Nature contents: 12 December 2013

Can't view this email? Click here to view in your browser.     Volume 504 Number 7479      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.               AIMResearch - Highlighting the latest research from the Advanced Institute for Materials Research (AIMR) at Tohoku University, Japan Latest highlights: Molecular magnets: Mathematical predictions | Batteries: The power of patterns In the spotlight: No bridge too far (Research support focus)  Register today for monthly email alerts from the AIMR!       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 ▼   An archaeal origin of eukaryotes supports only two primary domains of life   Ever since the unexpected discovery in 1977 of a group of microorganisms called the Archaea, researchers have generally assumed that life on Earth can be arranged in three domains: the Bacteria and Archaea, both lacking nuclei but different from one another, and the eukaryotes, with nucleated cells. But with the discovery of Archaea containing genes once thought unique to eukaryotes, there has been increasing support for a two-domain model, in which the eukaryotes evolved from within the Archaea. This review concludes that the two-domain view can now be regarded as the accepted model.       Physical Sciences More Physical sciences ▼   Ferromagnetism in suspensions of magnetic platelets in liquid crystal   The idea that magnetic particles suspended in a liquid crystal might spontaneously orient into a ferromagnetic state has been around for decades but had not confirmed experimentally. Alenka Mertelj and colleagues have now realized such a state using nanosized ferromagnetic platelets in a nematic liquid crystal. The resulting 'liquid magnet' phase responds to very small magnetic fields and may lead to novel magneto-optic devices.       Earth & Environmental Sciences More Earth & Environmental sciences ▼   Increased insolation threshold for runaway greenhouse processes on Earth-like planets   As the Sun increases in brightness there may one day be a 'runaway greenhouse' effect on Earth — a state in which a planet absorbs more energy from its host star than it can radiate back to space. Earth would become more like Venus, with no oceans and lots of heat. Jérémy Leconte et al. use a three-dimensional climate model to show that the threshold for the initiation of a runaway greenhouse is much higher than has been estimated by simpler one-dimensional models. This finding is of importance in relation to extrasolar planets, since it extends the size of the habitable zone around other stars.                 Podcast & Video     In this week's podcast: some species grow old gracefully, what lizard breath reveals about dinosaurs, and ways to avoid shortages of isotopes crucial in hospitals. In our latest video feature Joe Letteri of visual effects company Weta Digital reveals how they made Gollum look believable on screen.         News & Comment Read daily news coverage▶ ▲top               THIS WEEK           Editorials                   Failure of care ▶     Laboratory animals must have the very best standard of care if we are to justify their use in science. As one institution is found wanting, others should look to review their animal-welfare practices.             The patent bargain ▶     An open-source patent database highlights the need for more transparency worldwide.             Gender progress (?) ▶     Despite some success, the proportions of women in Nature’s pages and as referees are still too low.             World View                   Preserve the European Research Council's legacy ▶     A change in European Commission management styles under Horizon 2020 must not end the funding agency's focus on excellence, says Helga Nowotny.             Seven Days                   Seven days: 6–12 December 2013 ▶     The week in science: Criticism of animal welfare in research; hopes of HIV cure dashed; and new estimates for dementia worldwide.             NEWS IN FOCUS           Fungus threatens top banana ▶     Fears rise for Latin American industry as devastating disease hits leading variety in Africa and Middle East.             Florida forecasts sinkhole burden ▶     Predictive model will map areas vulnerable to collapse.             Diabetes drugs ride a bumpy road ▶     Safety worries hamper emerging therapies.             Food fuelled with fungi ▶     Ecologists are starting to appreciate the power of microbes to make crops hardier.             India faces uphill battle on biodiversity ▶     Government decision to limit protection for species-rich mountains angers conservationists.             