Nature contents: 04 April 2013

Can't view this email? Click here to view in your browser.     Volume 496 Number 7443      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.                       Hamamatsu's NanoZoomer-XR delivers faster, worry-free scanning of up to 320 slides. Our new NDP.view2 software allows faster viewing of your slides and an improved interface. Our new NDP.analyze software, powered by Visiopharm, allows you to extract subcellular morphometric details from brightfield and fluorescent whole slide images either locally or on the Cloud.             Jump to the content that matters to you View Table of Contents ▶ ▼ News & Comment   ▼ Biological Sciences   ▼ Chemical Sciences   ▼ Physical Sciences   ▼ Earth & Environmental Sciences   ▼ Careers & Jobs       This week's highlights     Biological Sciences More Biological sciences ▼   The genomes of four tapeworm species reveal adaptations to parasitism   Existing treatments for tapeworms are not always reliable and some have adverse side effects, so new drugs are urgently needed. The publication of four tapeworm genome sequences - human-infective species Echinococcus multilocularis, E. granulosus, Taenia solium and the laboratory model Hymenolepis microstoma - and the identification of potential new drug targets for treating tapeworm infections is therefore a welcome development. More than a thousand E. multilocularis proteins emerge as potential targets, and of these, close to 200 may be targeted by existing pharmaceuticals.       Chemical Sciences More Chemical sciences ▼   Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution   Three-dimensional images and movies of a platinum nanoparticle at atomic resolution published this week reveal details of defects in nanomaterials that have not been seen before. Jianwei Miao and colleagues describe a new combination of established techniques that combines electron tomographic reconstruction with 3D Fourier filtering. Possible applications include materials sciences, nanoscience, solid-state physics and chemistry.       Earth & Environmental Sciences More Earth & Environmental sciences ▼   July 2012 Greenland melt extent enhanced by low-level liquid clouds   The heatwave that struck Greenland in July 2012 melted surface ice across virtually the entire ice sheet, causing extensive flooding. Ice core data suggest that such events occur on average only about once every 150 years, with the last one in 1889. This study shows that thin, low-level, liquid clouds played a key role in the 2012 event. At high elevations these clouds enhance surface warming, as they were optically thick enough and low enough to significantly enhance the downwelling infrared flux at the surface. Yet they were thin enough to allow sufficient solar radiation through to raise surface temperatures above the melting point.                   Nature present: CNIO Cancer Symposium: Frontiers in Tumor Heterogeneity and Plasticity October 27-30, 2013 Madrid, Spain Click here for more information or to register for this conference today!                 Podcast & Video     In this week's podcast: what would happen to you if you fell in a black hole, Greenland's 2012 heat wave, and how North America swallowed some islands to make its mountainous western coast.         News & Comment Read daily news coverage▶ ▲top               THIS WEEK           Editorials                   A record made to be broken ▶     Japan's major science-funding agency has a clean record when it comes to research fraud. Now is the time for it to step up and resolve a long-running case of alleged scientific misconduct.             Against the law ▶     Behaviours proposed for black holes conflict with the laws of physics.             World View                   If a job is worth doing, it is worth doing twice ▶     Researchers and funding agencies need to put a premium on ensuring that results are reproducible, argues Jonathan F. Russell.             Seven Days                   Seven days: 29 March–4 April 2013 ▶     The week in science: Canada leaves UN desertification treaty, China reports first human deaths from H7N9 bird flu, and UK open-access policies take effect.             NEWS IN FOCUS           Crick's medal goes under the hammer ▶     Pending auction raises eyebrows but few objections.             Sizing up a slow assault on cancer ▶     Rise of immunotherapies spurs search for markers of response.             Detectors zero in on Earth's heat ▶     Geoneutrinos paint picture of deep-mantle processes.             