Nature contents: 11 September 2014

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Volume 513 Number 7517      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.               Starting a CRISPR/CAS9 project on genome editing? Come to OriGene for a wide selection of tools: All-in-one pCAS-Guide vectors gRNA and donor vector cloning services  Genome-wide gene knockout kit Learn about CRISPR technology from a Youtube video Go to http://www.origene.com/CRISPR-CAS9/ to learn more.       Jump to the content that matters to you View Table of Contents ▶ ▼ News & Comment   ▼ Biological Sciences   ▼ Health Sciences   ▼ Physical Sciences   ▼ Earth & Environmental Sciences   ▼ Careers & Jobs       This week's highlights     Specials — Outlook:Lung cancer     Lung cancer is the mortality king of malignancy. The disease kills almost 1.6 million people per year globally. Researchers are seeking insights into lung cancer's causes that could lead to better treatments and more effective prevention. ▼ more       Biological Sciences More Biological sciences ▼   Gibbon genome and the fast karyotype evolution of small apes   In their presentation of the genome of the northern white-cheeked gibbon, Lucia Carbone and colleagues provide intriguing insights into the biology and evolutionary history of a group that straddles the divide between Old World monkeys and the great apes. They identify a unique retrotransposon that might be the source of gibbons' remarkable genome plasticity. Positive selection on genes involved in forelimb development and connective tissue may relate to gibbons' unique mode of locomotion in the tropical canopy.       Physical Sciences More Physical sciences ▼   Assembly-line synthesis of organic molecules with tailored shapes   Living organisms use sophisticated assembly-lines to perform complex organic syntheses. Until now chemists have been able to mimic this approach only to synthesize peptides and oligonucleotides with simple amide or phosphate bonds. These authors create an impressive molecular assembly line through iterative reagent-controlled homologations of boronic esters. They use it to generate organic molecules containing ten contiguous, stereochemically defined methyl groups, an important step towards the synthesis of complex molecules with predictable shape.                 Earth & Environmental Sciences More Earth & Environmental sciences ▼   A global strategy for road building   New roads bring socioeconomic benefits, but road building is often a haphazard process, and much of it will occur in ecologically important areas. This study combines data on the predicted socioeconomic benefits of new roads with measures of environmental value across the world to develop a 'global roadmap' of the balance between human and environmental aspects of road-building. The map shows areas where road-building should be encouraged, where it should be avoided, and where conflicts of interest will require careful decision-making.     Podcast & Video     In this week's podcast: the gibbon genome gives scientists something to swing about, the quest to cure blindness, and the country producing the most energy from renewables.         News & Comment Read daily news coverage▶ ▲top               THIS WEEK           Editorials                   Genetic rights and wrongs ▶     Australia's decision to uphold a patent on biological material is in danger of hampering the development of diagnostic tests.             Ebola: time to act ▶     Governments and research organizations must mobilize to end the West African outbreak.             Orbital assembly ▶     The space launch of a 3D printer does not herald a brave new era — but it is a good start.             World View                   Make diagnostic centres a priority for Ebola crisis ▶     Bottlenecks in testing samples for Ebola leave patients stranded for days in isolation wards and raise fears of seeking treatment, says J. Daniel Kelly.             Seven Days                   Seven days: 5–11 September 2014 ▶     The week in science: NIH finds forgotten ricin, scientists discover massive dinosaur, and greenhouse gases hit record highs.             NEWS IN FOCUS           Scientists split over Scottish independence vote ▶     Research could founder or flourish if Scotland leaves the United Kingdom.             Plate tectonics found on Europa ▶     Discovery buoys bid for mission to Jovian moon.             Chinese data hint at trigger for fatal quake ▶     Seismic activity started to rise just as two giant reservoirs on upper Yangtze were being filled with water.             NASA to send 3D printer into space ▶     Machine will let astronauts create parts to order.             Features                   Wildlife energy: Survival of the fittest ▶     Using a wildlife version of fitness trackers, biologists can finally measure how much energy animals need to stay alive.             Curing blindness: Vision quest ▶     Technologies are allowing doctors to do what was once unheard of: restore blind people's sight. Now the real challenges begin.             COMMENT           Climate policy: Rethink IPCC reports ▶     Voluntary work alone cannot sustain the assessments carried out by the Intergovernmental Panel on Climate Change. Thomas F. Stocker and Gian-Kasper Plattner call for institutional support and a longer report cycle.             