Hot off the presses! Jun 25 Nature

The Jun 25 issue of the Nature is now up on Pubget (About Nature): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Cheerleader or watchdog?
  - Nature 459(7250):1033 (2009)
  Science journalism is under threat. What can scientists do to help?
• Raising the standards
  - Nature 459(7250):1033-1034 (2009)
  A fledgling effort in China will show people what is happening on the environmental front.
• Orphan giant
  - Nature 459(7250):1034 (2009)
  Strong advocacy is needed if progress is to be made against tuberculosis.
• Animal biology: Birds of a feather
  - Nature 459(7250):1036 (2009)
  
• Astronomy: Honing the Hubble constant
  - Nature 459(7250):1036 (2009)
  
• Neurobiology: Sweet memories
  - Nature 459(7250):1036 (2009)
  
• Chemistry: The tiniest acid drop
  - Nature 459(7250):1036 (2009)
  
• Nanotechnology: Mass spec goes mechanical
  - Nature 459(7250):1036 (2009)
  
• Atmospheric science: Rain on physics
  - Nature 459(7250):1036-1037 (2009)
  
• Biology: A light touch
  - Nature 459(7250):1037 (2009)
  
• Organic chemistry: Give and take
  - Nature 459(7250):1037 (2009)
  
• Genetics: Depression link revoked
  - Nature 459(7250):1037 (2009)
  
• Cognitive science: The tool becomes him
  - Nature 459(7250):1037 (2009)
  
• Journal club
  Fuhrer MS - Nature 459(7250):1037 (2009)
  
• US human spacefaring questioned
  Hand E - Nature 459(7250):1038-1039 (2009)
  When it comes to how NASA should spend its money putting people in space, just about everyone has an opinion — some of them strident. But at the moment, the opinions that matter most are those in a ten-person committee that listened quietly as key players pleaded their case at a meeting on 17 June in Washington DC.
• New protein structures replace the old
  Sanderson K - Nature 459(7250):1038-1039 (2009)
  Protein structures are getting regular makeovers with the help of 're-refinement' software developed by Dutch structural biologists. The Protein Data Bank (PDB) holds nearly 53,000 three-dimensional structures of protein molecules and nucleic acids that have mainly been deciphered through X-ray crystallography.
• Climate burden of refrigerants rockets
  - Nature 459(7250):1040 (2009)
  Modern refrigerants designed to protect the ozone layer are poised to become a major contributor to global warming because of their future explosive growth in the developing world, scientists report this week. Hydrofluorocarbon chemicals (HFCs) were developed to phase out ozone-depleting gases, in response to the Montreal Protocol.
• Deficit dooms Swedish gene institute
  Dalton R - Nature 459(7250):1040-1041 (2009)
  Cost overruns have sliced into the historically important biology programme of Sweden's Lund University, culminating in a departmental reorganization that has some scientists fuming. The Institute of Genetics, where in the winter of 1955–56 the correct number of human chromosomes was established (J.
• G8 cancels science parley
  Abbott A - Nature 459(7250):1041 (2009)
  The Italian government has caught scientists off guard by cancelling the G8 science and technology meeting that was to have begun on 25 June. The meeting would have brought together science ministers of the G8 nations to discuss issues such as how to monitor climate change and maintain environment-friendly energy supplies.
• Florida universities hit by funding crisis
  Schrope M - Nature 459(7250):1042-1043 (2009)
  This March, Michael Perfit, chair of the geology department at the University of Florida in Gainesville, learned that budget cuts might slash 11 of the 24 faculty and staff positions in his group. "It was like someone saying your whole family was killed in a car accident," he says.
• Biology society narrows Chinese rifts
  Cyranoski D - Nature 459(7250):1044 (2009)
  Scientific relations warm between mainland China and Taiwan. Warming scientific relations between Taiwan and mainland China were on view last week at a meeting in Taipei of the Society of Chinese Bioscientists in America (SCBA). Historically a Taiwanese-dominated academic networking group, the society last week announced its first president-elect born and raised in mainland China: Xiao-Fan Wang, a cancer biologist at Duke University in Durham, North Carolina. And a bill introduced in the Taiwanese legislature in January could mean that many more mainland Chinese scientists will be soon be living and working in Taiwan. The legislation would permit Taiwanese universities to recognize university degrees from mainland institutions such as Peking University and Tsinghua University. "It's ridiculous that we don't," says Ji-Wang Chern, dean of research and development at the National Taiwan University in Taipei. Carmay Lim, a computational biophysicist at the Academia Sinica in Taipei, says she has not been able to offer PhD positions to mainland students whom she wanted to stay on in her lab. "Because of the politics between Taiwan and [mainland] China, scientists like myself lose good students to universities in other parts of the world," she says. Few details of the bill are publicly available, but Chern says it is likely to be adopted. The proposal aligns with generally better relations between mainland China and Taiwan, especially since Ma Ying-jeou became president of Taiwan in May 2008. The easing of tensions could be seen in the relaxed atmosphere of the SCBA meeting. Society scientists recall past episodes in which a senior education ministry official from Beijing stormed out after not being allowed to move her talk ahead of a Taiwanese scientist, and a 2001 meeting where Nobel laureate Yuan Tseh Lee suggested that China was hurting chances for diplomacy and scientific collaboration by building up missiles aimed at Taiwan. His counterpart from the Chinese Academy of Sciences defended China's actions as a valid protection against imperialism. "There has been nothing like that here," says Chung S. Yang, a cancer researcher at Rutgers University in Piscataway, New Jersey, and former SCBA president. ADVERTISEMENT New society president Kuan-Teh Jeang, a virologist at the US National Institutes of Health in Bethesda, Maryland, says the SCBA will be changing dramatically in ways that could help to unite Chinese scientists. He hopes to turn it into an organization with more lobbying power, an enhanced role in advising government and academic institutions on interactions with Chinese institutions overseas and, possibly within a year, its own online open-access journal. "We need to be ready to extend beyond niche special interests," he says. "We should participate in the mainstream." Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Chemistry publisher in move from print journals
  - Nature 459(7250):1045 (2009)
  