Detective work uncovers under-reported overfishing ▶     Excessive catches by Chinese vessels threaten livelihoods and ecosystems in West Africa.             Feature                   Astrophysics: Fire in the hole! ▶     Will an astronaut who falls into a black hole be crushed or burned to a crisp?             COMMENT           Policy: Update the Chemical Weapons Convention ▶     Bring biological threats into the treaty and make chemists more aware of the dark side of their research, says Leiv K. Sydnes.             Collaboration: Link the world's best investigators ▶     Nurturing small groups of leading researchers — especially young scientists — is the way to break intellectual ground, says Alan Bernstein.             Books and Arts                   Anthropology: A monochrome Eden ▶     Bob Bloomfield assesses a haunting photographic record of remote environments and the indigenous peoples who live in them.             Books in brief ▶             Palaeontology: Giants unearthed ▶     Xu Xing revels in an enthusiast's tour of the Mesozoic era and its denizens.             Correspondence                   Sexism: Dearth of female role models Simon Williams, Christine Wood, Richard McGee | Sexism: A revealing experiment Tina M. Iverson | Sexism: Science biographer responds Marjorie Senechal | Gender gap: Nature's readers comment online             Obituary                   Donald Arthur Glaser (1926–2013) ▶     Physicist and biotechnologist who invented the bubble chamber.                         October 21 - 22 2013 The Royal Society, London Alfred Russel Wallace and his legacy This meeting will encompass Wallace's major scientific interests including evolution, natural history, biogeography, colouration, sexual selection and astronomy and, a hundred years after his death, will examine and debate current thinking on many of the issues that preoccupied him, including very briefly his contributions to the social sciences. Contact: discussion.meetings@royalsociety.org               Biological Sciences ▲top             RESEARCH           Latest Online                   Structural biology: A solution to the telomerase puzzle ▶     Benjamin M. Akiyama, Michael D. Stone             HIV: Roadmaps to a vaccine ▶     Hugo Mouquet, Michel C. Nussenzweig             Glucose–TOR signalling reprograms the transcriptome and activates meristems ▶     Yan Xiong, Matthew McCormack, Lei Li et al.     The authors show that photosynthetically derived glucose drives target-of-rapamycin signalling, resulting in transcriptional reprogramming of genes involved in cell cycle regulation.             Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus ▶     Hua-Xin Liao, Rebecca Lynch, Tongqing Zhou et al.     Longitudinal sampling is used to map the evolution of an HIV-1 virus from the time of infection, and the co-evolution of a broadly neutralizing antibody in the same infected patient; the findings have important implications for HIV vaccine development.             The architecture of Tetrahymena telomerase holoenzyme ▶     Jiansen Jiang, Edward J. Miracco, Kyungah Hong et al.     The long-awaited structure of a telomerase holoenzyme, from Tetrahymena, has been obtained by electron microscopy; affinity labelling of subunits and modelling with NMR and crystal structures of various components allowed the identification of the catalytic core and subunit interactions, and the functional role of the subunits in telomerase processivity was enabled by performing the first reconstitution of the holoenzyme in vitro.             Terrestrial water fluxes dominated by transpiration ▶     Scott Jasechko, Zachary D. Sharp, John J. Gibson et al.     An analysis of the relative effects of transpiration and evaporation, which can be distinguished by how they affect isotope ratios in water, shows that transpiration is by far the largest water flux from Earth's continents, representing 80 to 90 per cent of terrestrial evapotranspiration and using half of all solar energy absorbed by land surfaces.             Diverse and heritable lineage imprinting of early haematopoietic progenitors ▶     Shalin H. Naik, Leïla Perié, Erwin Swart et al.     In vivo 'cellular barcoding' shows that early haematopoietic progenitors are heterogeneous in the cell types that they produce, and this is partly due to an 'imprinting' of fate in progenitors, including for a separate dendritic cell lineage.             Rescuing cocaine-induced prefrontal cortex hypoactivity prevents compulsive cocaine seeking ▶     Billy T. Chen, Hau-Jie Yau, Christina Hatch et al.     