Economics: Manufacture renewables to build energy security ▶     Countries should follow China's lead and boost markets for water, wind and solar power technologies to drive down costs, say John A. Mathews and Hao Tan.             Books and Arts                   Science fiction: Verne and beyond ▶ nbsp;   Danièle Chatelain and George Slusser explore how French science fiction grapples with Cartesian duality.             Q&A: The sci-fi optimist ▶     Best-selling science-fiction writer Neal Stephenson's works cover everything from cryptography to Sumerian mythology. Ahead of next year's novel Seveneves, he talks about his influences, the stagnation in material technologies, and Hieroglyph, the forthcoming science-fiction anthology that he kick-started to stimulate the next generation of engineers.             Books in brief ▶     Barbara Kiser reviews five of the week's best science picks.             Correspondence                   Scientific record: Frame retractions so they hold firm Joachim Kirsch, Hans Schöler | Pregnancy: study the mother's DNA as well Hannah Landecker | Pregnancy: no safe level of alcohol Elizabeth R. Sowell, Michael E. Charness, Edward P. Riley | Policy: Count the social cost of oil sands too Stephanie Montesanti | Mental health: Consider human will in psychology studies Warren Mansell, Timothy A. Carey             Correction                   Correction ▶                 Biological Sciences ▲top             RESEARCH           Latest Online                   Structural biology: Ribosome revelations ▶     Nelson B. Olivier             Architecture of mammalian respiratory complex I ▶     Kutti R. Vinothkumar, Jiapeng Zhu, Judy Hirst     Complex I is the first enzyme of the mitochondrial electron transport chain and it is essential for oxidative phosphorylation in mammalian mitochondria; here the electron cryo-microscopy structure of complex I from bovine heart mitochondria is reported, advancing knowledge of its structure in mammals.             Three new Jurassic euharamiyidan species reinforce early divergence of mammals ▶     Shundong Bi, Yuanqing Wang, Jian Guan et al.     Three new euharamiyidan species from the Jurassic period of China are described, cementing the alliance with multituberculates and showing that the initial divergence between groups of extant mammals—monotremes on the one side, marsupials and placentals on the other—goes back to the Triassic period.             Structural basis for the inhibition of the eukaryotic ribosome ▶     Nicolas Garreau de Loubresse, Irina Prokhorova, Wolf Holtkamp et al.     Whereas previous structural investigation of ribosome inhibitors has been done using the prokaryotic ribosome, this work presents X-ray crystal structures of the yeast ribosome in complex with 16 inhibitors including eukaryotic-specific inhibitors; the inhibitors all bind the mRNA or tRNA binding sites, larger molecules appear to target specifically the first elongation cycle.             Non-equivalent contributions of maternal and paternal genomes to early plant embryogenesis ▶     Gerardo Del Toro-De León, Marcelina García-Aguilar, C. Stewart Gillmor     A functional assessment of paternal gene activation in Arabidopsis confirms that paternal genome activation does not occur in one early discrete step, shows that maternal and paternal genomes do not make equivalent contributions to early plant embryogenesis, and uncovers an unexpectedly large effect of hybrid genetic background on paternal gene activity.             The drivers of tropical speciation ▶     Brian Tilston Smith, John E. McCormack, Andrés M. Cuervo et al.     Diversification of Neotropical birds is not directly linked to the Andean uplift, the major landscape change of the Neogene period; instead, most diversification is post-Neogene and species diversity is dependent on how long lineages have persisted in the landscape and how easily they disperse.             Structural basis for the assembly of the Sxl–Unr translation regulatory complex ▶     Janosch Hennig, Cristina Militti, Grzegorz M. Popowicz et al.     The crystal structure of the RNA binding domains of Sxl and Unr with msl2 RNA shows that interwoven interactions establish cooperative assembly of the ternary complex, highlighting how binding of relatively general RNA binding domains to RNA can result in a unique and specific protein–RNA architecture.             A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing ▶     Sarah B. Miller, F. Zehra Yildiz, Jennifer A. Lo et al.     To prime reverse transcription of Moloney murine leukaemia virus, a transfer RNA molecule must bind two regions of the retroviral RNA, the primer binding site (PBS) and primer activation signal within the U5-PBS; here, the NMR structures of the U5-PBS RNA and tRNA primer are solved, with and without the retroviral nucleocapsid protein, which remodels these regions.             Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells ▶     Thomas M. Carlile, Maria F. Rojas-Duran, Boris Zinshteyn et al.     