of the 1992 Landers earthquake, a period of reduced strength probably triggered the 1993 Parkfield aseismic transient2, 3, 4, 5 as well as the accompanying cluster of four M > 4 earthquakes at Parkfield. The fault-strength changes produced by the distant 2004 Sumatra–Andaman earthquake are especially important, as they suggest that the very largest earthquakes may have a global influence on the strength of the Earth's fault systems. As such a perturbation would bring many fault zones closer to failure, it should lead to temporal clustering of global seismicity. This hypothesis seems to be supported by the unusually high number of M 8 earthquakes occurring in the few years following the 2004 Sumatra–Andaman earthquake.
• A pre-Archaeopteryx troodontid theropod from China with long feathers on the metatarsus
  - Nature 461(7264):640 (2009)
  The early evolution of the major groups of derived non-avialan theropods is still not well understood, mainly because of their poor fossil record in the Jurassic. A well-known result of this problem is the 'temporal paradox' argument that is sometimes made against the theropod hypothesis of avian origins1. Here we report on an exceptionally well-preserved small theropod specimen collected from the earliest Late Jurassic Tiaojishan Formation of western Liaoning, China2. The specimen is referable to the Troodontidae, which are among the theropods most closely related to birds. This new find refutes the 'temporal paradox'1 and provides significant information on the temporal framework of theropod divergence. Furthermore, the extensive feathering of this specimen, particularly the attachment of long pennaceous feathers to the pes, sheds new light on the early evolution of feathers and demonstrates the complex distribution of skeletal and integumentary features close to the! dinosaur–bird transition.
• Robust discrimination between self and non-self neurites requires thousands of Dscam1 isoforms
  - Nature 461(7264):644 (2009)
  Down Syndrome cell adhesion molecule (Dscam) genes encode neuronal cell recognition proteins of the immunoglobulin superfamily1, 2. In Drosophila, Dscam1 generates 19,008 different ectodomains by alternative splicing of three exon clusters, each encoding half or a complete variable immunoglobulin domain3. Identical isoforms bind to each other, but rarely to isoforms differing at any one of the variable immunoglobulin domains4, 5. Binding between isoforms on opposing membranes promotes repulsion6. Isoform diversity provides the molecular basis for neurite self-avoidance6, 7, 8, 9, 10, 11. Self-avoidance refers to the tendency of branches from the same neuron (self-branches) to selectively avoid one another12. To ensure that repulsion is restricted to self-branches, different neurons express different sets of isoforms in a biased stochastic fashion7, 13. Genetic studies demonstrated that Dscam1 diversity has a profound role in wiring the fly brain11. Here we show how man! y isoforms are required to provide an identification system that prevents non-self branches from inappropriately recognizing each other. Using homologous recombination, we generated mutant animals encoding 12, 24, 576 and 1,152 potential isoforms. Mutant animals with deletions encoding 4,752 and 14,256 isoforms14 were also analysed. Branching phenotypes were assessed in three classes of neurons. Branching patterns improved as the potential number of isoforms increased, and this was independent of the identity of the isoforms. Although branching defects in animals with 1,152 potential isoforms remained substantial, animals with 4,752 isoforms were indistinguishable from wild-type controls. Mathematical modelling studies were consistent with the experimental results that thousands of isoforms are necessary to ensure acquisition of unique Dscam1 identities in many neurons. We conclude that thousands of isoforms are essential to provide neurons with a robust discrimination mech! anism to distinguish between self and non-self during self-avo! idance.
• Direct reprogramming of human neural stem cells by OCT4
  Kim JB Greber B Araúzo-Bravo MJ Meyer J Park KI Zaehres H Schöler HR - Nature 461(7264):649 (2009)
  Induced pluripotent stem (iPS) cells have been generated from mouse and human somatic cells by ectopic expression of four transcription factors (OCT4 (also called POU5F1), SOX2, c-Myc and KLF4)1, 2, 3, 4, 5, 6, 7. We previously reported that Oct4 alone is sufficient to reprogram directly adult mouse neural stem cells to iPS cells8. Here we report the generation of one-factor human iPS cells from human fetal neural stem cells (one-factor (1F) human NiPS cells) by ectopic expression of OCT4 alone. One-factor human NiPS cells resemble human embryonic stem cells in global gene expression profiles, epigenetic status, as well as pluripotency in vitro and in vivo. These findings demonstrate that the transcription factor OCT4 is sufficient to reprogram human neural stem cells to pluripotency. One-factor iPS cell generation will advance the field further towards understanding reprogramming and generating patient-specific pluripotent stem cells.