• Researchers urge action on medical-isotope shortage
  - Nature 459(7250):1045 (2009)
  
• Climate projections taken to finest detail
  - Nature 459(7250):1045 (2009)
  
• EU legislation increases clinical-trial workloads
  - Nature 459(7250):1045 (2009)
  A review of the effects of the legislation governing clinical trials in the European Union has backed up some researchers' complaints about the regulations. The 2001 European Clinical Trials Directive, which came into force from 2004, was intended to harmonize the rules governing clinical trials. But it has faced criticism from researchers who think it is overly complex and bureaucratic (see Nature doi:10.1038/news.2009.163; 2009). Last week, the final report from the European Commission-funded project assessing the directive concluded that the measures increase workloads on trial sponsors and ethics committees, and delay the start of trials. The number of commercially-sponsored clinical trials in Europe increased by about 30% between 2003 and 2007, the report adds, whereas the number of non-commercially sponsored clinical trials remained constant. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• More financial woes for climate satellites
  - Nature 459(7250):1045 (2009)
  NOAA Ineffective management and cost overruns are plaguing an already troubled satellite system for tracking weather and climate, the US Government Accountability Office (GAO) reported to Congress on 17 June. The National Polar-orbiting Operational Environmental Satellite System (NPOESS; illustrated above) was conceived in 1994 as a three-way project between the Department of Defense, the National Oceanic and Atmospheric Administration (NOAA) and NASA. "This tri-agency experiment has been an epic failure," says the GAO's David Powner. In 2002, NPOESS was supposed to cost $7 billion for six satellites, with the first to launch in 2009 (Nature 782–785; 2007). Auditors now think that the current estimate — $14 billion for four satellites beginning in 2014 — is at least $1 billion off the mark. A separate report, conducted by an independent review team for NPOESS management, recommends that the White House appoint a top-level decision-maker, and suggests that NOAA should be made lead agency on the system. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Journal of the century
  - Nature 459(7250):1045 (2009)
  With a new impact factor of 31.434, up from 28.103 last year, Nature maintains its position as the leading weekly science journal, according to the 2008 Journal Citation Report. Also, Nature was last week named 'journal of the century' by the BioMedical & Life Sciences Division (DBIO) of the Special Libraries Association (SLA). Voted for by DBIO's 686 members, the award was given to celebrate the SLA's centenary and recognizes the most influential journal of the past 100 years. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Cyberinfrastructure: Feed me data
  Ledford H - Nature 459(7250):1047-1049 (2009)
  In April 2008, Richard Jorgensen found himself in front of a group of expectant researchers gathered in Cold Spring Harbor Laboratory, New York. The pressure was on: Jorgensen had recently been placed in charge of iPlant, a US$50-million, five-year programme funded by the National Science Foundation (NSF).
• Science journalism: Breaking the convention?
  Brumfiel G - Nature 459(7250):1050-1051 (2009)
  Blogs and Twitter are opening up meetings to those not actually there. Does that mean too much access to science in the raw, asks Geoff Brumfiel. Download a PDF of this story. Last July, Lars Jensen carried a small shoulder bag of equipment into the atrium of the glass-and-steel conference centre in Toronto, Ontario. Jensen, a bioinformatician at the University of Copenhagen, was one of about 1,400 researchers at the annual Intelligent Systems for Molecular Biology meeting. With him he had the tools of any modern conference attendee: a laptop, a handheld PDA and a digital camera to snap a few photos of his trip. Jensen immediately did what most researchers do: he logged on to the wireless network. He used his PDA to check FriendFeed — an online social network similar to Facebook that is popular among biologists. "Anyone else signed up for the 'orienteering' event today?" Shirley Wu, a graduate student at Stanford University, California, had written on a page that members had already devoted to the conference. "Nah," Jensen typed, "bloggers don't need icebreaker events ;-)" Jensen's joke about face-to-face contact proved prescient. Over the next few days, he and nearly 30 other researchers met mostly via their screens in the FriendFeed conference group. During sessions, many group members posted brief comments sent from their laptops or mobile phones to the popular website Twitter, and automatically cross-posted to FriendFeed. Some of these communiqués described a comment from a talk or the flavour of a session. Other posts were links to relevant papers, or photos from around the conference centre. At one point the group even served as a public address system: "HL33: Session Chair MIA — if anyone sees Yanay Ofran they may want to point him to the session," wrote Shannon McWeeney, a bioinformatics researcher at the Oregon Health & Science University in Portland. The virtual coverage "was not something that we had arranged beforehand", Jensen says. But by the time he and others were finished, hundreds of comments had been posted to the group. The information was so complete that Jensen, Wu and the other ring leaders were able to use it to write an authoritative conference summary that was later published (N. Saunders et al. PLoS Comp. Biol. e1000263; 2009). For technophiles and advocates of scientific openness, this is the way of the future. Online groups allow meeting attendees to post and discuss research as it is presented, and follow parallel sessions. They also provide an opportunity for researchers not at the meeting, as well