Nature contents: 25 September 2014

If you are unable to see the message below, click here to view.

Volume 513 Number 7519      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.               Nature Communications soon to be fully open access: From 20th October Nature Communications, will become fully open access for all new submissions. If an author has a manuscript they wish to submit to the journal via the subscription route, they must submit before 20th October. After this date all new submissions, if accepted, will be published open access and an article processing charge (APC) will apply. For any questions on the switch, open access or advice on policies and funding, visit our website, read the press release or contact our dedicated support team at openaccess@nature.com.         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     Physical Sciences More Physical sciences ▼   Water vapour absorption in the clear atmosphere of a Neptune-sized exoplanet   Jonathan Fraine et al. have obtained the transmission spectrum of the Neptune-sized exoplanet HAT-P-11b from the optical to the infrared. In it they detected water vapour absorption at 1.4-micrometre wavelength. HAT-P-11b is the smallest and coldest planet with an absorption signature measured by transmission. Previously it had been possible to measure atmosphere compositions only for large, Jupiter-sized, extroplanets but this latest advance now means that it is possible to measure atmospheric mean molecular weight, providing insights into the formation history of planets as small as four Earth masses.       Earth & Environmental Sciences More Earth & Environmental sciences ▼   Island biogeography of the Anthropocene   According to the theory of island biogeography, species richness is determined by how an island's area and isolation govern rates of colonization, extinction and speciation. This long-term test of the theory takes advantage of a long history of human introduction of anole lizards to Caribbean islands transported on crops such as pineapple, and recently on ornamental plants for hotel gardens. The results show that in a world dominated by humans, economic isolation has replaced geographic isolation as a negative predictor of species richness - illustrated by the fact that the US trade embargo has reduced the number of exotic anoles established on Cuba.       Biological Sciences More Biological sciences ▼   A faster Rubisco with potential to increase photosynthesis in crops   The carboxylating enzyme known as Rubisco is an important target for efforts to improve the photosynthetic efficiency of plants. This study reports the successful engineering of tobacco plants containing a functioning Rubisco from a cyanobacterium. The cyanobacterial (photosynthetic blue-green algal) enzyme has a much greater catalytic rate than the plant's normal enzyme. The lines generated here constitute an important step towards enhancing photosynthetic efficiency and improving crop yields.           Podcast & Video     In this week's podcast: how age determines bird migration, using lizards to test biodiversity theories, and translating cosmology using a simple set of words. Plus, what's hot elsewhere in Nature. In our latest video feature Geneticist Pardis Sabeti talks about the song she wrote in memory of colleagues who died in the 2014 Ebola outbreak.         News & Comment Read daily news coverage▶ ▲top               THIS WEEK           Editorials                   First response, revisited ▶     The Ebola outbreak in West Africa has starkly exposed major gaps in plans to tackle emerging infectious diseases. Lessons must be learned.             Staff support ▶     German research organizations need to help their workers to defend animal research.             Special interest ▶     As the Scottish referendum showed, scientists’ views can influence political debate.             World View                   Istanbul canal needs environmental study ▶     Scientists must ensure that the ambitious plan of Turkey’s president does not move forward without a thorough impact assessment, says Derin Orhon.             Seven Days                   Seven days: 19–25 September 2014 ▶     The week in science: NASA mission reaches Mars, Arctic sea-ice hits annual minimum, and extreme drought fuels California fires.             NEWS IN FOCUS           Brazil warming to ‘green’ policies ▶     Activist Marina Silva is gaining ground in presidential polls.             