Nature contents: 28 June 2012

Can't view this email? Click here to view in your browser.     Volume 486 Number 7404      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.                       RIKEN RESEARCH - The latest in news and research from RIKEN, Japan's flagship research organization Research highlights: A genetic alternative to fertilizer | Clones off to a bad start Old cells learn new tricks News, research highlights and in-depth interviews with RIKEN's leading researchers, updated weekly and all completely free. Keep up to date by registering for the weekly email alert!             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     Physical Sciences More Physical sciences ▼   Magnetic tornadoes as energy channels into the solar corona   At over a million degrees kelvin, the Sun's outer atmosphere is significantly hotter than the surface. That means there must be very efficient ways of getting heat to the solar extremities. Observations from NASA's Solar Dynamics Observatory spacecraft may have detected one such route for heat transfer — swirling events in the Sun's chromosphere that are linked to rapidly rotating magnetic structures lower in the chromosphere.       Biological Sciences More Biological sciences ▼   Three-dimensional limb joint mobility in the early tetrapod Ichthyostega   The early tetrapod Ichthyostega was around at a critical time — when animals were about to colonize the land. This paper presents a three-dimensional reconstruction and computer modelling of limb joint mobility based on Ichthyostega fossils. What we see is an ungainly animal that may have shuffled on land using movements similar to that seen in seals. This implies that the transition from swimming to walking was a gradual process.       Biological Sciences More Biological sciences ▼   The bonobo genome compared with the chimpanzee and human genomes   Sometimes called the 'forgotten ape', the bonobo is centre-stage this week with the publication of its genome sequence. Comparative genomic analyses reveal that more than 3% of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. Further comparisons may shed light on the genetic background of behavioural differences between the ape species — why for example, humans and chimpanzees use tools whereas bonobos do not.                   Nature Genetics and the Wellcome Trust present: The Genomics of Common Diseases 2012 September 19-22, 2012 - Potomac, MD, USA For more information and to register, visit: www.nature.com/natureconferences/gcd2012 Abstract submission deadline - June 28, 2012                 Podcast & Video     In this week's podcast: the Australopithecus diet, saving the Baltic Sea and five remaining puzzles about bird flu. Plus, the best of the rest from this week's Nature.         News & Comment Read daily news coverage▶ ▲top             THIS WEEK           Editorials                   Openness costs ▶     Two reports highlight key aspects of the global trend towards open access to research results: who will pay, and how much, to supply what to whom?             A first step ▶     Perhaps the Earth conference was not a wasted opportunity but the start of a new journey.             Pig out ▶     If farmers do not rein in the use of antibiotics for livestock, people will be severely affected.             World View                   Open your minds and share your results ▶     An open approach is the best way to maximize the benefits of research for both scientists and the public, says Geoffrey Boulton             Seven Days                   Seven days: 22–28 June 2012 ▶     The week in science: Galapagos giant tortoise 'Lonesome George' dies; United Nations to set up board of science advisers; and London's Royal Society urges an era of open data.           NEWS IN FOCUS           Wealth gap curbs Rio goals ▶     Outcome of last week's Earth Summit reflects the divided priorities of rich and poor nations.             Freeze on mutant-flu research set to thaw ▶     But some fear that if more labs work on the viruses, the risk of accidental release will multiply.             Sea versus senators ▶     North Carolina sea-level rise accelerates while state legislators put the brakes on research.             California condors face lead menace ▶     Signature species may need perpetual conservation.             Science at stake in Mexican election ▶     Presidential candidates vow to restore research reputation.             