as a far wider community, to actively participate in it. "I think it is extremely efficient," says Jean-Claude Bradley, a chemist at Drexel University in Philadelphia, Pennsylvania. Jonathan Eisen, an evolutionary biologist at the University of California, Davis, adds that 'twittering' about a presentation he is listening to helps him to focus. "I don't want to screw up and say something that's technically wrong or conceptually wrong," he says. But some worry that these tools will undermine meetings. By disseminating scientific results far beyond the lecture hall, blogging and social networking blurs the line between journalists and researchers. Scientists in competitive fields may be more reluctant to discuss new findings if they can be posted on the Internet within seconds. And at a time when many conference attendees are already surfing the web rather than paying attention to the presenter, messaging is yet another annoyance. "Frankly, it can be a distraction if people are typing on their keyboards in the meeting," says David Stewart, the director of meetings and courses at Cold Spring Harbor Laboratory in New York. "I could take pictures of every slide and it would be on the Internet within seconds." Lars Jensen Blogging without leave Last month, Stewart unwittingly found himself at the centre of the debate about such technologies at Cold Spring Harbor's annual Biology of Genomes meeting. The meeting was oversubscribed, and many researchers were interested in following the proceedings on the web. Cold Spring Harbor streamed video of the talks online for those who had registered and paid a fee, but an informal group of bloggers also began following events. Among them was Daniel MacArthur, a geneticist and author of the blog Genetic Future. MacArthur says that he decided to blog from the conference at the request of a number of people who couldn't attend. "They asked whether it would be possible to communicate interesting things during the sessions." MacArthur's comprehensive postings were read by many scientists but they irked journalists attending the meeting. The meeting rules stated that reporters had to seek permission from speakers before publishing material on their work, rules that Cold Spring Harbor instituted in part because some journals, such as Nature, discourage scientists from talking to the press before their work is published. But those rules didn't apply to scientist-bloggers like MacArthur and, after he posted details from a few talks, reporters contacted Stewart for clarification on the policies. The complaint was a wake-up call: "For the first time, I became aware that people were blogging about the data at the meeting," Stewart says. Blogging can create much thornier issues for researchers. Many presenters are already cautious about revealing unpublished results at meetings for fear that rivals in the audience might note them down. Now that the note-taking is taking place live and on the web, the speed and distance that information spreads has jumped to a new level. "With the set-up I have now, I would be able to sit in a conference, take pictures of every slide that is being shown, and it would be on the Internet within seconds, while the talk is still going on," says Jensen. This kind of direct-to-web exposure creates problems for many industrial and applied researchers. In the United States, patent applications must be filed within a year of any information becoming available to the public. The exact date of that 'public disclosure' used to be difficult to nail down, but no more, says Michael Natan, chief executive officer of Oxonica Materials, a nanotechnology company in Mountain View, California. In the Internet age, time-stamped photographs of a talk can let competitors know the exact minute a researcher presented a patentable result. Consequently, "people in industry will be much more circumspect about what they present in public", he says. Even basic researchers have reason to fret. Last year, a group of theoretical physicists photographed slides from a meeting presentation, extracted the data, and used them in their own analysis, which they published online (see Nature 7; 2008). In that case, the theorists were given permission by a presenter, and the photographs were properly cited, but the situation illustrates how easily data can find their way into the public sphere. In many fields, competition is so intense that you must conceal to survive, says Natan. "Frankly, it can be a distraction if people are typing on their keyboards in the meeting." David Stewart For denizens of the blogosphere, these sorts of concerns seem a little out of date. "I think scientific conferences are about your sharing with the world what you're doing," says Francis Ouellette, a researcher at the Ontario Institute for Cancer Research in Toronto, who twittered at the Cold Spring Harbor Meeting. "Whether or not the participant you're sharing with is in the room is somewhat inconsequential." Ouellette and many other active bloggers are also members of the 'open science' movement, which encourages researchers to make their data public as quickly as possible. Bradley sees this openness as a powerful deterrent to anyone hoping to scoop him at a conference because anything cribbed from his talk is already out on the Internet for everyone else to view. "If someone actually does copy something, I think it would be pretty embarrassing," he says, "it's already there, and it's indexed to Google." The rights of scientists Prompted by his recent experience, Stewart has come up with a pragmatic solution. At future meetings, anyone communicating information to third parties, whether by news story, blog or 'tweet', will now be required to ask presenters beforehand. "What we really want to do is to protect the rights of individual scientists to present their data in a pre-published form," he says. "I'm not saying don't blog, I'm saying blog by all means, but get permission." MacArthur