Chinese science gets mass transformation ▶     Teamwork at centre of Chinese Academy of Sciences reform.             Global Ebola response kicks into gear at last ▶     US and UN mobilizations are welcome but overdue.             Cheap solar cells tempt businesses ▶     Easy-to-make perovskite films rival silicon for efficiency.             US vows to combat antibiotic resistance ▶     Strategy lauded, but some fear it is lax on agricultural use.             Drug-safety pilot makes the grade ▶     FDA will continue to monitor safety from health records.             Features                   Infectious disease: Ebola’s lost ward ▶     A hospital in Sierra Leone has struggled to continue its research amid the worst Ebola outbreak in history.             Renewable energy: Wind power tests the waters ▶     The United States has plenty of strong winds offshore, but it has struggled to harness them for energy.             COMMENT           Chemistry: Chemical con artists foil drug discovery ▶     Naivety about promiscuous, assay-duping molecules is polluting the literature and wasting resources, warn Jonathan Baell and Michael A. Walters.             Books and Arts                   In retrospect: The Courtship Habits of the Great Crested Grebe ▶     Michael Brooke reappraises Julian Huxley's pioneering classic of animal behaviour on its centenary.             Cosmology: A few words on infinity ▶     Lucy Fortson enjoys a slim primer on cosmology that uses a cleverly constrained lexicon.             Q&A: Violin detective ▶     Peter Ratcliff uses dendrochronology — tree-ring dating — to pin down the age and suggest the provenance of stringed instruments. As he prepares to speak at the Woodmusick instrument identification conference in Cremona, Italy, on 30 September, he talks about the science of spotting fakes, and the 14 Stradivarius instruments made from the same spruce tree.             Correspondence                   Environment: Social change affects Antarctic priorities Nick Gales, Phil Trathan, Anthony Worby | Agriculture: Intensive dairy farms becoming greener Stephen LeBlanc | Social media: Research critics to be properly informed Robert B. Eckhardt, Maciej Henneberg | Society: Science should boost well-being, not GDP Mark A. de Vries             Correction                   Clarification ▶               Biological Sciences ▲top             RESEARCH           Latest Online                   Cancer: The origin of human retinoblastoma ▶     Rod Bremner, Julien Sage             Structural biology: Lariat lessons ▶     Robert T. Batey             Crystal structure of a eukaryotic group II intron lariat ▶     Aaron R. Robart, Russell T. Chan, Jessica K. Peters et al.     This study determines the structure of a branched lariat RNA, providing insights into rearrangement of the intron between the two steps of RNA splicing.             Individual improvements and selective mortality shape lifelong migratory performance ▶     Fabrizio Sergio, Alessandro Tanferna, Renaud De Stephanis et al.     A cross-sectional study of migrating raptors aged from 1 to 27 years old shows that migratory performance gradually improves with age and is driven both by selective mortality and individual improvement, with younger birds leaving progressively earlier as they age and becoming more proficient at coping with adverse environmental conditions, such as unfavourable winds.             Regulation of RNA polymerase II activation by histone acetylation in single living cells ▶     Timothy J. Stasevich, Yoko Hayashi-Takanaka, Yuko Sato et al.     The interplay of histone acetylation and RNA polymerase II activity is investigated using fluorescence microscopy; acetylation of H3 at Lys 27 enhances the recruitment of a transcriptional activator and accelerates the transition of RNA polymerase II from initiation to elongation, thus indicating that histone acetylation has a causal effect on two distinct steps in transcription activation.             Tyrosine phosphorylation of histone H2A by CK2 regulates transcriptional elongation ▶     Harihar Basnet, Xue B. Su, Yuliang Tan et al.     A conserved tyrosine residue, Tyr 57, of histone H2A is phosphorylated by an unsuspected tyrosine kinase activity of casein kinase 2, influencing a series of histone marks associated with active transcription and regulating transcription elongation.             Multiplex single-molecule interaction profiling of DNA-barcoded proteins ▶     Liangcai Gu, Chao Li, John Aach et al.     