Model pigs face messy path ▶     As approvals for engineered food animals stall, pigs may be US regulators' next challenge.             Fetal tests spur legal battle ▶     A newborn industry based on non-invasive genetic testing turns combative.             Features                   Influenza: Five questions on H5N1 ▶     Scientists now know that the deadly bird flu virus is capable of causing a human pandemic. That makes tackling the remaining unknowns all the more urgent.             Phylogeny: Rewriting evolution ▶     Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree.           COMMENT           Ecology: Save the Baltic Sea ▶     Geoengineering efforts to bring oxygen into the deep Baltic should be abandoned, says Daniel J. Conley.             Sustainable farming: Get pigs off antibiotics ▶     Frank Aarestrup explains how he helped Denmark to cut the use of antibiotics in its livestock by 60%, and calls on the rest of the world to follow suit.             Books and Arts                   Physics: A shining life ▶     Frank Close enjoys the life of Hans Bethe, a Manhattan Project veteran who probed the hearts of stars.             Books in brief ▶             Cities: Metropolitan mash-up ▶     Anthony King enters a parallel city that teems with hackers innovating for the public good.             Fiction: Ray Bradbury, an appreciation ▶     Astronomer and author David Brin celebrates the legacy of a literary titan whose life-long pursuit of new horizons changed the face of science fiction.             Q&A: The sound catcher ▶     Tom Mitchell uses engineering and computing to enable people to play and sample live music using gestures. With the latest version of his co-creation 'The Gloves' about to debut at TEDGlobal 2012 in Edinburgh, UK, he talks about adaptive musical interaction.             Correspondence                   Environment: Carson no 'beacon of reason' on DDT Tony Trewavas | Neuroscience: Help to survey the use of smart drugs Imre Bard & Ilina Singh | Tumours: Less lactation may explain cancer rise Anne Marie Oudesluys-Murphy | Sustainability: Limit consumption to preserve habitats Marco Sakai | Astronomy: Clue to an ancient cosmic-ray event? Jonathon Allen           Obituary                   Andrew Fielding Huxley (1917–2012) ▶     Biophysicist who showed how nerves carry electrical signals and muscles contract.                 Biological Sciences ▲top             RESEARCH           Latest Online                   Evolutionary physiology: A bone for all seasons ▶     Kevin Padian             Biophysical mechanism of T-cell receptor triggering in a reconstituted system ▶     John R. James & Ronald D. Vale     After introducing the T-cell receptor and other essential signalling genes, a non-immune cell is capable of displaying the early events of T-cell activation when placed in contact with antigen-presenting cells, and the initial signalling in this reconstituted system is shown to require the spatial reorganization of molecules at the cell interface.             Myocardial infarction accelerates atherosclerosis ▶     Partha Dutta, Gabriel Courties, Ying Wei, Florian Leuschner, Rostic Gorbatov et al.     Myocardial infarction accelerates atherosclerosis through activation of the sympathetic nervous system, and the consequent release of haematopoietic stem and progenitor cells.             Independent evolution of striated muscles in cnidarians and bilaterians ▶     Patrick R. H. Steinmetz, Johanna E. M. Kraus, Claire Larroux, Jörg U. Hammel, Annette Amon-Hassenzahl et al.     This phylogenomic study shows that core muscle proteins were already present in unicellular organisms before the origin of multicellular animals, and supports a convergent evolutionary model for striated muscles in which new proteins are added to ancient contractile apparatus during independent evolution of bilaterians and some non-bilaterians, resulting in very similar ultrastructures.             The diet of Australopithecus sediba ▶     Amanda G. Henry, Peter S. Ungar, Benjamin H. Passey, Matt Sponheimer, Lloyd Rossouw et al.     Phytolith, stable carbon isotope, and dental microwear texture data for two individuals of Au. sediba, 2-million-year-old hominins from South Africa, show that they consumed a mostly C3 diet that probably included harder foods, and both dicotyledons (for example, tree leaves, fruits, and wood or bark) and monocotyledons (for example, grasses and sedges); this diet contrasts with previously described diets of other early hominin species.             