A study of compulsive drug-seeking behaviour in rats reveals that prolonged cocaine self-administration decreases prelimbic cortex activity resulting in increased compulsive drug-seeking actions; conversely, increasing activity in the prelimbic cortex decreases drug-seeking behaviour, a finding relevant to addiction treatment.             Manipulation of small Rho GTPases is a pathogen-induced process detected by NOD1 ▶     A. Marijke Keestra, Maria G. Winter, Josef J. Auburger et al.     Salmonella effector proteins trigger host innate immunity through the activation of small Rho GTPases, which, in turn, is sensed by the NOD1/2 signalling pathway.             A pathogenic picornavirus acquires an envelope by hijacking cellular membranes ▶     Zongdi Feng, Lucinda Hensley, Kevin L. McKnight et al.     Hepatitis A virus particles released from cells can hijack and become wrapped in host-derived membranes by using proteins that facilitate the budding of many enveloped viruses, calling into question the traditional distinction between enveloped and non-enveloped viruses.             Crystal structure of a eukaryotic phosphate transporter ▶     Bjørn P. Pedersen, Hemant Kumar, Andrew B. Waight et al.     The X-ray crystal structure of a high-affinity phosphate importer in an inward-facing, occluded state in the presence of phosphate is reported; this is the first structure of a membrane protein involved in inorganic phosphate uptake and the first crystal structure of a eukaryotic MFS transporter.             Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors ▶     Alistair B. Russell, Michele LeRoux, Krisztina Hathazi et al.     A functionally diverse superfamily of bacterial phospholipase enzymes that mediate antagonisitc interactions as effectors of the type VI secretion system is uncovered; these enzymes degrade the bacterial membrane, representing a novel mechanism of bacterial competition.             Articles and Letters                   The genomes of four tapeworm species reveal adaptations to parasitism OPEN ▶     Isheng J. Tsai, Magdalena Zarowiecki, Nancy Holroyd et al.     Genome sequences of human-infective tapeworm species reveal extreme losses of genes and pathways that are ubiquitous in other animals, species-specific expansions of non-canonical heat shock proteins and families of known antigens, specialized detoxification pathways, and metabolism that relies on host nutrients; this information is used to identify new potential drug targets.             SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket ▶     Weiman Xing, Luca Busino, Thomas R. Hinds et al.     Crystal structures of mammalian CRY2, one of the cryptochrome flavoproteins that have light-independent functions at the core of the circadian clock, show that it binds FAD dynamically and that the F-box protein FBXL3 captures CRY2 by occupying its FAD-binding pocket and burying its PER-binding interface.             Draft genome of the wheat A-genome progenitor Triticum urartu  ▶     Hong-Qing Ling, Shancen Zhao, Dongcheng Liu et al.     The genome sequence and its analysis of the diploid wild wheat Triticum urartu (progenitor of the wheat A genome) represent a tool for studying the complex, polyploid wheat genomes and should be a valuable resource for the genetic improvement of wheat.             Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation OPEN ▶     Jizeng Jia, Shancen Zhao, Xiuying Kong et al.     Sequencing and analysing the diploid genome and transcriptome of Aegilops tauschii provide new insights into the role of this genome in enabling the adaptation of bread wheat and are a step towards understanding the very large and complicated hexaploid genomes of wheat species.             The emergence of functional microcircuits in visual cortex ▶     Ho Ko, Lee Cossell, Chiara Baragli et al.     A study of mouse visual cortex relating patterns of excitatory synaptic connectivity to visual response properties of neighbouring neurons shows that, after eye opening, local connectivity reorganizes extensively: more connections form selectively between neurons with similar visual responses and connections are eliminated between visually unresponsive neurons, but the overall connectivity rate does not change.             Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway ▶     Jaekyoung Son, Costas A. Lyssiotis, Haoqiang Ying et al.     Pancreatic cancers use a novel glutamine metabolism pathway, regulated by oncogenic KRAS, to maintain redox balance; these findings add to the understanding of the mechanisms by which oncogenic alterations reprogram cellular metabolism to promote tumour growth.             