says that the new policies seem like a fairly good compromise, but, he adds: "I'm hopeful that other conferences will tend to adopt more open policies." Conference organizers contacted by Nature had a wide range of policies on social networking. Many societies have banned digital photography in talks and poster sessions and some consider bloggers to be members of the media and subject them to certain reporting restrictions. However, almost nobody has developed a policy on when twittering is fair play. "This has not come up in the past but it may be something we consider in the future," says Kevin Wilson, a spokesman for the American Society for Cell Biology in Bethesda, Maryland. Journals are also pondering how best to handle social networking at meetings. Nature generally supports social media tools, says Philip Campbell, Nature's editor-in-chief. And as long as it's not a deliberate attempt to hype a new finding, he says that researchers should feel free to talk to colleagues who blog or twitter. Ginger Pinholster, the director of public programmes for the American Association for the Advancement of Science, the publisher of Science, agrees. As long as the scientist wasn't trying to promote his or her work to the public, it wouldn't be a problem. She adds that blogging unpublished results is a problem that "we just haven't run into yet". ADVERTISEMENT Although Cold Spring Harbor has opted for control, the organizers of the Intelligent Systems for Molecular Biology meeting are choosing total openness. When this year's meeting opens in Stockholm later this week, they are planning to fully embrace social networking tools. FriendFeed entries will be created for each talk at the meeting, and the entries for the keynote sessions will be posted directly to the meeting's main website. That means some people could get the buzz of the meeting without travelling to Stockholm at all. But that's not why Lars Jensen is staying at home this year. The main papers being presented have already been published, he says, so there won't be much new. He might follow the sessions online, but then again, he might catch up the old-fashioned way. "I have colleagues who are going," he says. "I can always ask them afterwards whether anything interesting happened." Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Interrogation: hard for psychologists to act as whistleblowers
  Jackson MR - Nature 459(7250):1052 (2009)
  I was disappointed in your Editorial 'Responsible interrogation' (Nature 459, 300; 2009). You accept the role of psychologists in secret interrogations because they can supposedly act as whistleblowers against inhumane treatment.
• Interrogation: our professional body forbids involvement
  Wagner LB - Nature 459(7250):1052 (2009)
  Your Editorial 'Responsible interrogation' (Nature 459, 300; 2009) takes a remarkably unscientific approach to the topic of psychologists' participation in national-security interrogations, in that it omits important current facts. The scale of this omission is comparable to failing to mention Helicobacter pylori in a discussion of peptic ulcers, the treatment of which was revolutionized by the discovery that most are caused by H. pylori
• Free will: it's a normal biological property, not a gift or a mystery
  Doyle RO - Nature 459(7250):1052 (2009)
  In his Essay 'Is free will an illusion?' (Nature 459, 164–165; 2009), Martin Heisenberg argues that humans must have free will because freedom of action has been demonstrated in other animals — including those as small as fruitflies and bacteria.
• Free will: emotions and consciousness could contribute
  Vermeersch E - Nature 459(7250):1052-1053 (2009)
  In his Essay 'Is free will an illusion?' (Nature 459, 164–165; 2009), Martin Heisenberg suggests that belief in free will is supported by quantum events.
• How air capture could help to promote a Copenhagen solution
  Chichilnisky G Eisenberger P - Nature 459(7250):1053 (2009)
  Your News Feature 'Sucking it up' (Nature 458, 1094–1097; 2009) reports on the issue of the capture of carbon dioxide from air. This is timely, as in February this year, President Obama and the Canadian Prime Minister, Stephen Harper, agreed to work together on carbon capture and sequestration as part of an effort to build a North American environmental and energy accord.
• Planck's power lies in its unique instrument combination
  Mandolesi N Planck LFI co-investigators - Nature 459(7250):1053 (2009)
  Your News Feature 'The test of inflation' (Nature 458, 820–824; 2009) highlights some of the exciting scientific data to be collected by the European Space Agency's Planck spacecraft, and the theoretical issues underlying its objectives to study the moments after the Big Bang.You discuss the new high-frequency 52-bolometer detector, but do not mention the 22-radiometer low-frequency instrument (LFI).
• Science journalism: Toppling the priesthood
  Murcott T - Nature 459(7250):1054-1055 (2009)
  In the first of three essays, Toby Murcott argues that the process of science needs to be opened up if journalists are to provide proper critique.
• Science journalism: Too close for comfort
  Rensberger B - Nature 459(7250):1055-1056 (2009)
  In the second of three essays, Boyce Rensberger tracks the progression of scientific correspondents from cheerleaders to watchdogs.
• Science journalism: The Arab boom
  El-Awady N - Nature 459(7250):1057 (2009)
  As research increases in Arab countries, the media is stepping up to report on it. In the third of three essays, Nadia El-Awady says the local journalism has much room for improvement.
• From rubber ducks to ocean gyres
  - Nature 459(7250):1058-1059 (2009)
  The tale of Curtis Ebbesmeyer's use of beachcombing to reveal patterns of ocean circulation conveys the romance of early marine science, but his lessons for today are serious, finds Simon Boxall.
• Cooking debate goes off the boil
  - Nature 459(7250):1059-1060 (2009)
  