Atmospheric CO2 forces abrupt vegetation shifts locally, but not globally ▶     Steven I. Higgins & Simon Scheiter     A model of the effects of climate change on African vegetation from 1850 to 2100 predicts increases in woody plant cover, but considerable heterogeneity in the timing of these shifts dampens the shock that these changes in land-surface properties may represent to the Earth system.             Seasonal bone growth and physiology in endotherms shed light on dinosaur physiology ▶     Meike Köhler, Nekane Marín-Moratalla, Xavier Jordana & Ronny Aanes     Dinosaurs were not necessarily cold-blooded: the main argument in favour of this, namely the presence of seasonal lines of arrested bone growth, has been demolished by a comprehensive study of extant ruminants.             Proto-genes and de novo gene birth ▶     Anne-Ruxandra Carvunis, Thomas Rolland, Ilan Wapinski, Michael A. Calderwood, Muhammed A. Yildirim et al.     Novel protein-coding genes can arise either from pre-existing genes or de novo; here it is shown that functional genes emerge de novo through transitory proto-genes generated by widespread translational activity in non-genic sequences.             Universal species–area and endemics–area relationships at continental scales ▶     David Storch, Petr Keil & Walter Jetz     The change in number of terrestrial vertebrate species or endemics with sampled area is characterized by universal curves whose properties depend only on the mean geographic range size of species.             Human dorsal anterior cingulate cortex neurons mediate ongoing behavioural adaptation ▶     Sameer A. Sheth, Matthew K. Mian, Shaun R. Patel, Wael F. Asaad, Ziv M. Williams et al.     Functional imaging, single-cell recording and targeted surgical lesions were used in human patients undergoing cingulotomy to show that the dorsal anterior cingulate cortex provides a continuously updated prediction of expected cognitive demand.             Articles and Letters                   Dimensionality of consumer search space drives trophic interaction strengths ▶     Samraat Pawar, Anthony I. Dell & Van M. Savage     Consumption rates vary substantially between consumers searching in three dimensions (for example, arboreal and pelagic zones), with consumption rates scaling superlinearly with consumer body mass, and those searching in two dimensions (for example, terrestrial and benthic zones), with consumption rates scaling sublinearly with consumer body mass.             mTORC1 in the Paneth cell niche couples intestinal stem-cell function to calorie intake ▶     Ömer H. Yilmaz, Pekka Katajisto, Dudley W. Lamming, Yetis Gültekin, Khristian E. Bauer-Rowe et al.     In the mouse intestine, calorie restriction enhances the regenerative capacity of intestinal stem cells by reducing mTORC1 signalling in their Paneth cell niche.             A map of nucleosome positions in yeast at base-pair resolution ▶     Kristin Brogaard, Liqun Xi, Ji-Ping Wang & Jonathan Widom     A new technique for mapping nucleosomes genome-wide with single-base-pair accuracy, by chemical modification of engineered histones.             Activation of remote meta-C–H bonds assisted by an end-on template ▶     Dasheng Leow, Gang Li, Tian-Sheng Mei & Jin-Quan Yu     Rapid synthesis of complex molecules via selective functionalization of unactivated carbon–hydrogen bonds is here made easier with the use of removable ‘templates’ that enable the activation of distal bonds.             Three-dimensional limb joint mobility in the early tetrapod Ichthyostega ▶     Stephanie E. Pierce, Jennifer A. Clack & John R. Hutchinson     Three-dimensional reconstruction and modelling of limb joint mobility in the early tetrapod Ichthyostega is used to provide insights into an important step in vertebrate evolution—the transition from swimming to walking.             The bonobo genome compared with the chimpanzee and human genomes ▶     Kay Prüfer, Kasper Munch, Ines Hellmann, Keiko Akagi, Jason R. Miller et al.     Sequencing of the bonobo genome shows that more than three per cent of the human genome is more closely related to either the bonobo genome or the chimpanzee genome than those genomes are to each other.             Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer ▶     Sandra Misale, Rona Yaeger, Sebastijan Hobor, Elisa Scala, Manickam Janakiraman et al.     