Life possible in the early Universe ▶     Planets orbiting the first stars could have been habitable, challenging arguments for a multiverse.             Features                   Radioisotopes: The medical testing crisis ▶     With a serious shortage of medical isotopes looming, innovative companies are exploring ways to make them without nuclear reactors.             Earth science: Under the volcano ▶     Geophysicists are scouring the globe for evidence of mantle plumes — the presumed source of some mega-eruptions.             COMMENT           Developmental biology: Support mothers to secure future public health ▶     Evidence that long-term health is shaped by the environment in early life calls for prenatal interventions to tackle chronic disease, argue David Barker and colleagues.             Bibliometrics: Global gender disparities in science ▶     Cassidy R. Sugimoto and colleagues present a bibliometric analysis confirming that gender imbalances persist in research output worldwide.             Books and Arts                   Computer animation: Digital heroes and computer-generated worlds ▶     Joe Letteri, Oscar-winning co-creator of Gollum on screen, looks at the evolution of computer animation as the next instalment of The Hobbit trilogy reaches cinemas.             Geology: The maverick founder of modern seismology ▶     George Helffrich relishes a film on John Milne, whose work in Japan put earthquake science on the map.             Books in brief ▶             Correspondence                   Marine infrastructure: NSF fleet vital for ocean science Peter B. Ortner | Pathogens: Appeal for funds to fight banana blight Gert H. J. Kema, Stephan Weise | Cross-border science: Universities aid EU research mobility David J. Drewry | Training: African database for education schemes Fanuel Muindi, Moytrayee Guha             Correction                   Correction ▶                 NatureJournals app for iPad The NatureJournals app for iPad now boasts over 25 Nature-branded titles. Subscribe to any journal in the app for $35.99* and gain access to world class research on the move. www.nature.com/content/app/anytitleoffer   *Apple exchange rates apply. Limited time offer available on all journals except Scientific Reports. iPad is a trademark of Apple Inc.         Biological Sciences ▲top             RESEARCH           Latest Online                   Plant biology: Witchcraft and destruction ▶     Steven M. Smith             Diversity of ageing across the tree of life ▶     Owen R. Jones, Alexander Scheuerlein, Roberto Salguero-Gómez et al.     Examination of demographic age trajectories for species from a wide range of taxonomic groups shows that these species have very diverse life-history patterns; mortality and reproduction vary greatly with age for both long- and short-lived species, and the relationships between ageing, mortality and reproduction are clearly complex.             DWARF 53 acts as a repressor of strigolactone signalling in rice ▶     Liang Jiang, Xue Liu, Guosheng Xiong et al.     Strigolactones (SLs), key regulators of plant growth, are believed to mediate their responses through a proposed receptor (D14) that interacts with an F-box protein (D3) to form a D14–SCFD3 protein complex; here the perception of SLs by the D14–SCFD3 complex and the control of gene expression are linked by the finding that DWARF 53, a repressor protein of SL signalling, interacts with the D14–SCFD3 complex and is ubiquitinated and degraded in a SL-dependent manner.             D14–SCFD3-dependent degradation of D53 regulates strigolactone signalling ▶     Feng Zhou, Qibing Lin, Lihong Zhu et al.     Strigolactones (SLs), key regulators of plant growth, are believed to mediate their responses through a proposed receptor (D14) that interacts with an F-box protein (D3) to form a D14–SCFD3 protein complex; here the perception of SLs by the D14–SCFD3 complex and the control of gene expression are linked by the finding that DWARF 53, a repressor protein of SL function, interacts with the D14–SCFD3 complex and is ubiquitinated and degraded in a SL-dependent manner.             Muc5b is required for airway defence ▶     Michelle G. Roy, Alessandra Livraghi-Butrico, Ashley A. Fletcher et al.     The airway mucin Muc5b (but not Muc5ac) is required for mucociliary clearance, defence against bacterial infection in the airways and middle ear, and maintenance of immune homeostasis in the lungs; Muc5b deficiency causes accumulation of apoptotic macrophages, impairment of phagocytosis and reduced production of interleukin-23, leading to infection and inflammation.             Transcranial amelioration of inflammation and cell death after brain injury ▶     Theodore L. Roth, Debasis Nayak, Tatjana Atanasijevic et al.     