• Our changing body image
  - Nature 459(7250):1060-1061 (2009)
  
• Science journalism: From the newsroom
  - Nature 459(7250):1061 (2009)
  The Washington Post's national environmental reporter Juliet Eilperin and its executive editor Marcus Brauchli discuss the future of science coverage in their newspaper.
• Structural biology: Protein dynamics from disorder
  Tolman JR - Nature 459(7250):1063-1064 (2009)
  The functions of proteins are often crucially dependent on how they move, but measuring the absolute magnitudes of protein motions hasn't been possible. A spectroscopic method looks set to change all that.
• Granular media: Structures in sand streams
  Lohse D van der Meer D - Nature 459(7250):1064-1065 (2009)
  An ingenious experiment that involves dropping a costly, high-speed video camera from a height of several metres reveals how free-falling streams of granular matter, such as sand, break up into grain clusters.
• Cell biology: A score for membrane fusion
  Collins RN Zimmerberg J - Nature 459(7250):1065-1066 (2009)
  Intracellular membrane fusion has been mimicked in vitro using a mix of 17 purified proteins and lipid bilayers. This technical tour de force allows the study of how cells orchestrate and perform such fusion events.
• 50 & 100 years ago
  - Nature 459(7250):1067 (2009)
  In 1956, as an experiment, an agency was started in the London area to put women graduates in touch with any suitable part-time work ... Many potential employers are prejudiced against part-time workers; it was felt that they might have more confidence if they could interview not one but a number of suitable candidates for each vacancy ... It also seemed clear that much of this work could be done at home and that it would be greatly welcomed, especially by mothers of young children ... Many employers were sympathetic to the idea and more jobs gradually became available ... Fewer permanent than temporary jobs are filled. This seems to reflect a general reluctance on the part of married women to commit themselves to permanent work.
• Planetary science: Enceladus with a grain of salt
  Spencer J - Nature 459(7250):1067-1068 (2009)
  The observation that water plumes erupt from cracks on Saturn's moon Enceladus has fired speculation about a possible subsurface ocean. The latest searches for sodium salts point to the existence of such an ocean.
• Stem cells: The stress of forming blood cells
  Pardanaud L Eichmann A - Nature 459(7250):1068-1069 (2009)
  The first heartbeat is an important moment in an embryo's life. The biomechanical forces created by pulsatile flow promote the formation of haematopoietic stem cells that equip the body with its mature blood cells.
• Nuclear physics: Unexpected doubly magic nucleus
  Janssens RV - Nature 459(7250):1069-1070 (2009)
  Nuclei with a 'magic' number of both protons and neutrons, dubbed doubly magic, are particularly stable. The oxygen isotope 24O has been found to be one such nucleus — yet it lies just at the limit of stability.
• Recent advances and emerging trends in plant hormone signalling
  Santner A Estelle M - Nature 459(7250):1071-1078 (2009)
  Plant growth and development is regulated by a structurally unrelated collection of small molecules called plant hormones. During the last 15 years the number of known plant hormones has grown from five to at least ten. Furthermore, many of the proteins involved in plant hormone signalling pathways have been identified, including receptors for many of the major hormones. Strikingly, the ubiquitin–proteasome pathway plays a central part in most hormone-signalling pathways. In addition, recent studies confirm that hormone signalling is integrated at several levels during plant growth and development.
• A soma-to-germline transformation in long-lived Caenorhabditis elegans mutants
  Curran SP Wu X Riedel CG Ruvkun G - Nature 459(7250):1079-1084 (2009)
  Unlike the soma, which ages during the lifespan of multicellular organisms, the germ line traces an essentially immortal lineage. Genomic instability in somatic cells increases with age, and this decline in somatic maintenance might be regulated to facilitate resource reallocation towards reproduction at the expense of cellular senescence. Here we show that Caenorhabditis elegans mutants with increased longevity exhibit a soma-to-germline transformation of gene expression programs normally limited to the germ line. Decreased insulin-like signalling causes the somatic misexpression of the germline-limited pie-1 and pgl family of genes in intestinal and ectodermal tissues. The forkhead boxO1A (FOXO) transcription factor DAF-16, the major transcriptional effector of insulin-like signalling, regulates pie-1 expression by directly binding to the pie-1 promoter. The somatic tissues of insulin-like mutants are more germline-like and protected from genotoxic stress. Gene inact! ivation of components of the cytosolic chaperonin complex that induce increased longevity also causes somatic misexpression of PGL-1. These results indicate that the acquisition of germline characteristics by the somatic cells of C. elegans mutants with increased longevity contributes to their increased health and survival.
• GOLPH3 modulates mTOR signalling and rapamycin sensitivity in cancer
  Scott KL Kabbarah O Liang MC Ivanova E Anagnostou V Wu J Dhakal S Wu M Chen S Feinberg T Huang J Saci A Widlund HR Fisher DE Xiao Y Rimm DL Protopopov A Wong KK Chin L - Nature 459(7250):1085-1090 (2009)
  Genome-wide copy number analyses of human cancers identified a frequent 5p13 amplification in several solid tumour types, including lung (56%), ovarian (38%), breast (32%), prostate (37%) and melanoma (32%). Here, using integrative analysis of a genomic profile of the region, we identify a Golgi protein, GOLPH3, as a candidate targeted for amplification. Gain- and loss-of-function studies in vitro and in vivo validated GOLPH3 as a potent oncogene. Physically, GOLPH3 localizes to the trans-Golgi network and interacts with components of the retromer complex, which in yeast has been linked to target of rapamycin (TOR) signalling. Mechanistically, GOLPH3 regulates cell size, enhances growth-factor-induced mTOR (also known as FRAP1) signalling in human cancer cells, and alters the response to an mTOR inhibitor in vivo. Thus, genomic and genetic, biological, functional and biochemical data in yeast and humans establishes GOLPH3 as a new oncogene that is commonly targeted for! amplification in human cancer, and is capable of modulating the response to rapamycin, a cancer drug in clinical use.
• Reconstitution of Rab- and SNARE-dependent membrane fusion by synthetic endosomes
  Ohya T Miaczynska M Coskun U Lommer B Runge A Drechsel D Kalaidzidis Y Zerial M - Nature 459(7250):1091-1097 (2009)
