Nature contents: 09 January 2014

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Can't view this email? Click here to view in your browser.     Volume 505 Number 7482      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.               nature.com webcasts Nature Protocols presents a webcast on: Transformative Technologies in Neuroscience: Optogenetics   23 January 9am PST/12pm EST/5pm GMT/6pm CET   Free webcast and live Q & A session    This material is based upon work supported by the National Science Foundation under Grant No. 1348284.       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 ▼   Elephant shark genome provides unique insights into gnathostome evolution   The 'living fossil' fish, the coelacanth, has changed little in the past several million years. But the slowest evolving genome of all known vertebrates is now revealed as the elephant shark, Callorhinchus milii. The genome of this cartilaginous fish, a native of temperate waters off southern Australia and New Zealand, has now been sequenced. Genome analysis points to an unusual adaptive immune system, lacking the CD4 receptor and associated cytokines. Also absent are genes encoding secreted calcium-binding phosphoproteins, in line with the absence of bone in cartilaginous fish.       Physical Sciences More Physical sciences ▼   A metal-free organic–inorganic aqueous flow battery   In a flow battery the electro-active components are fluids held external to the battery itself, making it theoretically possible to store arbitrarily large amounts of energy. Flow batteries are attractive as a potential means for regulating the output of intermittent sources of electricity such as wind or solar power. The snag is the high cost of most electro-active materials. Now Brian Huskinson and colleagues have developed an aqueous flow battery based on inexpensive, non-metallic commodity chemicals.       Chemical Sciences More Chemical sciences ▼   Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform   Brown macroalgae are seen as a potential feedstock for biofuel manufacture, with the advantage that they can be farmed in coastal waters without using valuable arable land. However, the sugars that they produce are not readily processed by the biotechnology workhorse, Saccharomyces cerevisiae yeast. This paper reports the engineering of a yeast strain that can utilize the unique sugars in brown macroalgae for high-efficiency ethanol fermentation. With appropriate modifications, this synthetic biology platform can be used to produce many other biofuels and renewable chemicals.                 Podcast & Video     In this week's podcast: storing solar power in your basement, the colour of long-extinct sea monsters, and preventing violent attacks on university campuses.         News & Comment Read daily news coverage▶ ▲top               THIS WEEK           Editorials                   Data sharing will pay dividends ▶     As public pressure builds for drug companies to make more results available from clinical trials, the industry should not forget that it relies on collective goodwill to test new therapies.             Risk management ▶     Teams aimed at preventing violence on campus can offer a lifeline to those in crisis.             Conflict of interest ▶     How two world wars affected scientific research, and vice versa.             World View                   This was no Antarctic pleasure cruise ▶     After his polar vessel became trapped in shifting sea ice, Chris Turney defends the scientific basis of the expedition.             Seven Days                   Seven days: 3–9 January 2014 ▶     The week in science: China crushes seized ivory, smuggled dinosaur skull recovered, and incoming asteroid spotted.             NEWS IN FOCUS           Leaked files slam stem-cell therapy ▶     Disclosures and resignations reveal scientific concerns over methods of Italy's Stamina Foundation.             Particle-physics papers set free ▶     Tensions as open-access initiative goes live — without the field's leading journal.             Projects set to tackle neglected diseases ▶     But they do little to alter the process of drug development.             Many eyes on Earth ▶     Swarms of small satellites set to deliver close to real-time imagery of swathes of the planet.             China tops Europe in R&D intensity ▶     Reforms to commercial and academic research systems still needed despite reaching spending milestone, say scientists.             Features                   Computer science: The learning machines ▶     Using massive amounts of data to recognize photos and speech, deep-learning computers are taking a big step towards true artificial intelligence.             Workplace violence: Caught on campus ▶     Violent incidents at academic institutions have spurred universities to adopt formal procedures designed to keep campuses safer. But do the tactics work?             COMMENT           History: Shut up and calculate! ▶     Practical, interdisciplinary ways of working forged during the Second World War had a lasting impact on a generation of physicists and their findings, says David Kaiser.             Books and Arts                   Military science: The evolving science of war ▶     Sharon Weinberger assesses two studies probing the roles of physics and psychology in conflicts past, present and future.             Psychology: Feeling the fear ▶     David Adam applauds the autobiography of a high-flyer confronting his own nervous suffering head-on.             Ornithology: Under their wing ▶     Ben Sheldon relishes a study of the broad-ranging impact of ornithology on modern biology.             Q&A: Tinnitus tunesmith ▶     Sound artist Daniel Fishkin tries to convey the experience of tinnitus. As the latest incarnation of his installation series Composing the Tinnitus Suites opens in Brooklyn, New York, he talks about building a mechanical model of the inner ear.             