Using long-term intravital photography to explore the cellular changes after compression-induced traumatic brain injury in a murine model, it is shown that parenchymal and meningeal inflammation as well as cell death can be modulated by topical treatment with purinergic receptor antagonists and glutathione.             Structural basis of the alternating-access mechanism in a bile acid transporter ▶     Xiaoming Zhou, Elena J. Levin, Yaping Pan et al.     Inhibitors of the bile acid transporter ASBT may be useful therapeutics for treating hypercholesterolaemia and type 2 diabetes; here, two X-ray crystal structures of an ASBT homologue from Yersinia frederiksenii are solved.             Diet rapidly and reproducibly alters the human gut microbiome ▶     Lawrence A. David, Corinne F. Maurice, Rachel N. Carmody et al.     Consuming diets rich in plant versus animal products changes the microbes found in the human gut within days, with important implications for our health and evolution.             Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease ▶     Carlos Cruchaga, Celeste M. Karch, Sheng Chih Jin et al.     Whole-exome sequencing reveals that a rare variant of phospholipase D3 (PLD3(V232M)) segregates with Alzheimer’s disease status in two independent families and doubles risk for the disease in case–control series, and that several other PLD3 variants increase risk for Alzheimer’s disease in African Americans and people of European descent.             Unidirectional pulmonary airflow patterns in the savannah monitor lizard ▶     Emma R. Schachner, Robert L. Cieri, James P. Butler et al.     Unlike the tidal (in and out) breathing of mammals, bird lungs have unidirectional airflow patterns; here the savannah monitor lizard is shown to have unidirectional airflow too, with profound implications for the evolution of unidirectional airflow in reptiles, predating the origin of birds.             A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis  ▶     G. W. Liechti, E. Kuru, E. Hall et al.     Peptidoglycan is an essential structural component of the cell wall in the majority of bacteria, but the obligate intracellular human pathogen Chlamydia trachomatis was thought to be one of the few exceptions; here a click chemistry approach is used to label peptidoglycan in replicating C. trachomatis with novel d-amino acid dipeptide probes.             Articles and Letters                   Ultrafast endocytosis at mouse hippocampal synapses ▶     Shigeki Watanabe, Benjamin R. Rost, Marcial Camacho-Pérez et al.     Sustained neurotransmission requires recycling of synaptic vesicles, but the proposed mechanisms have been controversial; here a ‘flash-and-freeze’ method for electron microscopy reveals a new ultrafast form of endocytosis that is actin- and dynamin-dependent and occurs within 100 milliseconds of stimulation.             Targeting Plasmodium PI(4)K to eliminate malaria ▶     Case W. McNamara, Marcus C. S. Lee, Chek Shik Lim et al.     The lipid kinase phosphatidylinositol-4-OH kinase (PI(4)K) is identified as a target of the imidazopyrazines, a new antimalarial compound class that can inhibit several Plasmodium species at each stage of the parasite life cycle; the imidazopyrazines exert their inhibitory action by interacting with the ATP-binding pocket of PI(4)K.             Structural mechanism of ligand activation in human GABAB receptor ▶     Yong Geng, Martin Bush, Lidia Mosyak et al.     Crystallographic structural analysis of bound states of the GBR1 and GBR2 subunits of human GABAB receptor shows that both subunits adopt an open conformation at rest — represented by the apo and antagonist-bound structures — and that only GBR1 closes in the activated state — represented by the agonist-bound structure.             Parvalbumin-expressing basket-cell network plasticity induced by experience regulates adult learning ▶     Flavio Donato, Santiago Belluco Rompani, Pico Caroni     In adult mouse hippocampus, a learning-associated plasticity mechanism may exist that depends on the configuration of parvalbumin(PV)-expressing basket cell networks; trial and error learning initially promotes a higher fraction of cells with low PV expression, whereas learning completion promotes a higher fraction of cells with high PV expression, and these opposite configurations modulate learning and the underlying structural plasticity.             Distinct fibroblast lineages determine dermal architecture in skin development and repair ▶     Ryan R. Driskell, Beate M. Lichtenberger, Esther Hoste et al.     