  Rab GTPases and SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) are evolutionarily conserved essential components of the eukaryotic intracellular transport system. Although pairing of cognate SNAREs is sufficient to fuse membranes in vitro, a complete reconstitution of the Rab–SNARE machinery has never been achieved. Here we report the reconstitution of the early endosomal canine Rab5 GTPase, its key regulators and effectors together with SNAREs into proteoliposomes using a set of 17 recombinant human proteins. These vesicles behave like minimal 'synthetic' endosomes, fusing with purified early endosomes or with each other in vitro. Membrane fusion measured by content-mixing and morphological assays requires the cooperativity between Rab5 effectors and cognate SNAREs which, together, form a more efficient 'core machinery' than SNAREs alone. In reconstituting a fusion mechanism dependent on both a Rab GTPase and SNAREs, our work shows t! hat the two machineries act coordinately to increase the specificity and efficiency of the membrane tethering and fusion process.
• Sodium salts in E-ring ice grains from an ocean below the surface of Enceladus
  Postberg F Kempf S Schmidt J Brilliantov N Beinsen A Abel B Buck U Srama R - Nature 459(7250):1098-1101 (2009)
  Saturn's moon Enceladus emits plumes of water vapour and ice particles from fractures near its south pole1, 2, 3, 4, 5, suggesting the possibility of a subsurface ocean5, 6, 7. These plume particles are the dominant source of Saturn's E ring7, 8. A previous in situ analysis9 of these particles concluded that the minor organic or siliceous components, identified in many ice grains, could be evidence for interaction between Enceladus' rocky core and liquid water9, 10. It was not clear, however, whether the liquid is still present today or whether it has frozen. Here we report the identification of a population of E-ring grains that are rich in sodium salts (0.5–2% by mass), which can arise only if the plumes originate from liquid water. The abundance of various salt components in these particles, as well as the inferred basic pH, exhibit a compelling similarity to the predicted composition of a subsurface Enceladus ocean in contact with its rock core11. The plume vapou! r is expected to be free of atomic sodium. Thus, the absence of sodium from optical spectra12 is in good agreement with our results. In the E ring the upper limit for spectroscopy12 is insufficiently sensitive to detect the concentrations we found.
• No sodium in the vapour plumes of Enceladus
  Schneider NM Burger MH Schaller EL Brown ME Johnson RE Kargel JS Dougherty MK Achilleos NA - Nature 459(7250):1102-1104 (2009)
  The discovery of water vapour and ice particles erupting from Saturn's moon Enceladus fuelled speculation that an internal ocean was the source1, 2, 3. Alternatively, the source might be ice warmed, melted or crushed by tectonic motions4. Sodium chloride (that is, salt) is expected to be present in a long-lived ocean in contact with a rocky core. Here we report a ground-based spectroscopic search for atomic sodium near Enceladus that places an upper limit on the mixing ratio in the vapour plumes orders of magnitude below the expected ocean salinity5. The low sodium content of escaping vapour, together with the small fraction of salt-bearing particles6, argues against a situation in which a near-surface geyser is fuelled by a salty ocean through cracks in the crust1. The lack of observable sodium in the vapour is consistent with a wide variety of alternative eruption sources, including a deep ocean6, a freshwater reservoir, or ice. The existing data may be insufficient ! to distinguish between these hypotheses.
• Optically controlled locking of the nuclear field via coherent dark-state spectroscopy
  Xu X Yao W Sun B Steel DG Bracker AS Gammon D Sham LJ - Nature 459(7250):1105-1109 (2009)
  A single electron or hole spin trapped inside a semiconductor quantum dot forms the foundation for many proposed quantum logic devices1, 2, 3, 4, 5, 6. In group III–V materials, the resonance and coherence between two ground states of the single spin are inevitably affected by the lattice nuclear spins through the hyperfine interaction7, 8, 9, while the dynamics of the single spin also influence the nuclear environment10, 11, 12, 13, 14, 15. Recent efforts12, 16 have been made to protect the coherence of spins in quantum dots by suppressing the nuclear spin fluctuations. However, coherent control of a single spin in a single dot with simultaneous suppression of the nuclear fluctuations has yet to be achieved. Here we report the suppression of nuclear field fluctuations in a singly charged quantum dot to well below the thermal value, as shown by an enhancement of the single electron spin dephasing time T 2*, which we measure using coherent dark-state spectroscopy. The! suppression of nuclear fluctuations is found to result from a hole-spin assisted dynamic nuclear spin polarization feedback process, where the stable value of the nuclear field is determined only by the laser frequencies at fixed laser powers. This nuclear field locking is further demonstrated in a three-laser measurement, indicating a possible enhancement of the electron spin T 2* by a factor of several hundred. This is a simple and powerful method of enhancing the electron spin coherence time without use of 'spin echo'-type techniques8, 12. We expect that our results will enable the reproducible preparation of the nuclear spin environment for repetitive control and measurement of a single spin with minimal statistical broadening.
• High-speed tracking of rupture and clustering in freely falling granular streams
  Royer JR Evans DJ Oyarte L Guo Q Kapit E Möbius ME Waitukaitis SR Jaeger HM - Nature 459(7250):1110-1113 (2009)
  Thin streams of liquid commonly break up into characteristic droplet patterns owing to the surface-tension-driven Plateau–Rayleigh instability1, 2, 3. Very similar patterns are observed when initially uniform streams of dry granular material break up into clusters of grains4, 5, 6, even though flows of macroscopic particles are considered to lack surface tension7, 8. Recent studies on freely falling granular streams tracked fluctuations in the stream profile9, but the clustering mechanism remained unresolved because the full evolution of the instability could not be observed. Here we demonstrate that the cluster formation is driven by minute, nanoNewton cohesive forces that arise from a combination of van der Waals interactions and capillary bridges between nanometre-scale surface asperities. Our experiments involve high-speed video imaging of the granular stream in the co-moving frame, control over the properties of the grain surfaces and the use of atomic force mic! roscopy to measure grain–grain interactions. The cohesive forces that we measure correspond to an equivalent surface tension five orders of magnitude below that of ordinary liquids. We find that the shapes of these weakly cohesive, non-thermal clusters of macroscopic particles closely resemble droplets resulting from thermally induced rupture of liquid nanojets10, 11, 12.
• Enhanced carbon pump inferred from relaxation of nutrient limitation in the glacial ocean
  Pichevin LE Reynolds BC Ganeshram RS Cacho I Pena L Keefe K Ellam RM - Nature 459(7250):1114-1117 (2009)