Molecular alterations in KRAS are associated with acquired resistance to anti-epidermal growth factor receptor (EGFR) treatment in colorectal cancer; resistant mutations can be identified in the blood of patients, months before clinical evidence of disease progression.             The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers ▶     Luis A. Diaz Jr, Richard T. Williams, Jian Wu, Isaac Kinde, J. Randolph Hecht et al.     This work on colorectal cancer shows that secondary mutations in KRAS that confer resistance to panitumumab, an anti-EGFR monoclonal antibody, are already present when antibody treatment begins; the apparent inevitability of resistance suggests that combinations of drugs targeting at least two different oncogenic pathway will be needed for treatment.             Autoregulation of microRNA biogenesis by let-7 and Argonaute ▶     Dimitrios G. Zisoulis, Zoya S. Kai, Roger K. Chang & Amy E. Pasquinelli     MicroRNA in worms is shown to target non-coding primary microRNA transcripts through interaction with the Argonaute protein, promoting the production of further microRNA and thus generating a positive-feedback loop.             Generalized Lévy walks and the role of chemokines in migration of effector CD8+ T cells ▶     Tajie H. Harris, Edward J. Banigan, David A. Christian, Christoph Konradt, Elia D. Tait Wojno et al.     T cells in the brains of Toxoplasma-infected mice are shown to move by Lévy-like walks.             PPAR-γ is a major driver of the accumulation and phenotype of adipose tissue Treg cells ▶     Daniela Cipolletta, Markus Feuerer, Amy Li, Nozomu Kamei, Jongsoon Lee et al.     T regulatory (Treg) cells in visceral adipose tissue express high levels of the nuclear receptor peroxisome proliferator-activated receptor (PPAR)-γ, and fat-specific adaptation of Treg cells is dependent on PPAR-γ.             Immune self-reactivity triggered by drug-modified HLA-peptide repertoire ▶     Patricia T. Illing, Julian P. Vivian, Nadine L. Dudek, Lyudmila Kostenko, Zhenjun Chen et al.     The paper describes the mechanism by which small-molecule drugs such as abacavir affect antigen presentation and consequently T-cell response in immunologically based drug reactions such as abacavir hypersensitivity syndrome (AHS) and carbamazepine-induced Stevens–Johnson syndrome (SJS).             News & Views                   Ageing: A healthy diet for stem cells ▶     Fresnida J. Ramos & Matt Kaeberlein             Pharmacology: A false sense of non-self ▶     Ellis L. Reinherz             Neuroscience: Genes and human brain evolution ▶     Daniel H. Geschwind & Genevieve Konopka             Cancer: Pinprick diagnostics ▶     Eduardo Vilar & Josep Tabernero             Evolutionary physiology: A bone for all seasons ▶     Kevin Padian             Research Highlights                   Palaeontology: Turtle sex recorded in rock | Developmental biology: Blood vessel directs cells | Ecology: One ring species to rule them all | Cell biology: p53 triggers cell death in stroke | Molecular biology: Protein crawls on chromosome         NEWS & COMMENT           A first step | Freeze on mutant-flu research set to thaw | California condors face lead menace | Model pigs face messy path | Fetal tests spur legal battle | Influenza: Five questions on H5N1 | Phylogeny: Rewriting evolution | Ecology: Save the Baltic Sea | Sustainable farming: Get pigs off antibiotics | Environment: Carson no 'beacon of reason' on DDT Tony Trewavas | Neuroscience: Help to survey the use of smart drugs Imre Bard & Ilina Singh | Tumours: Less lactation may explain cancer rise Anne Marie Oudesluys-Murphy | Sustainability: Limit consumption to preserve habitats Marco Sakai | Andrew Fielding Huxley (1917–2012)           CAREERS           Pay rise recommended             More Biological Sciences ▶                         Differentiation of Lethal and Non-Lethal Prostate Cancer The Asian Journal of Andrology is proud to present a special issue and web focus on the Differentiation of Lethal and Non-Lethal Prostate Cancer which outline a diverse and comprehensive series of potential differentiation factors. Access the Special Issue and Web Focus today!               