Single-molecular-interaction-sequencing involves attaching DNA barcodes to proteins, assaying these barcoded proteins en masse in an aqueous solution, followed by immobilization in a polyacrylamide film and amplifying and analysing the barcoding DNAs—the method allows for precise protein quantification and simultaneous interrogation of molecular binding affinity and specificity.             Cell differentiation and germ–soma separation in Ediacaran animal embryo-like fossils ▶     Lei Chen, Shuhai Xiao, Ke Pang et al.     Spheroidal microfossils from the Ediacaran Doushantuo phosphorites show clear signs of cell differentiation, programmed cell death, and separation between soma and germline, and seem to represent a hitherto unknown experiment in multicellular life like nothing on Earth today.             Rb suppresses human cone-precursor-derived retinoblastoma tumours ▶     Xiaoliang L. Xu, Hardeep P. Singh, Lu Wang et al.     The nature of the retinal cell-type-specific circuitry that predisposes to retinoblastoma is demonstrated, in which a program that is unique to post-mitotic human cone precursors sensitizes to the oncogenic effects of retinoblastoma (Rb) protein depletion; hence, the loss of Rb collaborates with the molecular framework of cone precursors to initiate tumorigenesis.             Articles and Letters                   Statin treatment rescues FGFR3 skeletal dysplasia phenotypes ▶     Akihiro Yamashita, Miho Morioka, Hiromi Kishi et al.     This study reprograms fibroblasts from thanatophoric dysplasia type I (TD1) and achondroplasia (ACH) patients into induced pluripotent stem cells (iPSCs), finding that chondrogenic differentiation results in the formation of degraded cartilage; statin treatment led to significant recovery of bone growth in a mouse model of ACH.             Loss of oncogenic Notch1 with resistance to a PI3K inhibitor in T-cell leukaemia ▶     Monique Dail, Jason Wong, Jessica Lawrence et al.     Mutations that dysregulate Notch1 and Ras/PI3K signalling are common in T-cell acute lymphoblastic leukaemia; here, treatment with a PI3K inhibitor is shown to induce drug resistance that is associated with downregulation of activated Notch1 signalling, suggesting that inhibition of both Notch1 and PI3K could promote drug resistance.             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.             Brain structure resolves the segmental affinity of anomalocaridid appendages ▶     Peiyun Cong, Xiaoya Ma, Xianguang Hou et al.     An anomalocaridid from the Cambrian period of China is so well preserved that its anterior nervous system can be resolved.             Island biogeography of the Anthropocene ▶     Matthew R. Helmus, D. Luke Mahler, Jonathan B. Losos     A contemporary test of the theory of island biogeography, in which species richness is determined by an island’s area and isolation, shows that geographic area is still a good positive predictor of species richness, but that geographic isolation as a negative predictor has been replaced by economic isolation.             A faster Rubisco with potential to increase photosynthesis in crops ▶     Myat T. Lin, Alessandro Occhialini, P. John Andralojc et al.     The plant enzyme Rubisco is the main enzyme converting atmospheric carbon dioxide into biological compounds, however, this enzymatic process is inefficient in vascular plants; this study demonstrates that tobacco plants can be engineered to fix carbon with a faster cyanobacterial Rubisco, thus potentially improving plant photosynthesis.             Glial origin of mesenchymal stem cells in a tooth model system ▶     Nina Kaukua, Maryam Khatibi Shahidi, Chrysoula Konstantinidou et al.     In the mouse, nerve-associated peripheral glial cells give rise to mesenchymal stem cells that contribute to the development and growth of adult teeth.             Antifungal drug resistance evoked via RNAi-dependent epimutations ▶     Silvia Calo, Cecelia Shertz-Wall, Soo Chan Lee et al.     The human fungal pathogen Mucor circinelloides develops spontaneous resistance to an antifungal drug both through mutation and through a newly identified epigenetic RNA-mediated pathway; RNA interference is spontaneously triggered to silence the fkbA gene, giving rise to drug-resistant epimutants that revert to being drug-sensitive once again when grown in the absence of drug.             Functional polarization of tumour-associated macrophages by tumour-derived lactic acid ▶     Oscar R. Colegio, Ngoc-Quynh Chu, Alison L. Szabo et al.     