Proteolytic elimination of N-myristoyl modifications by the Shigella virulence factor IpaJ ▶     Nikolay Burnaevskiy, Thomas G. Fox, Daniel A. Plymire et al.     An irreversible mechanism of protein demyristoylation catalysed by invasion plasmid antigen J (IpaJ), a Shigella flexneri type III effector protein with cysteine protease activity, is described.             SIRT6 regulates TNF-α secretion through hydrolysis of long-chain fatty acyl lysine ▶     Hong Jiang, Saba Khan, Yi Wang et al.     The sirtuin family of enzymes are known as NAD-dependent deacetylases, although some of them have very weak deacetylase activity; here human SIRT6, an enzyme important for DNA repair and transcription, is shown to remove long-chain fatty acyl groups from protein lysine residues, and to have a function in promoting tumour necrosis factor alpha secretion.             Mechanistic studies of an unprecedented enzyme-catalysed 1,2-phosphono-migration reaction ▶     Wei-chen Chang, Mishtu Dey, Pinghua Liu et al.     The non-haem-iron-dependent enzyme HppE catalyses the final step in the biosynthesis of fosfomycin, a broad-spectrum, clinically useful antibiotic; here it is shown that HppE can also catalyse a 1,2-phosphono-migration reaction, previously undocumented for any enzyme.             A solution to release twisted DNA during chromosome replication by coupled DNA polymerases ▶     Isabel Kurth, Roxana E. Georgescu, Mike E. O'Donnell     During chromosome replication, coupled polymerases introduce topological changes that cause lower processivity and transient lagging-strand polymerase dissociation from DNA.             Structures of protein–protein complexes involved in electron transfer ▶     Svetlana V. Antonyuk, Cong Han, Robert R. Eady et al.     Structures of a newly characterized three-domain haem-c-Cu nitrite reductase are reported at 1.01 Å resolution, indicating how electron transfer may occur in protein–protein complexes.             News & Views                   Biochemistry: Positive and radical ▶     Spencer C. Peck, Wilfred A. van der Donk             Cancer: A metabolic metamorphosis ▶     Abigail S. Krall, Heather R. Christofk             Biochemistry: Sirtuin on a high-fat diet ▶     Poonam Bheda, Cynthia Wolberger             Structural biology: A solution to the telomerase puzzle ▶     Benjamin M. Akiyama, Michael D. Stone             HIV: Roadmaps to a vaccine ▶     Hugo Mouquet, Michel C. Nussenzweig             Research Highlights                   Animal communication: Bees of bigger hives forage better | Neuroscience: Faulty link in schizophrenia | Animal behaviour: Chemically camouflaged fish | Microbiology: Whole sequence, no culture | Neuroscience: Fickle wiring in ageing brains | Applied maths: Mechanics behind seashell spines         NEWS & COMMENT           Sizing up a slow assault on cancer | Policy: Update the Chemical Weapons Convention | Books in brief | Palaeontology: Giants unearthed | Donald Arthur Glaser (1926–2013) | Crick's medal goes under the hammer             More Biological Sciences ▶                         Subscribe to Nature this Spring for only $60/£60/EUR60 Nature brings you the finest peer-reviewed research in all scientific disciplines, not to mention an enticing round up of news, features and commentaries by global experts. Join our expanding community of scientific leaders and subscribe today!               Chemical Sciences ▲top             RESEARCH           Research Highlights                   Emulsion chemistry: Russian-doll-style droplets         NEWS & COMMENT           Policy: Update the Chemical Weapons Convention             More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Articles and Letters                   Femtosecond switching of magnetism via strongly correlated spin–charge quantum excitations ▶     Tianqi Li, Aaron Patz, Leonidas Mouchliadis et al.     Magnetic order in a manganite can be switched during femtosecond photo-excitation via coherent superpositions of quantum states; this is analogous to processes in femtosecond chemistry where photoproducts of chemical and biochemical reactions can be influenced by creating suitable superpositions of molecular states.             Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution ▶     Chien-Chun Chen, Chun Zhu, Edward R. White et al.     A new combination of established techniques is used to produce three-dimensional (3D) images and a video of almost all the atoms in a platinum nanoparticle, revealing the 3D core structure of edge and screw dislocations and 3D twin boundaries in the nanoparticle at atomic resolution.             Colossal injection of catalyst atoms into silicon nanowires ▶     Oussama Moutanabbir, Dieter Isheim, Horst Blumtritt et al.     