Fibroblasts constitute the major mesenchymal cell type in the connective tissue and their functions are remarkably diverse: here, by characterising lineages of mouse skin fibroblasts, it is shown that distinct subpopulations contribute to skin development and repair during injury.             Derivation of novel human ground state naive pluripotent stem cells ▶     Ohad Gafni, Leehee Weinberger, Abed AlFatah Mansour et al.     It is known that human embryonic stem (ES) cells are more similar to mouse primed epiblast stem cells than to naive mouse ES cells; here culture conditions are determined that allow human ES and induced pluripotent stem cells to acquire a pluripotent state that retains growth characteristics highly similar to mouse naive ES cells, and competence in generating cross-species human-mouse embryonic chimaerism.             A chain mechanism for flagellum growth ▶     Lewis D. B. Evans, Simon Poulter, Eugene M. Terentjev et al.     Growth of a flagellum outside the bacterial cell proceeds by successive subunit acquisition from the cell export machinery to form a chain that is pulled to the flagellum tip, where subunit crystallization provides the entropic force to drive the process.             High-content genome-wide RNAi screens identify regulators of parkin upstream of mitophagy ▶     Samuel A. Hasson, Lesley A. Kane, Koji Yamano et al.     Mitophagy is the elimination of damaged mitochondria by the autophagosome regulated by the ubiquitin ligase, parkin and the kinase PINK1; a genome-wide RNAi screen with high-content microscopy has identified new genes that have an upstream role in parkin translocation to the mitochondria.             p53 status determines the role of autophagy in pancreatic tumour development ▶     Mathias T. Rosenfeldt, Jim O’Prey, Jennifer P. Morton et al.     In a mouse model of pancreatic tumours driven by Kras mutations, the outcome of suppressing autophagy is shown to depend on the status of p53: if p53 is intact, deletion of key autophagy genes blocks the progression of pre-cancerous lesions to aggressive carcinomas; however, in the absence of p53, loss of autophagy accelerates tumorigenesis, accompanied by deregulation of cancer cell metabolism.             Mechanism of farnesylated CAAX protein processing by the intramembrane protease Rce1 ▶     Ioannis Manolaridis, Kiran Kulkarni, Roger B. Dodd et al.     The crystal structure of an archaeal Rce1 protein has been determined; this protein represents a novel type of intramembrane protease, with a distinct architecture and catalytic site.             Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations ▶     Yubo Zhang, Chee-Hong Wong, Ramon Y. Birnbaum et al.     A chromatin interaction analysis with paired-end tagging (ChIA-PET) approach is used to delineate chromatin interactions mediated by RNA polymerase II in several different stem-cell populations; putative long-range promoter–enhancer interactions are inferred, indicating that linear juxtaposition does not necessarily guide enhancer target selection and prevalent cell-specific enhancer usage.             Primary cilia are specialized calcium signalling organelles ▶     Markus Delling, Paul G. DeCaen, Julia F. Doerner et al.     Primary cilia are known as specialized calcium signalling compartments on the cell surface, but the ionic permeability and other physiological properties of these protrusions are unknown—this is one of two studies identifying the ion channels that densely populate primary cilia, with direct measurements revealing cilia as a unique, functionally independent calcium signalling compartment that modulates hedgehog signalling pathways.             Direct recording and molecular identification of the calcium channel of primary cilia ▶     Paul G. DeCaen, Markus Delling, Thuy N. Vien et al.     Primary cilia are known as specialized calcium signalling compartments on the cell surface, but the ionic permeability and other physiological properties of these protrusions are unknown—this is one of two studies identifying the ion channels that densely populate primary cilia, with direct measurements revealing cilia as a unique, functionally independent calcium signalling compartment that modulates hedgehog signalling pathways.             Reviews and Perspectives                   An archaeal origin of eukaryotes supports only two primary domains of life ▶     Tom A. Williams, Peter G. Foster, Cymon J. Cox et al.     Accumulating evidence that the eukaryotic nuclear lineage originated from within the Archaea provides support for a tree containing only two primary domains of life—the Achaea and Bacteria—over the currently accepted ‘three-domains tree’.             