Correspondence                   Taxonomy: Call for ecosystem modelling data Mike Harfoot, Dave Roberts | Publishing: Halt self-citation in impact measures Elissa Z. Cameron, Amy M. Edwards, Angela M. White | Environment: Himalayas already have hazard network Yadav Uprety, Ram P. Chaudhary, Nakul Chettri | Pollinator declines: Avoid pitfalls of consensus methods Ian Bateman, Matthew Agarwala, Tomáš Bad'ura             Correction                   Correction ▶                     Biological Sciences ▲top             RESEARCH           Latest Online                   Ecology: Good dirt with good friends ▶     Mark A. Bradford             Molecular biology: The tug of DNA repair ▶     Irina Artsimovitch             Discovery and saturation analysis of cancer genes across 21 tumour types ▶     Michael S. Lawrence, Petar Stojanov, Craig H. Mermel et al.     Large-scale genomic analysis of somatic point mutations in exomes from tumour–normal pairs across 21 cancer types identifies most known cancer genes in these tumour types as well as 33 genes not known to be significantly mutated, and down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies.             UvrD facilitates DNA repair by pulling RNA polymerase backwards ▶     Vitaly Epshtein, Venu Kamarthapu, Katelyn McGary et al.     UvrD acts in nucleotide excision repair by using its helicase/translocase activity to induce RNA polymerase backtracking, enabling repair enzymes to access DNA lesions.             Convergent evolution of a fused sexual cycle promotes the haploid lifestyle ▶     Racquel Kim Sherwood, Christine M. Scaduto, Sandra E. Torres et al.     In the predominantly diploid yeast Saccharomyces cerevisiae, regulatory control of mating is separate from meiosis; here the related hemiascomycete yeast Candida lusitaniae is shown to have coordinated regulatory control of mating and meiosis, favouring the formation of haploids.             Skin pigmentation provides evidence of convergent melanism in extinct marine reptiles ▶     Johan Lindgren, Peter Sjövall, Ryan M. Carney et al.     Dark melanin pigment was detected in the fossilized skin of three distantly related marine reptiles (a leatherback turtle, mosasaur and ichthyosaur); benefits of thermoregulation and/or crypsis may have contributed to this melanisation, which therefore has implications for our understanding of how these animals may have lived.             Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage ▶     Colin Averill, Benjamin L. Turner, Adrien C. Finzi     Ecosystem mycorrhizal type is shown to have a stronger effect on soil carbon storage than temperature, precipitation, clay content and primary production; ecosystems dominated by ectomycorrhizal and ericoid mycorrhizal fungi contain 70% more soil carbon per unit nitrogen than do ecosystems dominated by arbuscular mycorrhizal fungi.             Genetics of single-cell protein abundance variation in large yeast populations ▶     Frank W. Albert, Sebastian Treusch, Arthur H. Shockley et al.     A new method for identifying genetic loci that influence protein expression in budding yeast reveals considerable complexity in how genetic variation shapes the proteome.             Articles and Letters                   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.             Elephant shark genome provides unique insights into gnathostome evolution OPEN ▶     Byrappa Venkatesh, Alison P. Lee, Vydianathan Ravi et al.     Whole-genome analysis of the elephant shark, a cartilaginous fish, shows that it is the slowest evolving of all known vertebrates, lacks critical bone formation genes and has an unusual adaptive immune system.             Patterning and growth control by membrane-tethered Wingless ▶     Cyrille Alexandre, Alberto Baena-Lopez, Jean-Paul Vincent     Replacement of the wingless (wg) gene in Drosophila with one that expresses a membrane-tethered form of Wg results in viable flies with normally patterned appendages of nearly the right size; early wg transcription and memory of signalling ensure continued target-gene expression in the absence of Wg release, even though the spread of Wg could boost cell proliferation.             The effects of genetic variation on gene expression dynamics during development ▶     Mirko Francesconi, Ben Lehner     A comprehensive study into the effects of polymorphisms on gene expression dynamics during a 12-hour development period of Caenorhabditis elegans shows that both cis and trans expression quantitative trait loci (eQTLs) can increase and decrease gene expression, depending on the time point, and that trans eQTLs can act as modifiers of expression during a given period of development.             HMGA2 functions as a competing endogenous RNA to promote lung cancer progression ▶     Madhu S. Kumar, Elena Armenteros-Monterroso, Philip East et al.     HMGA2 promotes lung cancer progression in mice and humans; in mouse and human lung cancer cells, HMGA2 competes with mRNAs like TGFBR3 for the let-7 microRNA family, and in human non-small-cell lung cancer tissue, expression levels of HMGA2 and TGFBR3 are correlated, suggesting that HMGA2 functions both as a protein-coding gene and as a non-coding RNA.             Mycobacteria manipulate macrophage recruitment through coordinated use of membrane lipids ▶     C. J. Cambier, Kevin K. Takaki, Ryan P. Larson et al.     The bacteria responsible for causing tuberculosis in mammals and zebrafish are shown to preferentially recruit and infect permissive macrophages while evading microbicidal ones.             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 for hijacking CBF-β and CUL5 E3 ligase complex by HIV-1 Vif ▶     Yingying Guo, Liyong Dong, Xiaolin Qiu et al.     This study provides a crystal structure of the Vif–CBF-β–CUL5–ELOB–ELOC complex, which shows that Vif mimics the action of SOCS2 to interact with CUL5 and ELOC.             Structural basis of lentiviral subversion of a cellular protein degradation pathway ▶     David Schwefel, Harriet C. T. Groom, Virginie C. Boucherit et al.     