The growth of tumours is supported by tumour production of lactic acid, which polarizes tumour-associated macrophages to an M2 phenotype through a pathway dependent on hypoxia-inducible factor 1α.             The alarmin IL-33 promotes regulatory T-cell function in the intestine ▶     Chris Schiering, Thomas Krausgruber, Agnieszka Chomka et al.     The alarmin interleukin-33 is constitutively expressed at barrier sites and released in response to tissue damage; here, the IL-33 receptor ST2 is shown to be preferentially expressed on colonic regulatory T cells, where it promotes regulatory T-cell function and adaptation to the inflammatory tissue environment.             Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease ▶     Carolin Anders, Ole Niewoehner, Alessia Duerst et al.     Crystal structure of the RNA-guided endonuclease Cas9 bound to a guide RNA and a target DNA duplex reveals how base-specific recognition of a short motif known as PAM in the DNA target results in localized strand separation in the DNA immediately upstream of the PAM, allowing the target DNA strand to hybridize to the guide RNA.             News & Views                   Structural biology: Ribosome revelations ▶     Nelson B. Olivier             Biodiversity: Leaping lizards ▶     Patrick Goymer             Disease models: Statins give bone growth a boost ▶     Bjorn R. Olsen             Inorganic chemistry: How calcium affects oxygen formation ▶     Davide Lionetti, Theodor Agapie             50 & 100 Years Ago ▶             Plant Science: Towards turbocharged photosynthesis ▶     G. Dean Price, Susan M. Howitt             Network biology: A compass for stem-cell differentiation ▶     Franz-Josef Müller, Jeanne F. Loring             Cancer: The origin of human retinoblastoma ▶     Rod Bremner, Julien Sage             Structural biology: Lariat lessons ▶     Robert T. Batey             Brief Communications Arising                   Mitochondrial Ca2+ uniporter and CaMKII in heart ▶     Francesca Fieni, Derrick E. Johnson, Andy Hudmon et al.             Joiner et al. reply ▶     Mei-ling A. Joiner, Olha M. Koval, Jingdong Li et al.             Corrigenda                   Corrigendum: Quantitative flux analysis reveals folate-dependent NADPH production ▶     Jing Fan, Jiangbin Ye, Jurre J. Kamphorst et al.             Corrigendum: Elephant shark genome provides unique insights into gnathostome evolution ▶     Byrappa Venkatesh, Alison P. Lee, Vydianathan Ravi et al.             Corrigendum: Coupling of angiogenesis and osteogenesis by a specific vessel subtype in bone ▶     Anjali P. Kusumbe, Saravana K. Ramasamy, Ralf H. Adams             Research Highlights                   Zoology: Clock ticks for tiny group of fish | Stem cells: Cord-blood cells made plentiful | Ecology: Boring invaders held at the border | Virology: Flu virus comes in various flavours | Cancer immunology: Therapy broadens immune response | Genomics: Mutation has big disease effect         NEWS & COMMENT           Staff support | Infectious disease: Ebola’s lost ward | Chemistry: Chemical con artists foil drug discovery | In retrospect: The Courtship Habits of the Great Crested Grebe | Q&A: Violin detective | Social media: Research critics to be properly informed | First response, revisited | Chinese science gets mass transformation | Global Ebola response kicks into gear at last | US vows to combat antibiotic resistance | Drug-safety pilot makes the grade             More Biological Sciences ▶                 A picture of health In a series of four films reporter Lorna Stewart travels to the German island of Lindau to meet 600 of science’s brightest young minds and 37 rock stars – Nobel laureates. Watch the full series of films including this week’s release HIV in hiding with Francoise Barré-Sinoussi. nature.com/lindau/2014 Supported by Mars, Incorporated and published weekly from Sep 24th - Oct 15th         Health Sciences ▲top             RESEARCH           Latest Online                   Cancer: The origin of human retinoblastoma ▶     Rod Bremner, Julien Sage             Rb suppresses human cone-precursor-derived retinoblastoma tumours ▶     Xiaoliang L. Xu, Hardeep P. Singh, Lu Wang et al.     The nature of the retinal cell-type-specific circuitry that predisposes to retinoblastoma is demonstrated, in which a program that is unique to post-mitotic human cone precursors sensitizes to the oncogenic effects of retinoblastoma (Rb) protein depletion; hence, the loss of Rb collaborates with the molecular framework of cone precursors to initiate tumorigenesis.             