Chemical Sciences ▲top             RESEARCH           Latest Online                   Organic chemistry: Reactions at the end of a tether ▶     Stefan Roesner & Varinder K. Aggarwal             Biophysical mechanism of T-cell receptor triggering in a reconstituted system ▶     John R. James & Ronald D. Vale     After introducing the T-cell receptor and other essential signalling genes, a non-immune cell is capable of displaying the early events of T-cell activation when placed in contact with antigen-presenting cells, and the initial signalling in this reconstituted system is shown to require the spatial reorganization of molecules at the cell interface.             Direct and highly regioselective and enantioselective allylation of β-diketones ▶     Wesley A. Chalifoux, Samuel K. Reznik & James L. Leighton     A simple, regioselective and enantioselective method for allylating β-diketones has been developed, significantly expanding the pool of easily accessible enantiomerically enriched and functionally complex tertiary carbinols.             Articles and Letters                   Activation of remote meta-C–H bonds assisted by an end-on template ▶     Dasheng Leow, Gang Li, Tian-Sheng Mei & Jin-Quan Yu     Rapid synthesis of complex molecules via selective functionalization of unactivated carbon–hydrogen bonds is here made easier with the use of removable ‘templates’ that enable the activation of distal bonds.             Immune self-reactivity triggered by drug-modified HLA-peptide repertoire ▶     Patricia T. Illing, Julian P. Vivian, Nadine L. Dudek, Lyudmila Kostenko, Zhenjun Chen et al.     The paper describes the mechanism by which small-molecule drugs such as abacavir affect antigen presentation and consequently T-cell response in immunologically based drug reactions such as abacavir hypersensitivity syndrome (AHS) and carbamazepine-induced Stevens–Johnson syndrome (SJS).             News & Views                   Organic chemistry: Directors extend their reach ▶     Matthew O. Kitching & Victor Snieckus             Organic chemistry: Reactions at the end of a tether ▶     Stefan Roesner & Varinder K. Aggarwal             More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   Atmospheric CO2 forces abrupt vegetation shifts locally, but not globally ▶     Steven I. Higgins & Simon Scheiter     A model of the effects of climate change on African vegetation from 1850 to 2100 predicts increases in woody plant cover, but considerable heterogeneity in the timing of these shifts dampens the shock that these changes in land-surface properties may represent to the Earth system.             Articles and Letters                   The signature of orbital motion from the dayside of the planet τ Boötis b ▶     Matteo Brogi, Ignas A. G. Snellen, Remco J. de Kok, Simon Albrecht, Jayne Birkby et al.     The detection of carbon monoxide absorption in the spectrum of the extrasolar planet τ Boötis b, and its tracing of the change in the radial velocity of the planet, demonstrates that atmospheric characterization is possible for non-transiting planets.             Magnetic tornadoes as energy channels into the solar corona ▶     Sven Wedemeyer-Böhm, Eamon Scullion, Oskar Steiner, Luc Rouppe van der Voort, Jaime de la Cruz Rodriguez et al.     Rotating magnetic structures in the Sun can channel energy outwards from the convection zone and may explain how the energy required to heat the outer layers of the Sun reaches its upper atmosphere.             The limits of the nuclear landscape ▶     Jochen Erler, Noah Birge, Markus Kortelainen, Witold Nazarewicz, Erik Olsen et al.     Nuclear density functional theory is used to calculate the uncertainty in the positions of the neutron and proton ‘drip lines’, and to estimate that there are around 7,000 bound nuclides containing between 2 and 120 protons.             Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight ▶     N. D. Loh, C. Y. Hampton, A. V. Martin, D. Starodub, R. G. Sierra et al.     Intense, coherent X-ray pulses from a free-electron laser can be used to obtain high-resolution morphology of individual sub-micrometre particles in their native state, while at the same time their composition is analysed by mass spectrometry.             Generalized Lévy walks and the role of chemokines in migration of effector CD8+ T cells ▶     Tajie H. Harris, Edward J. Banigan, David A. Christian, Christoph Konradt, Elia D. Tait Wojno et al.     T cells in the brains of Toxoplasma-infected mice are shown to move by Lévy-like walks.             News & Views                   Solar physics: Swirls in the corona ▶     Stephen J. Bradshaw             Brief Communications Arising                   No inter-hemispheric δ13CH4 trend observed ▶     I. Levin, C. Veidt, B. H. Vaughn, G. Brailsford, T. Bromley et al.             