News & Views                   Neuroscience: Faster than kiss-and-run ▶     Soyoun Cho, Henrique von Gersdorff             Developmental biology: Mechanics in the embryo ▶     Stefano Piccolo             Cancer: A suppression switch ▶     Hanna Starobinets, Jayanta Debnath             Neuroscience: The highs and lows of memory ▶     Kevin Allen, Hannah Monyer             Plant biology: Witchcraft and destruction ▶     Steven M. Smith             Corrigendum                   Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome ▶     Kerstin Howe, Matthew D. Clark, Carlos F. Torroja et al.             Retraction                   Retraction: GlcNAcylation of a histone methyltransferase in retinoic-acid-induced granulopoiesis ▶     Ryoji Fujiki, Toshihiro Chikanishi, Waka Hashiba et al.             Research Highlights                   Animal behaviour: Baboons know when to be noisy | Agroecology: Bees are better for strawberries | Biotechnology: CRISPR corrects genetic disease | Neuroscience: Primate brain makes oestrogen | Ecology: Why rabies hangs on after bat culls | Palaeontology: Ancient reptiles stuck to the air         NEWS & COMMENT           Fungus threatens top banana | Radioisotopes: The medical testing crisis | Developmental biology: Support mothers to secure future public health | India faces uphill battle on biodiversity | Books in brief | Pathogens: Appeal for funds to fight banana blight | Failure of care | Diabetes drugs ride a bumpy road | Food fuelled with fungi             More Biological Sciences ▶                 Empower your cancer research with our end-to-end patient-derived xenografts solution  First-in-kind to predict somatic mutations under the normal-absent condition. Comprehensive cancer genome database for cross-validation and auto-correction of genetic variants. Accelerate your translational research and drug discovery. Learn more...         Chemical Sciences ▲top             RESEARCH           Latest Online                   Merging allylic carbon–hydrogen and selective carbon–carbon bond activation ▶     Ahmad Masarwa, Dorian Didier, Tamar Zabrodski et al.     A method of selectively activating both allylic carbon–hydrogen bonds and carbon–carbon bonds can furnish sophisticated molecular scaffolds with all-carbon quaternary stereogenic centres that can themselves be derivatized.             More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   Merging allylic carbon–hydrogen and selective carbon–carbon bond activation ▶     Ahmad Masarwa, Dorian Didier, Tamar Zabrodski et al.     A method of selectively activating both allylic carbon–hydrogen bonds and carbon–carbon bonds can furnish sophisticated molecular scaffolds with all-carbon quaternary stereogenic centres that can themselves be derivatized.             Face-to-face transfer of wafer-scale graphene films ▶     Libo Gao, Guang-Xin Ni, Yanpeng Liu et al.     High-quality graphene is grown on copper and then transferred to the underlying substrate, typically silicon oxide or quartz, by simply etching away the copper; the graphene is held in place during etching by capillary bridges.             The rarity of dust in metal-poor galaxies ▶     David B. Fisher, Alberto D. Bolatto, Rodrigo Herrera-Camus et al.     Observations of local galaxy I Zw 18 imply that the dust mass in star-forming, metal-poor environments is much lower than expected, and, therefore, that the amount of dust in young galaxies of the early Universe, such as redshift-6.6 galaxy Himiko, is probably a factor of about 100 less than previously thought.             Nanoparticle solutions as adhesives for gels and biological tissues ▶     Séverine Rose, Alexandre Prevoteau, Paul Elzière et al.     Strong, rapid adhesion between two hydrogels and even slices of animal tissue can be achieved at room temperature by using a silica nanoparticle solution as a ‘glue’.             Articles and Letters                   Ferromagnetism in suspensions of magnetic platelets in liquid crystal ▶     Alenka Mertelj, Darja Lisjak, Miha Drofenik et al.     The idea that magnetic particles suspended in a liquid crystal might spontaneously orient into a ferromagnetic state has hitherto not been confirmed experimentally, but such a state has now been realized using nanometre-sized ferromagnetic platelets in a nematic liquid crystal.             Baryons in the relativistic jets of the stellar-mass black-hole candidate 4U 1630-47 ▶     María Díaz Trigo, James C. A. Miller-Jones, Simone Migliari et al.     Doppler-shifted X-ray emission lines from highly-ionized atoms, appearing together with radio emission from the relativistic jets of the black-hole candidate X-ray binary 4U 1630-47, indicate that the X-ray emission lines arise in a jet travelling at approximately two-thirds the speed of light and imply that the jet contains baryons.             