Articles and Letters                   Statin treatment rescues FGFR3 skeletal dysplasia phenotypes ▶     Akihiro Yamashita, Miho Morioka, Hiromi Kishi et al.     This study reprograms fibroblasts from thanatophoric dysplasia type I (TD1) and achondroplasia (ACH) patients into induced pluripotent stem cells (iPSCs), finding that chondrogenic differentiation results in the formation of degraded cartilage; statin treatment led to significant recovery of bone growth in a mouse model of ACH.             Loss of oncogenic Notch1 with resistance to a PI3K inhibitor in T-cell leukaemia ▶     Monique Dail, Jason Wong, Jessica Lawrence et al.     Mutations that dysregulate Notch1 and Ras/PI3K signalling are common in T-cell acute lymphoblastic leukaemia; here, treatment with a PI3K inhibitor is shown to induce drug resistance that is associated with downregulation of activated Notch1 signalling, suggesting that inhibition of both Notch1 and PI3K could promote drug resistance.             News & Views                   Disease models: Statins give bone growth a boost ▶     Bjorn R. Olsen             50 & 100 Years Ago ▶             Cancer: The origin of human retinoblastoma ▶     Rod Bremner, Julien Sage             Research Highlights                   Cancer immunology: Therapy broadens immune response         NEWS & COMMENT           Staff support | Infectious disease: Ebola’s lost ward | First response, revisited | Global Ebola response kicks into gear at last | US vows to combat antibiotic resistance | Drug-safety pilot makes the grade             More Health Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   Lithium–antimony–lead liquid metal battery for grid-level energy storage ▶     Kangli Wang, Kai Jiang, Brice Chung et al.     All-liquid batteries comprising a lithium negative electrode and an antimony–lead positive electrode have a higher current density and a longer cycle life than conventional batteries, can be more easily used to make large-scale storage systems, and so potentially present a low-cost means of grid-level energy storage.             Articles and Letters                   Early turbulent mixing as the origin of chemical homogeneity in open star clusters ▶     Yi Feng, Mark R. Krumholz     Simulations tracing the mixing of chemical elements as star-forming clouds assemble and collapse show that turbulent mixing during cloud assembly naturally produces a scatter of stellar abundance much smaller than that in the gas, explaining why stars in the same cluster appear to be nearly identical in their chemical abundances.             Water vapour absorption in the clear atmosphere of a Neptune-sized exoplanet ▶     Jonathan Fraine, Drake Deming, Bjorn Benneke et al.     Space telescope observations of the transmission spectrum of the extrasolar planet HAT-P-11b, which is about the same size as Neptune, reveal water vapour absorption at a wavelength of 1.4 micrometres and indicate that the planetary atmosphere is predominantly clear down to an altitude corresponding to about 1 millibar.             News & Views                   Extrasolar planets: Window on a watery world ▶     Eliza M. R. Kempton             Inorganic chemistry: How calcium affects oxygen formation ▶     Davide Lionetti, Theodor Agapie             Research Highlights                   Quantum optics: Photons made to dance together | Chemistry: On the trail of a drug in plants | Materials: Squid skin inspires colourful display         NEWS & COMMENT           Renewable energy: Wind power tests the waters | Chemistry: Chemical con artists foil drug discovery | Cheap solar cells tempt businesses | Cosmology: A few words on infinity             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Latest Online                   Global covariation of carbon turnover times with climate in terrestrial ecosystems ▶     Nuno Carvalhais, Matthias Forkel, Myroslava Khomik et al.     A global, observation-based assessment of whole-ecosystem carbon turnover times shows that the overall mean global carbon turnover time is about 23 years and that locally its spatial variability depends on precipitation at least as strongly as on temperature.             Cell differentiation and germ–soma separation in Ediacaran animal embryo-like fossils ▶     Lei Chen, Shuhai Xiao, Ke Pang et al.     Spheroidal microfossils from the Ediacaran Doushantuo phosphorites show clear signs of cell differentiation, programmed cell death, and separation between soma and germline, and seem to represent a hitherto unknown experiment in multicellular life like nothing on Earth today.             