  The modern Eastern Equatorial Pacific (EEP) Ocean is a large oceanic source of carbon to the atmosphere1. Primary productivity over large areas of the EEP is limited by silicic acid and iron availability, and because of this constraint the organic carbon export to the deep ocean is unable to compensate for the outgassing of carbon dioxide that occurs through upwelling of deep waters. It has been suggested that the delivery of dust-borne iron to the glacial ocean2, 3 could have increased primary productivity and enhanced deep-sea carbon export in this region, lowering atmospheric carbon dioxide concentrations during glacial periods. Such a role for the EEP is supported by higher organic carbon burial rates documented in underlying glacial sediments4, 5, but lower opal accumulation rates cast doubts on the importance of the EEP as an oceanic region for significant glacial carbon dioxide drawdown6, 7. Here we present a new silicon isotope record that suggests the paradoxi! cal decline in opal accumulation rate in the glacial EEP results from a decrease in the silicon to carbon uptake ratio of diatoms under conditions of increased iron availability from enhanced dust input. Consequently, our study supports the idea of an invigorated biological pump in this region during the last glacial period that could have contributed to glacial carbon dioxide drawdown. Additionally, using evidence from silicon and nitrogen isotope changes, we infer that, in contrast to the modern situation, the biological productivity in this region is not constrained by the availability of iron, silicon and nitrogen during the glacial period. We hypothesize that an invigorated biological carbon dioxide pump constrained perhaps only by phosphorus limitation was a more common occurrence in low-latitude areas of the glacial ocean.
• 142Nd evidence for an enriched Hadean reservoir in cratonic roots
  Upadhyay D Scherer EE Mezger K - Nature 459(7250):1118-1121 (2009)
  The isotope 146Sm undergoes -decay to 142Nd, with a half-life of 103 million years. Measurable variations in the 142Nd/144Nd values of rocks resulting from Sm–Nd fractionation could therefore only have been produced within about 400 million years of the Solar System's formation (that is, when 146Sm was extant). The 142Nd/144Nd compositions of terrestrial rocks1, 2, 3, 4, 5, 6, 7 are accordingly a sensitive monitor of the main silicate differentiation events that took place in the early Earth. High 142Nd/144Nd values measured in some Archaean rocks from Greenland1, 2, 3, 4, 5 hint at the existence of an early incompatible-element-depleted mantle. Here we present measurements of low 142Nd/144Nd values in 1.48-gigayear-(Gyr)-old lithospheric mantle-derived alkaline rocks from the Khariar nepheline syenite complex in southeastern India8. These data suggest that a reservoir that was relatively enriched in incompatible elements formed at least 4.2 Gyr ago and traces of its! isotopic signature persisted within the lithospheric root of the Bastar craton until at least 1.48 Gyr ago. These low 142Nd/144Nd compositions may represent a diluted signature of a Hadean (4 to 4.57 Gyr ago) enriched reservoir that is characterized by even lower values. That no evidence of the early depleted mantle has been observed in rocks younger than 3.6 Gyr (refs 3, 4, 7) implies that such domains had effectively mixed back into the convecting mantle by then. In contrast, some early enriched components apparently escaped this fate. Thus, the mantle sampled by magmatism since 3.6 Gyr ago may be biased towards a depleted composition that would be balanced by relatively more enriched reservoirs that are 'hidden' in Hadean crust6, the D'' layer9, 10, 11 of the lowermost mantle or, as we propose here, also within the roots of old cratons.
• Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
  Smith GJ Vijaykrishna D Bahl J Lycett SJ Worobey M Pybus OG Ma SK Cheung CL Raghwani J Bhatt S Peiris JS Guan Y Rambaut A - Nature 459(7250):1122-1125 (2009)
  In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States1. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before emergence in humans, and! that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans2.
• Down's syndrome suppression of tumour growth and the role of the calcineurin inhibitor DSCR1
  Baek KH Zaslavsky A Lynch RC Britt C Okada Y Siarey RJ Lensch MW Park IH Yoon SS Minami T Korenberg JR Folkman J Daley GQ Aird WC Galdzicki Z Ryeom S - Nature 459(7250):1126-1130 (2009)
  The incidence of many cancer types is significantly reduced in individuals with Down's syndrome1, 2, 3, 4, and it is thought that this broad cancer protection is conferred by the increased expression of one or more of the 231 supernumerary genes on the extra copy of chromosome 21. One such gene is Down's syndrome candidate region-1 (DSCR1, also known as RCAN1), which encodes a protein that suppresses vascular endothelial growth factor (VEGF)-mediated angiogenic signalling by the calcineurin pathway5, 6, 7, 8, 9, 10. Here we show that DSCR1 is increased in Down's syndrome tissues and in a mouse model of Down's syndrome. Furthermore, we show that the modest increase in expression afforded by a single extra transgenic copy of Dscr1 is sufficient to confer significant suppression of tumour growth in mice, and that such resistance is a consequence of a deficit in tumour angiogenesis arising from suppression of the calcineurin pathway. We also provide evidence that attenuati! on of calcineurin activity by DSCR1, together with another chromosome 21 gene Dyrk1a, may be sufficient to markedly diminish angiogenesis. These data provide a mechanism for the reduced cancer incidence in Down's syndrome and identify the calcineurin signalling pathway, and its regulators DSCR1 and DYRK1A, as potential therapeutic targets in cancers arising in all individuals.
• Biomechanical forces promote embryonic haematopoiesis
  Adamo L Naveiras O Wenzel PL McKinney-Freeman S Mack PJ Gracia-Sancho J Suchy-Dicey A Yoshimoto M Lensch MW Yoder MC García-Cardeña G Daley GQ - Nature 459(7250):1131-1135 (2009)
  Biomechanical forces are emerging as critical regulators of embryogenesis, particularly in the developing cardiovascular system1, 2. After initiation of the heartbeat in vertebrates, cells lining the ventral aspect of the dorsal aorta, the placental vessels, and the umbilical and vitelline arteries initiate expression of the transcription factor Runx1 (refs 3–5), a master regulator of haematopoiesis, and give rise to haematopoietic cells4. It remains unknown whether the biomechanical forces imposed on the vascular wall at this developmental stage act as a determinant of haematopoietic potential6. Here, using mouse embryonic stem cells differentiated in vitro, we show that fluid shear stress increases the expression of Runx1 in CD41+c-Kit+ haematopoietic progenitor cells7, concomitantly augmenting their haematopoietic colony-forming potential. Moreover, we find that shear stress increases haematopoietic colony-forming potential and expression of haematopoietic markers! in the para-aortic splanchnopleura/aorta–gonads–mesonephros of mouse embryos and that abrogation of nitric oxide, a mediator of shear-stress-induced signalling8, compromises haematopoietic potential in vitro and in vivo. Collectively, these data reveal a critical role for biomechanical forces in haematopoietic development.