• Discovery of Atg5/Atg7-independent alternative macroautophagy
  - Nature 461(7264):654 (2009)
  Macroautophagy is a process that leads to the bulk degradation of subcellular constituents by producing autophagosomes/autolysosomes1, 2, 3. It is believed that Atg5 (ref. 4) and Atg7 (ref. 5) are essential genes for mammalian macroautophagy. Here we show, however, that mouse cells lacking Atg5 or Atg7 can still form autophagosomes/autolysosomes and perform autophagy-mediated protein degradation when subjected to certain stressors. Although lipidation of the microtubule-associated protein light chain 3 (LC3, also known as Map1lc3a) to form LC3-II is generally considered to be a good indicator of macroautophagy6, it did not occur during the Atg5/Atg7-independent alternative process of macroautophagy. We also found that this alternative process of macroautophagy was regulated by several autophagic proteins, including Unc-51-like kinase 1 (Ulk1) and beclin 1. Unlike conventional macroautophagy, autophagosomes seemed to be generated in a Rab9-dependent manner by the fusion! of isolation membranes with vesicles derived from the trans-Golgi and late endosomes. In vivo, Atg5-independent alternative macroautophagy was detected in several embryonic tissues. It also had a function in clearing mitochondria during erythroid maturation. These results indicate that mammalian macroautophagy can occur through at least two different pathways: an Atg5/Atg7-dependent conventional pathway and an Atg5/Atg7-independent alternative pathway.
• Membrane-bound Fas ligand only is essential for Fas-induced apoptosis
  - Nature 461(7264):659 (2009)
  Fas ligand (FasL), an apoptosis-inducing member of the TNF cytokine family, and its receptor Fas are critical for the shutdown of chronic immune responses1, 2, 3 and prevention of autoimmunity4, 5. Accordingly, mutations in their genes cause severe lymphadenopathy and autoimmune disease in mice6, 7 and humans8, 9. FasL function is regulated by deposition in the plasma membrane and metalloprotease-mediated shedding10, 11. Here we generated gene-targeted mice that selectively lack either secreted FasL (sFasL) or membrane-bound FasL (mFasL) to resolve which of these forms is required for cell killing and to explore their hypothesized non-apoptotic activities. Mice lacking sFasL (FasLs/s) appeared normal and their T cells readily killed target cells, whereas T cells lacking mFasL (FasLm/m) could not kill cells through Fas activation. FasLm/m mice developed lymphadenopathy and hyper-gammaglobulinaemia, similar to FasLgld/gld mice, which express a mutant form of FasL that ca! nnot bind Fas, but surprisingly, FasLm/m mice (on a C57BL/6 background) succumbed to systemic lupus erythematosus (SLE)-like autoimmune kidney destruction and histiocytic sarcoma, diseases that occur only rarely and much later in FasLgld/gld mice. These results demonstrate that mFasL is essential for cytotoxic activity and constitutes the guardian against lymphadenopathy, autoimmunity and cancer, whereas excess sFasL appears to promote autoimmunity and tumorigenesis through non-apoptotic activities.
• Cooperative binding of two acetylation marks on a histone tail by a single bromodomain
  - Nature 461(7264):664 (2009)
  A key step in many chromatin-related processes is the recognition of histone post-translational modifications by effector modules such as bromodomains and chromo-like domains of the Royal family1, 2. Whereas effector-mediated recognition of single post-translational modifications is well characterized3, how the cell achieves combinatorial readout of histones bearing multiple modifications is poorly understood. One mechanism involves multivalent binding by linked effector modules4. For example, the tandem bromodomains of human TATA-binding protein-associated factor-1 (TAF1) bind better to a diacetylated histone H4 tail than to monoacetylated tails, a cooperative effect attributed to each bromodomain engaging one acetyl-lysine mark5. Here we report a distinct mechanism of combinatorial readout for the mouse TAF1 homologue Brdt, a testis-specific member of the BET protein family6. Brdt associates with hyperacetylated histone H4 (ref. 7) and is implicated in the marked chr! omatin remodelling that follows histone hyperacetylation during spermiogenesis, the stage of spermatogenesis in which post-meiotic germ cells mature into fully differentiated sperm7, 8, 9, 10. Notably, we find that a single bromodomain (BD1) of Brdt is responsible for selectively recognizing histone H4 tails bearing two or more acetylation marks. The crystal structure of BD1 bound to a diacetylated H4 tail shows how two acetyl-lysine residues cooperate to interact with one binding pocket. Structure-based mutagenesis that reduces the selectivity of BD1 towards diacetylated tails destabilizes the association of Brdt with acetylated chromatin in vivo. Structural analysis suggests that other chromatin-associated proteins may be capable of a similar mode of ligand recognition, including yeast Bdf1, human TAF1 and human CBP/p300 (also known as CREBBP and EP300, respectively). Our findings describe a new mechanism for the combinatorial readout of histone modifications in which a s! ingle effector module engages two marks on a histone tail as a! composite binding epitope.