The modification of uridine to pseudouridine is widespread in transfer and ribosomal RNAs but not observed so far in a coding RNA; here a new technique is used to detect this modification on a genome-wide scale, leading to the identification of pseudouridylation in messenger RNAs as well as almost 100 new sites in non-coding RNAs.             Articles and Letters                   A synaptic and circuit basis for corollary discharge in the auditory cortex ▶     David M. Schneider, Anders Nelson, Richard Mooney     Here auditory cortex excitatory neurons are shown to decrease their activity during locomotion, grooming and vocalization, and this decrease was paralleled by increased activity in inhibitory interneurons; these findings provide a circuit basis for how self-motion and external sensory signals can be integrated to potentially facilitate hearing.             Gibbon genome and the fast karyotype evolution of small apes OPEN ▶     Lucia Carbone, R. Alan Harris, Sante Gnerre et al.     The genome of the gibbon, a tree-dwelling ape from Asia positioned between Old World monkeys and the great apes, is presented, providing insights into the evolutionary history of gibbon species and their accelerated karyotypes, as well as evidence for selection of genes such as those for forelimb development and connective tissue that may be important for locomotion through trees.             Comprehensive molecular characterization of gastric adenocarcinoma OPEN ▶     The Cancer Genome Atlas reports on molecular evaluation of 295 primary gastric adenocarcinomas and proposes a new classification of gastric cancers into 4 subtypes, which should help with clinical assessment and trials of targeted therapies.             The evolution of the placenta drives a shift in sexual selection in livebearing fish ▶     B. J. A. Pollux, R. W. Meredith, M. S. Springer et al.     In poeciliid fish, the evolution of the placenta is associated with polyandry in females and correlates with a suite of phenotypic and behavioural traits in males.             Innate immune sensing of bacterial modifications of Rho GTPases by the Pyrin inflammasome ▶     Hao Xu, Jieling Yang, Wenqing Gao et al.     The Pyrin inflammasome detects the presence of a pathogen not through recognition of a microbial molecule but by the activity of a bacterial toxin that modifies host Rho activity.             Viral tagging reveals discrete populations in Synechococcus viral genome sequence space ▶     Li Deng, J. Cesar Ignacio-Espinoza, Ann C. Gregory et al.     The metagenome of uncultured, Pacific Ocean viruses linked to a ubiquitous cyanobacteria is characterized using viral-tagging, revealing discrete populations in viral sequence space that includes previously cultivated populations and new populations missed in isolate-based studies.             Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development ▶     Cawas B. Engineer, Majid Ghassemian, Jeffrey C. Anderson et al.     The continuing rise in atmospheric carbon dioxide concentrations suppresses the development of stomatal pores, and thus gas exchange, in plant leaves on a global scale; now, a framework of mechanisms by which carbon dioxide represses development has been identified.             Fructose-1,6-bisphosphatase opposes renal carcinoma progression ▶     Bo Li, Bo Qiu, David S. M. Lee et al.     Fructose-1,6-bisphosphatase is shown to be depleted in clear cell renal cell carcinoma (ccRCC) and inhibits ccRCC progression by antagonizing glycolytic flux in renal tubular epithelial cells and by restraining cell proliferation, glycolysis, and the pentose phosphate pathway in von Hippel–Lindau-protein-deficient ccRCC cells by blocking hypoxia-inducible factor function.             Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins ▶     Hani Goodarzi, Steven Zhang, Colin G. Buss et al.     Linear sequence elements within messenger RNAs are known to be targeted by regulatory factors such as microRNAs for degradation, a process that has been implicated in disease; now, non-linear regulatory structural elements within mRNAs are shown also to be targeted, with the resulting mRNA destabilization mediating breast cancer metastasis.             Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser ▶     Christopher Kupitz, Shibom Basu, Ingo Grotjohann et al.     Femtosecond X-ray pulses were used to obtain diffraction data on photosystem II, revealing conformational changes as the complex transitions from the dark S1 state to the double-pumped S3 state; the time-resolved serial femtosecond crystallography technique enables structural determination of protein conformations that are highly prone to traditional radiation damage.             News & Views                   Genomics: Something to swing about ▶     Michael J. O'Neill, Rachel J. O'Neill             Microbiology: Bacteria get vaccinated ▶     Rodolphe Barrangou, Todd R. Klaenhammer             Sustainable Development: The promise and perils of roads ▶     Stephen G. Perz             Sensory systems: Sound processing takes motor control ▶     Uri Livneh, Anthony Zador             Structural biology: Ribosome revelations ▶     Nelson B. Olivier             Corrigenda                   Corrigendum: Mitofusin 2 tethers endoplasmic reticulum to mitochondria ▶     Olga Martins de Brito, Luca Scorrano             Corrigendum: Direct recording and molecular identification of the calcium channel of primary cilia ▶     Paul G. DeCaen, Markus Delling, Thuy N. Vien et al.             