Articles and Letters                   Asian monsoons in a late Eocene greenhouse world ▶     A. Licht, M. van Cappelle, H. A. Abels et al.     Asian monsoons were strongly active 40 million years ago and were enhanced by high atmospheric CO2 content. They were significantly weakened when CO2 levels decreased 34 million years ago and then reinitiated several million years later.             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.             Flow in bedrock canyons ▶     Jeremy G. Venditti, Colin D. Rennie, James Bomhof et al.     A survey along the Fraser Canyon in Canada reveals complex flow dynamics involving velocity inversions and upwelling, which suggests ways to improve flow and bedrock incision modelling.             News & Views                   Earth science: A fresh look at river flow ▶     Nicole M. Gasparini             Extrasolar planets: Window on a watery world ▶     Eliza M. R. Kempton             Research Highlights                   Chemistry: On the trail of a drug in plants         NEWS & COMMENT           Brazil warming to ‘green’ policies | Istanbul canal needs environmental study | Environment: Social change affects Antarctic priorities | Agriculture: Intensive dairy farms becoming greener             More Earth & Environmental Sciences ▶                 Nature Outlook Lung Cancer   Lung cancer is the mortality king of malignancy, killing 1.6 million people yearly, with a five-year survival rate under 20%. With such grim statistics in mind, researchers are examining the causes of lung cancer with the aim of creating better treatments or even preventing it.  Access the Outlook free online for six months.   Produced with support from Boehringer Ingelheim and Cancer Research UK.         Careers & Jobs ▲top               Work–life balance: Kid-friendly digs ▶     How to blend fieldwork and far-flung travel with raising little people.                   Gender gaps ▶     Report confirms broad gender pay disparity in United States.                   Cross-discipline focus ▶     Institutions globally aim to support interdisciplinarity.                   Wellcome re-entry ▶     Foundation provides a roadmap back to the bench.             Careers related news & comment                   Chemistry: Chemical con artists foil drug discovery Jonathan Baell, Michael A. Walters | Staff support | Special interest | Seven days: 19–25 September 2014 | Cosmology: A few words on infinity Lucy Fortson | Environment: Social change affects Antarctic priorities Nick Gales, Phil Trathan, Anthony Worby | Chinese science gets mass transformation David Cyranoski               naturejobs.com Science jobs of the week       Postdoctoral Research Associate     University of Edinburgh            PhD Student     University of Kansas Medical Center (KUMC)            Research worker     King's College London            Research Associate     University of Cambridge          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. Keep up-to-date with the latest sector trends, vote in our reader poll and sign-up to receive the monthly Naturejobs newsletter.           • events Directory featured events           natureevents directory featured events         Stem cells: from basic research to bioprocessing     09.06.15 London, UK         Natureevents Directory is the premier resource for scientists looking for the latest scientific conferences, courses, meetings and symposia. Featured across Nature Publishing Group journals and centrally at natureevents.com it is an essential reference guide to scientific events worldwide.               Futures                   Post-apocalyptic conversations with a sidewalk ▶     Beth Cato                 Your email address is in the Nature mailing list. You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/nams/svc/myaccount (You will need to log in to be recognised as a nature.com registrant). For further technical assistance, please contact subscriptions@nature.com For other enquiries, please contact feedback@nature.com Nature Publishing Group | 75 Varick Street, 9th floor | New York | NY 10013-1917 | USA Nature Publishing Group's offices: Principal offices: London - New York - Tokyo Worldwide offices: Basingstoke - Boston - Buenos Aires - Delhi - Hong Kong - Madrid - Melbourne - Munich - Paris - San Francisco - Seoul - Washington DC Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.