• Substrate interactions and promiscuity in a viral DNA packaging motor
  - Nature 461(7264):669 (2009)
  The ASCE (additional strand, conserved E) superfamily of proteins consists of structurally similar ATPases associated with diverse cellular activities involving metabolism and transport of proteins and nucleic acids in all forms of life1. A subset of these enzymes consists of multimeric ringed pumps responsible for DNA transport in processes including genome packaging in adenoviruses, herpesviruses, poxviruses and tailed bacteriophages2. Although their mechanism of mechanochemical conversion is beginning to be understood3, little is known about how these motors engage their nucleic acid substrates. Questions remain as to whether the motors contact a single DNA element, such as a phosphate or a base, or whether contacts are distributed over several parts of the DNA. Furthermore, the role of these contacts in the mechanochemical cycle is unknown. Here we use the genome packaging motor of the Bacillus subtilis bacteriophage 29 (ref. 4) to address these questions. The full! mechanochemical cycle of the motor, in which the ATPase is a pentameric-ring5 of gene product 16 (gp16), involves two phases—an ATP-loading dwell followed by a translocation burst of four 2.5-base-pair (bp) steps6 triggered by hydrolysis product release7. By challenging the motor with a variety of modified DNA substrates, we show that during the dwell phase important contacts are made with adjacent phosphates every 10-bp on the 5'–3' strand in the direction of packaging. As well as providing stable, long-lived contacts, these phosphate interactions also regulate the chemical cycle. In contrast, during the burst phase, we find that DNA translocation is driven against large forces by extensive contacts, some of which are not specific to the chemical moieties of DNA. Such promiscuous, nonspecific contacts may reflect common translocase–substrate interactions for both the nucleic acid and protein translocases of the ASCE superfamily1.
• A human 5'-tyrosyl DNA phosphodiesterase that repairs topoisomerase-mediated DNA damage
  - Nature 461(7264):674 (2009)
  Topoisomerases regulate DNA topology and are fundamental to many aspects of chromosome metabolism1, 2. Their activity involves the transient cleavage of DNA, which, if it occurs near sites of endogenous DNA damage or in the presence of topoisomerase poisons, can result in abortive topoisomerase-induced DNA strand breaks3, 4, 5. These breaks feature covalent linkage of the enzyme to the DNA termini by a 3'- or 5'-phosphotyrosyl bond and are implicated in hereditary human disease6, 7, 8, chromosomal instability and cancer4, 9, and underlie the clinical efficacy of an important class of anti-tumour poisons3, 9, 10. The importance of liberating DNA termini from trapped topoisomerase is illustrated by the progressive neurodegenerative disease observed in individuals containing a mutation in tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that cleaves 3'-phosphotyrosyl bonds6, 7, 8. However, a complementary human enzyme that cleaves 5'-phosphotyrosyl bonds has not been rep! orted, despite the effect of DNA double-strand breaks containing such termini on chromosome instability and cancer6, 7, 8. Here we identify such an enzyme in human cells and show that this activity efficiently restores 5'-phosphate termini at DNA double-strand breaks in preparation for DNA ligation. This enzyme, TTRAP, is a member of the Mg2+/Mn2+-dependent family of phosphodiesterases. Cellular depletion of TTRAP results in increased susceptibility and sensitivity to topoisomerase-II-induced DNA double-strand breaks. TTRAP is, to our knowledge, the first human 5'-tyrosyl DNA phosphodiesterase to be identified, and we suggest that this enzyme is denoted tyrosyl DNA phosphodiesterase-2 (TDP2).
• Quality control
  - Nature 461(7264):686 (2009)
  A palpable hit.