An exactly solvable model for quantum communications ▶     Graeme Smith, John A. Smolin     An exactly solvable information-theoretical model of communications with a fully quantum electromagnetic field yields explicit expressions for all point-to-point capacities—the maximum possible rates of data transmission—of noisy quantum channels, with implications for quantum key distribution and fibre-optic communications.             Increased insolation threshold for runaway greenhouse processes on Earth-like planets ▶     Jérémy Leconte, Francois Forget, Benjamin Charnay et al.     A three-dimensional global climate model shows that the loss of a planet’s oceans through complete vaporization or evaporative escape to space will occur at considerably higher insolation than previously thought, owing to stabilizing atmospheric effects.             A chain mechanism for flagellum growth ▶     Lewis D. B. Evans, Simon Poulter, Eugene M. Terentjev et al.     Growth of a flagellum outside the bacterial cell proceeds by successive subunit acquisition from the cell export machinery to form a chain that is pulled to the flagellum tip, where subunit crystallization provides the entropic force to drive the process.             News & Views                   Extrasolar planets: Inner edge of the habitable zone ▶     James F. Kasting, Chester E. Harman             Astrophysics: Tracking our neighbours' past ▶     Alan McConnachie             Soft-matter physics: Ferromagnetic ferrofluids ▶     Noel A. Clark             Research Highlights                   Astrophysics: Trio of distant quasars found         NEWS & COMMENT           Radioisotopes: The medical testing crisis | Computer animation: Digital heroes and computer-generated worlds | Books in brief | Life possible in the early Universe             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Articles and Letters                   Increased insolation threshold for runaway greenhouse processes on Earth-like planets ▶     Jérémy Leconte, Francois Forget, Benjamin Charnay et al.     A three-dimensional global climate model shows that the loss of a planet’s oceans through complete vaporization or evaporative escape to space will occur at considerably higher insolation than previously thought, owing to stabilizing atmospheric effects.             News & Views                   Extrasolar planets: Inner edge of the habitable zone ▶     James F. Kasting, Chester E. Harman             Corrigendum                   Corrigendum: Deglacial pulses of deep-ocean silicate into the subtropical North Atlantic Ocean ▶     A. N. Meckler, D. M. Sigman, K. A. Gibson et al.             Research Highlights                   Climate change: Melting ice spurs wild weather | Meteorology: Satellite improves storm forecasts | Environmental science: Gas production contaminates water         NEWS & COMMENT           India faces uphill battle on biodiversity | Geology: The maverick founder of modern seismology | Books in brief | Marine infrastructure: NSF fleet vital for ocean science | Florida forecasts sinkhole burden | Food fuelled with fungi | Earth science: Under the volcano             More Earth & Environmental Sciences ▶                 Nature Collections TCGA pan-cancer analysis   Access the Collection and accompanying Podcast, FREE at: www.nature.com/tcga    Produced with support from  Illumina         Careers & Jobs ▲top               Computing: Out of the hood ▶     Biologists frustrated with wet-lab work can find rewards in a move to computational research.                   A faulty hypothesis ▶     Carolyn Beans says that some of the most interesting results are negative ones — but it still hurts to be wrong.             Careers related news & comment                   The patent bargain | Gender progress (?) | Preserve the European Research Council's legacy Helga Nowotny | Seven days: 6–12 December 2013 | Bibliometrics: Global gender disparities in science Vincent Larivière, Chaoqun Ni, Yves Gingras et al. | Training: African database for education schemes Fanuel Muindi, Moytrayee Guha | Books in brief Barbara Kiser | Diabetes drugs ride a bumpy road Heidi Ledford               naturejobs.com Science jobs of the week       Postdoctoral Associate     University of Illinois            Postdoctoral Scientist     Laboratory of Molecular Biology            Postdoctoral Research Assistant     University of Oxford            Lecturers / Senior Lecturers (open call)     Imperial 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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