Kai, Tyler, Randerson & Blake reply ▶     Fuu Ming Kai, Stanley C. Tyler, James T. Randerson & Donald R. Blake             Research Highlights                   Astronomy: Similar orbits but not densities | Photonics: Data travel on spiralled light | Climate change: Cyclones on the move         NEWS & COMMENT           Sea versus senators | Physics: A shining life | Cities: Metropolitan mash-up | Q&A: The sound catcher | Astronomy: Clue to an ancient cosmic-ray event? Jonathon Allen             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Latest Online                   Atmospheric CO2 forces abrupt vegetation shifts locally, but not globally ▶     Steven I. Higgins & Simon Scheiter     A model of the effects of climate change on African vegetation from 1850 to 2100 predicts increases in woody plant cover, but considerable heterogeneity in the timing of these shifts dampens the shock that these changes in land-surface properties may represent to the Earth system.             Articles and Letters                   Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight ▶     N. D. Loh, C. Y. Hampton, A. V. Martin, D. Starodub, R. G. Sierra et al.     Intense, coherent X-ray pulses from a free-electron laser can be used to obtain high-resolution morphology of individual sub-micrometre particles in their native state, while at the same time their composition is analysed by mass spectrometry.             Three-dimensional limb joint mobility in the early tetrapod Ichthyostega ▶     Stephanie E. Pierce, Jennifer A. Clack & John R. Hutchinson     Three-dimensional reconstruction and modelling of limb joint mobility in the early tetrapod Ichthyostega is used to provide insights into an important step in vertebrate evolution—the transition from swimming to walking.             Brief Communications Arising                   No inter-hemispheric δ13CH4 trend observed ▶     I. Levin, C. Veidt, B. H. Vaughn, G. Brailsford, T. Bromley et al.             Kai, Tyler, Randerson & Blake reply ▶     Fuu Ming Kai, Stanley C. Tyler, James T. Randerson & Donald R. Blake             Research Highlights                   Astronomy: Similar orbits but not densities | Planetary science: Carbon dioxide snow on Mars | Climate change: Cyclones on the move | Environmental science: Biodiverse and language-diverse         NEWS & COMMENT           Pig out | Wealth gap curbs Rio goals | Sea versus senators | California condors face lead menace | Ecology: Save the Baltic Sea | Environment: Carson no 'beacon of reason' on DDT Tony Trewavas | Sustainability: Limit consumption to preserve habitats Marco Sakai             More Earth & Environmental Sciences ▶                         Hot off the press!! Did you know this article from Molecular Psychiatry recently appeared in the press? Cocaine dependence: a fast-track for brain ageing? K D Ersche, P S Jones et al. Read this article now!               Careers & Jobs ▲top               Grant applications: Find me the money ▶     Some consultants offer to help researchers to find and secure grants. But scientists should carefully consider whether and how a consultant is worth the time and expense.                   Pay rise recommended ▶     US postdocs deserve increased compensation and benefits, says National Institutes of Health report.                   Career paths mixed ▶     Most graduates from professional science master's programmes head to industry, says study.                   Universities must evolve ▶     Graduate programmes focus too narrowly on academic careers, says US National Academies report.                   Careers related news & comment                   Wealth gap curbs Rio goals | Freeze on mutant-flu research set to thaw | Science at stake in Mexican election             naturejobs.com Science jobs of the week       Postdoc fellow     Indiana University School of Medicine            PhD in Physical Organic Chemistry: Non-covalent interactions     School of Chemistry, University of Edinburgh            Postdocs in Evolutionary Biology     University of Konstanz - Germany            Lecturer     King's College London          No matter what your career stage, student, postdoc or senior scientist, you will find articles on naturejobs.com to help guide you in your science career. 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