• Subcellular homeostasis of phytohormone auxin is mediated by the ER-localized PIN5 transporter
  Mravec J Skůpa P Bailly A Hoyerová K Krecek P Bielach A Petrásek J Zhang J Gaykova V Stierhof YD Dobrev PI Schwarzerová K Rolcík J Seifertová D Luschnig C Benková E Zazímalová E Geisler M Friml J - Nature 459(7250):1136-1140 (2009)
  The plant signalling molecule auxin provides positional information in a variety of developmental processes by means of its differential distribution (gradients) within plant tissues1. Thus, cellular auxin levels often determine the developmental output of auxin signalling. Conceptually, transmembrane transport and metabolic processes regulate the steady-state levels of auxin in any given cell2, 3. In particular, PIN auxin-efflux-carrier-mediated, directional transport between cells is crucial for generating auxin gradients2, 4, 5. Here we show that Arabidopsis thaliana PIN5, an atypical member of the PIN gene family, encodes a functional auxin transporter that is required for auxin-mediated development. PIN5 does not have a direct role in cell-to-cell transport but regulates intracellular auxin homeostasis and metabolism. PIN5 localizes, unlike other characterized plasma membrane PIN proteins, to endoplasmic reticulum (ER), presumably mediating auxin flow from the cyt! osol to the lumen of the ER. The ER localization of other PIN5-like transporters (including the moss PIN) indicates that the diversification of PIN protein functions in mediating auxin homeostasis at the ER, and cell-to-cell auxin transport at the plasma membrane, represent an ancient event during the evolution of land plants.
• Yurt, Coracle, Neurexin IV and the Na+,K+-ATPase form a novel group of epithelial polarity proteins
  - Nature 459(7250):1141-1145 (2009)
  The integrity of polarized epithelia is critical for development and human health. Many questions remain concerning the full complement and the function of the proteins that regulate cell polarity1. Here we report that the Drosophila FERM proteins Yurt (Yrt)2 and Coracle (Cora)3 and the membrane proteins Neurexin IV (Nrx-IV)4 and Na+,K+-ATPase5 are a new group of functionally cooperating epithelial polarity proteins. This 'Yrt/Cora group' promotes basolateral membrane stability and shows negative regulatory interactions with the apical determinant Crumbs (Crb). Genetic analyses indicate that Nrx-IV and Na+,K+-ATPase act together with Cora in one pathway, whereas Yrt acts in a second redundant pathway. Moreover, we show that the Yrt/Cora group is essential for epithelial polarity during organogenesis but not when epithelial polarity is first established or during terminal differentiation. This property of Yrt/Cora group proteins explains the recovery of polarity in embr! yos lacking the function of the Lethal giant larvae (Lgl) group of basolateral polarity proteins6, 7. We also find that the mammalian Yrt orthologue EPB41L5 (also known as YMO1 and Limulus)8, 9, 10 is required for lateral membrane formation, indicating a conserved function of Yrt proteins in epithelial polarity.
• Structural insight into the autoinhibition mechanism of AMP-activated protein kinase
  Chen L Jiao ZH Zheng LS Zhang YY Xie ST Wang ZX Wu JW - Nature 459(7250):1146-1149 (2009)
  The AMP-activated protein kinase (AMPK) is characterized by its ability to bind to AMP, which enables it to adjust enzymatic activity by sensing the cellular energy status and maintain the balance between ATP production and consumption in eukaryotic cells1, 2. It also has important roles in the regulation of cell growth and proliferation, and in the establishment and maintenance of cell polarity3. These important functions have rendered AMPK an important drug target for obesity, type 2 diabetes and cancer treatments4. However, the regulatory mechanism of AMPK activity by AMP binding remains unsolved. Here we report the crystal structures of an unphosphorylated fragment of the AMPK -subunit (KD-AID) from Schizosaccharomyces pombe that contains both the catalytic kinase domain and an autoinhibitory domain (AID), and of a phosphorylated kinase domain from Saccharomyces cerevisiae (Snf1-pKD). The AID binds, from the 'backside', to the hinge region of its kinase domain, for! ming contacts with both amino-terminal and carboxy-terminal lobes. Structural analyses indicate that AID binding might constrain the mobility of helix C, hence resulting in an autoinhibited KD-AID with much lower kinase activity than that of the kinase domain alone. AMP activates AMPK both allosterically and by inhibiting dephosphorylation5, 6. Further in vitro kinetic studies demonstrate that disruption of the KD-AID interface reverses the autoinhibition and these AMPK heterotrimeric mutants no longer respond to the change in AMP concentration. The structural and biochemical data have shown the primary mechanism of AMPK autoinhibition and suggest a conformational switch model for AMPK activation by AMP.
• dUTP incorporation into genomic DNA is linked to transcription in yeast
  Kim N Jinks-Robertson S - Nature 459(7250):1150-1153 (2009)
  Highly activated transcription is associated with eukaryotic genome instability, resulting in increased rates of mitotic recombination and mutagenesis. The association between high transcription and genome stability is probably due to a variety of factors including an enhanced accumulation of DNA damage, transcription-associated supercoiling, collision between replication forks and the transcription machinery, and the persistence of RNA–DNA hybrids1. In the case of transcription-associated mutagenesis, we previously showed that there is a direct proportionality between the level of transcription and the mutation rate in the yeast Saccharomyces cerevisiae 2, and that the molecular nature of the mutations is affected by highly activated transcription2, 3. Here we show that the accumulation of apurinic/apyrimidinic sites is greatly enhanced in highly transcribed yeast DNA. We further demonstrate that most apurinic/apyrimidinic sites in highly transcribed DNA are derived! from the removal of uracil, the presence of which is linked to direct incorporation of dUTP in place of dTTP. These results show an unexpected relationship between transcription and the fidelity of DNA synthesis, and raise intriguing cell biological issues with regard to nucleotide pool compartmentalization.
• Self-assembly of DNA into nanoscale three-dimensional shapes
  Douglas SM Dietz H Liedl T Högberg B Graf F Shih WM - Nature 459(7250):1154 (2009)
  Nature 459, 414–418 (2009) In this Letter, Figure 3 was printed incorrectly. The corrected figure is presented below.
• The missing memristor found
  Strukov DB Snider GS Stewart DR Williams RS - Nature 459(7250):1154 (2009)
  Nature 453, 80–83 (2008) In Fig. 2a of this Letter, the resistance for the right-hand element of the bottom circuit should be ROFF(1 - w/D), instead of the shown value ROFFw/D. Also, the correct value of window function should be w(D - W)/D2, rather than w(1 - W)/D2. All simulation results presented in the paper use the correct formulae.
• Codename: Phoenix
  Tang J - Nature 459(7250):1160 (2009)
  Here comes the rain.