Aluminium catalyst is trapped during growth of a silicon nanowire from vapour phase at concentrations vastly beyond equilibrium solid solubility, but is homogeneously distributed as atoms and not found as clusters or precipitates; this is a potential route to tailoring the composition and properties of nanowires.             News & Views                   Techniques: 3D imaging of crystal defects ▶     Patrick J. McNally             Materials science: The same, but better ▶     Teri W. Odom             Erratum                   Erratum: A sub-Mercury-sized exoplanet ▶     Thomas Barclay, Jason F. Rowe, Jack J. Lissauer et al.             Research Highlights                   Emulsion chemistry: Russian-doll-style droplets | Quantum information: Quality photons from nanocrystals | Particle Physics: Symmetry affirmed | Applied maths: Mechanics behind seashell spines | Materials science: Making films on the edge         NEWS & COMMENT           Astrophysics: Fire in the hole! | Policy: Update the Chemical Weapons Convention | Donald Arthur Glaser (1926–2013) | Detectors zero in on Earth's heat             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Latest Online                   Terrestrial water fluxes dominated by transpiration ▶     Scott Jasechko, Zachary D. Sharp, John J. Gibson et al.     An analysis of the relative effects of transpiration and evaporation, which can be distinguished by how they affect isotope ratios in water, shows that transpiration is by far the largest water flux from Earth's continents, representing 80 to 90 per cent of terrestrial evapotranspiration and using half of all solar energy absorbed by land surfaces.             Articles and Letters                   Patterns and mechanisms of early Pliocene warmth ▶     A. V. Fedorov, C. M. Brierley, K. T. Lawrence et al.     A synthesis of geochemical proxy records of sea surface temperature shows that the early Pliocene climate was little different from today in terms of maximum ocean temperatures but had substantially lower meridional and zonal temperature gradients.             Intra-oceanic subduction shaped the assembly of Cordilleran North America ▶     Karin Sigloch, Mitchell G. Mihalynuk     A new explanation for the origin of the accreted terranes that form the mountainous Cordillera of western North America is proposed and tested: stationary, intra-oceanic subduction deposited massive slab walls in the mantle and grew volcanic archipelagos at the surface, which were overridden by and accreted to North America during Cretaceous times.             July 2012 Greenland melt extent enhanced by low-level liquid clouds ▶     R. Bennartz, M. D. Shupe, D. D. Turner et al.     In July 2012, a heat wave swept across Greenland, resulting in extensive melting of surface ice and flooding; this is shown to have been enhanced by liquid clouds forming in such a way that sufficient incoming shortwave radiation could penetrate to the surface while downwelling longwave radiation increased.             News & Views                   Earth science: Western North America's jigsaw ▶     Saskia Goes             50 & 100 Years Ago ▶           NEWS & COMMENT           Anthropology: A monochrome Eden | Books in brief | Detectors zero in on Earth's heat | Detective work uncovers under-reported overfishing             More Earth & Environmental Sciences ▶                         Special Issue on Falling Sperm Counts and Global Estrogen Pollution: Lessons Learned 20 Years On The March special issue of Asian Journal of Andrology discusses the claim that falling sperm counts worldwide are due to global estrogen pollution, which, when published in 1992, raised the most public, fervent and durable controversy in the short history of Andrology. Take advantage of FREE access to select articles today!               Careers & Jobs ▲top               RNA: The genome's rising stars ▶     As the once-fringe field of long non-coding RNA moves into the limelight, young researchers could reap the benefits.                   Time to reflect ▶     A lab retreat provides a chance to rethink and advance the research programme, says Eleftherios Diamandis.             Careers related news & comment                   If a job is worth doing, it is worth doing twice Jonathan F. Russell | Seven days: 29 March–4 April 2013 | Collaboration: Link the world's best investigators Alan Bernstein | Sexism: Dearth of female role models Simon Williams, Christine Wood, Richard McGee | Sexism: A revealing experiment Tina M. 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