Research Highlights                   The language of deception | Animal behaviour: Videos teach tricks to wild monkeys | Genomics: How coffee got its buzz | Evolution: Wooing frogs are bat bait | Marine ecology: Blue whales bounce back | Microbiology and immunology: Early diet shapes gut flora | Neuroscience: Music training aids speech processing | Biofuels: Bacteria generate propane gas | Zoology: Archer fish show how to sharpshoot         NEWS & COMMENT           Wildlife energy: Survival of the fittest | Curing blindness: Vision quest | Books in brief | Pregnancy: study the mother's DNA as well | Pregnancy: no safe level of alcohol | Mental health: Consider human will in psychology studies | Genetic rights and wrongs | Ebola: time to act | Make diagnostic centres a priority for Ebola crisis             More Biological Sciences ▶                   nature.com webcasts Macmillan Science Communication presents a custom webcast on: Targeting the untargeted in translational research Thursday September 11, 2014 Session 1: Europe and the Middle East 2PM BST, 3pm CEST, 5PM GST Session 2: USA 9AM PDT, 11AM CDT, 12PM EDT Register forthe webcast and live Q andA Session  Sponsored by:           Health Sciences ▲top             RESEARCH           Articles and Letters                   Comprehensive molecular characterization of gastric adenocarcinoma OPEN ▶     The Cancer Genome Atlas reports on molecular evaluation of 295 primary gastric adenocarcinomas and proposes a new classification of gastric cancers into 4 subtypes, which should help with clinical assessment and trials of targeted therapies.             Fructose-1,6-bisphosphatase opposes renal carcinoma progression ▶     Bo Li, Bo Qiu, David S. M. Lee et al.     Fructose-1,6-bisphosphatase is shown to be depleted in clear cell renal cell carcinoma (ccRCC) and inhibits ccRCC progression by antagonizing glycolytic flux in renal tubular epithelial cells and by restraining cell proliferation, glycolysis, and the pentose phosphate pathway in von Hippel–Lindau-protein-deficient ccRCC cells by blocking hypoxia-inducible factor function.             Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins ▶     Hani Goodarzi, Steven Zhang, Colin G. Buss et al.     Linear sequence elements within messenger RNAs are known to be targeted by regulatory factors such as microRNAs for degradation, a process that has been implicated in disease; now, non-linear regulatory structural elements within mRNAs are shown also to be targeted, with the resulting mRNA destabilization mediating breast cancer metastasis.             News & Views                   Sensory systems: Sound processing takes motor control ▶     Uri Livneh, Anthony Zador           NEWS & COMMENT           Curing blindness: Vision quest | Pregnancy: study the mother's DNA as well | Ebola: time to act | Make diagnostic centres a priority for Ebola crisis             More Health Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   Evanescent-wave and ambient chiral sensing by signal-reversing cavity ringdown polarimetry ▶     Dimitris Sofikitis, Lykourgos Bougas, Georgios E. Katsoprinakis et al.     By passing light through a chiral sample — here vapours and solutions — in a specially designed ring cavity, the resulting chiral signals can be isolated from the achiral backgrounds and enhanced by a factor of more than 1,000, making them detectable in situations where conventional means of measurement fail.             Articles and Letters                   Assembly-line synthesis of organic molecules with tailored shapes ▶     Matthew Burns, Stéphanie Essafi, Jessica R. Bame et al.     The iterative, reagent-controlled homologation of a boronic ester is used to create an 'assembly line' capable of synthesizing organic molecules that contain ten contiguous, stereochemically defined methyl groups and which have different shapes depending on the stereochemistry of those groups.             The diversity of quasars unified by accretion and orientation ▶     Yue Shen, Luis C. Ho     Analysis of archival quasar data reveals that two quantities — the Eddington ratio and orientation — explain most of the diverse characteristics of quasars.             Probing excitonic dark states in single-layer tungsten disulphide ▶     Ziliang Ye, Ting Cao, Kevin O'Brien et al.     A series of long-lived excitons in a monolayer of tungsten disulphide are found to have strong binding energy and an energy dependence on orbital momentum that significantly deviates from conventional, three-dimensional, behaviour.             News & Views                   Astrophysics: Quasar complexity simplified ▶     Michael S. Brotherton             Research Highlights                   Physics: Magnets used in suspension act         NEWS & COMMENT           NASA to send 3D printer into space | Economics: Manufacture renewables to build energy security | Science fiction: Verne and beyond | Q&A: The sci-fi optimist             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Latest Online                   Placing an upper limit on cryptic marine sulphur cycling ▶     D. T. Johnston, B. C. Gill, A. Masterson et al.     The oxygen isotopic composition of seawater sulphate in oxygen-deficient waters records the degree of in situ sulphur cycling.             Articles and Letters                   Observational evidence for interhemispheric hydroxyl-radical parity ▶     P. K. Patra, M. C. Krol, S. A. Montzka et al.     Observations of methyl chloroform combined with an atmospheric transport model predict a Northern to Southern Hemisphere hydroxyl ratio of slightly less than 1, whereas commonly used atmospheric chemistry models predict ratios 15–45% higher.             A major advance of tropical Andean glaciers during the Antarctic cold reversal ▶     V. Jomelli, V. Favier, M. Vuille et al.     A moraine chronology determined by surface exposure dating shows that glaciers in the northern tropical Andes expanded to a larger extent during the Antarctic cold reversal (14,500 to 12,900 years ago) than during the Younger Dryas stadial (12,800 to 11,500 years ago), contrary to previous studies; as a result, previous chronologies and climate interpretations from tropical glaciers may need to be revisited.             A global strategy for road building ▶     William F. Laurance, Gopalasamy Reuben Clements, Sean Sloan et al.     A global zoning scheme is proposed to limit the environmental costs of road building while maximizing its benefits for human development, by discriminating among areas where road building would have high environmental costs but relatively low agricultural advantage, areas where strategic road improvements could promote agricultural production with relatively modest environmental costs, and 'conflict areas' where road building may have large agricultural benefits but also high environmental costs.             Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development ▶     Cawas B. Engineer, Majid Ghassemian, Jeffrey C. Anderson et al.     The continuing rise in atmospheric carbon dioxide concentrations suppresses the development of stomatal pores, and thus gas exchange, in plant leaves on a global scale; now, a framework of mechanisms by which carbon dioxide represses development has been identified.             News & Views                   Atmospheric chemistry: No equatorial divide for a cleansing radical ▶     Arlene M. Fiore             Oceanography: What goes down must come up ▶     Raffaele Ferrari           NEWS & COMMENT           Climate policy: Rethink IPCC reports | Chinese data hint at trigger for fatal quake | Policy: Count the social cost of oil sands too | Plate tectonics found on Europa             More Earth & Environmental Sciences ▶               Specials - Nature Outlook: Lung Cancer Free Access ▲top               Lung cancer ▶     Herb Brody             Epidemiology: The dominant malignancy ▶     Lung cancer is the leading cause of cancer mortality. In some countries, incidence rates are dropping but survival rates for those with the disease remain low. By Eric Bender.             Diagnosis: Early warning system ▶     The costs of lung-cancer screening overshadow the benefits of swift diagnosis — but ingenious technologies could help.             Perspective: The screening imperative ▶     Lung cancer kills more people than any other malignancy. Let's not delay in implementing a screening programme, says John K. Field.             Personalized medicine: Special treatment ▶     Therapies targeted at the specific genetics of a patient's lung cancer have proved harder to realize than expected.             Immunotherapy: Chemical tricks ▶     Lung cancer uses cunning mechanisms to evade the immune system. Can new antibody therapies outwit the disease?             Aetiology: Crucial clues ▶     Studies in never-smokers have revealed key lung-cancer mutations — but the cause of the disease is still a mystery.             Environment: Breathing trouble ▶     Large-scale studies are confirming suspicions that air pollution significantly increases the risk of lung cancer.             Public health: A burning issue ▶     An unusually high number of women from east Asia develop lung cancer. Few smoke, but that's only part of the mystery.         Sponsors             Nature Biotechnology  ANIMATION: ANTIBODY-DRUG CONJUGATES   The challenges facing targeted delivery of antibody-drug conjugates to a tumor are presented in a 3D animation that describes some of the mechanisms by which these agents target cells.   Animation by Nucleus Inc.   Produced with support from Daiichi Sankyo  and Takeda Pharmaceuticals         Careers & Jobs ▲top                     Job satisfaction: Divided opinions ▶     Financial woes are marring researchers' enjoyment of their work.             Careers related news & comment                   Seven days: 5–11 September 2014 | Genetic rights and wrongs | Scientists split over Scottish independence vote Elizabeth Gibney               naturejobs.com Science jobs of the week       Post Doctoral Fellow     University of Pittsburgh            PhD position     Istituto Clinico Humanitas            Post-Doctoral Research Fellow     Anglia Ruskin University            2 Full-time Research Fellow Positions     ETH Zurich          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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