The crystal structure of a ternary complex of the lentiviral accessory protein Vpx with the E3 ligase substrate adaptor DCAF1 and the HIV-1 restriction factor SAMHD1 shows how Vpx recruits SAMHD1 to the cell's ubiquitination machinery.             Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform ▶     Maria Enquist-Newman, Ann Marie E. Faust, Daniel D. Bravo et al.     Saccharomyces cerevisiae bearing engineered alginate and mannitol catabolic pathways can ferment sugars from brown macroalgae to produce ethanol, potentially allowing the use of brown macroalgae as a viable feedstock for the production of biofuels and renewable chemicals.             De novo protein crystal structure determination from X-ray free-electron laser data ▶     Thomas R. M. Barends, Lutz Foucar, Sabine Botha et al.     Femtosecond crystallography with an X-ray free-electron laser is used to analyse micrometre-sized protein crystals, generating a high-resolution structure of the protein without previous knowledge of what it looks like.             News & Views                   Developmental biology: Tethered wings ▶     Ginés Morata, Gary Struhl             50 & 100 Years Ago ▶             Therapeutics: Detective work on drug dosage ▶     Richard M. Crooks             HIV: Ringside views ▶     Michael H. Malim             Ecology: Good dirt with good friends ▶     Mark A. Bradford             Molecular biology: The tug of DNA repair ▶     Irina Artsimovitch             Corrigendum                   Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome ▶     Kerstin Howe, Matthew D. Clark, Carlos F. Torroja et al.             Research Highlights                   Neuroscience: In vivo cell switch for brain repair | Immunology: Dietary fibre dampens asthma | Zoology: Tobacco breath aids defence | Genomics: CRISPR screen identifies genes | Structural biology: Better pictures of protein structures | Cancer: How drugs boost resistance         NEWS & COMMENT           Risk management | Workplace violence: Caught on campus | Psychology: Feeling the fear | Ornithology: Under their wing | Taxonomy: Call for ecosystem modelling data | Environment: Himalayas already have hazard network | Pollinator declines: Avoid pitfalls of consensus methods | Correction | Data sharing will pay dividends | Leaked files slam stem-cell therapy | Projects set to tackle neglected diseases             More Biological Sciences ▶                 AIMResearch - Highlighting research from the Advanced Institute for Materials Research (AIMR) in Japan, which promotes mathematics-materials science collaboration Latest highlights: Superhard materials: Shear resolution In the spotlight: Reaping the rewards of a mathematics-materials approach (Roundtable interview) Register today for monthly email alerts from the AIMR!         Chemical Sciences ▲top             RESEARCH           Articles and Letters                   A metal-free organic–inorganic aqueous flow battery ▶     Brian Huskinson, Michael P. Marshak, Changwon Suh et al.     Flow batteries, in which the electro-active components are held in fluid form external to the battery itself, are attractive as a potential means for regulating the output of intermittent renewable sources of electricity; an aqueous flow battery based on inexpensive commodity chemicals is now reported that also has the virtue of enabling further improvement of battery performance through organic chemical design.             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.             News & Views                   Electrochemistry: Metal-free energy storage ▶     Grigorii L. Soloveichik             More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   A millisecond pulsar in a stellar triple system ▶     S. M. Ransom, I. H. Stairs, A. M. Archibald et al.     Precision timing and multiwavelength observations of a millisecond pulsar in a triple system show that the gravitational interactions between the bodies are strong; this allows the mass of each body to be determined accurately and means that the triple system will provide precise tests of the strong equivalence principle of general relativity.             Articles and Letters                   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.             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.             A metal-free organic–inorganic aqueous flow battery ▶     Brian Huskinson, Michael P. Marshak, Changwon Suh et al.     Flow batteries, in which the electro-active components are held in fluid form external to the battery itself, are attractive as a potential means for regulating the output of intermittent renewable sources of electricity; an aqueous flow battery based on inexpensive commodity chemicals is now reported that also has the virtue of enabling further improvement of battery performance through organic chemical design.             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.             News & Views                   Electrochemistry: Metal-free energy storage ▶     Grigorii L. Soloveichik             50 & 100 Years Ago ▶             Quantum physics: An atomic SQUID ▶     Charles A. Sackett             Research Highlights                   Astrophysics: Comets hint at cosmic encounter | Materials: Extra-stretchy graphene gloves         NEWS & COMMENT           Computer science: The learning machines | History: Shut up and calculate! | Particle-physics papers set free             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Articles and Letters                   Primitive layered gabbros from fast-spreading lower oceanic crust ▶     Kathryn M. Gillis, Jonathan E. Snow, Adam Klaus et al.     Drilling by the Integrated Ocean Drilling Program has recovered primitive, modally layered, orthopyroxene-bearing cumulate rocks from the lower plutonic crust formed at a fast-spreading ridge, leading to a better-constrained estimate of the bulk composition of fast-spreading oceanic crust.             Research Highlights                   Geology: Radar signals sinkhole to come         NEWS & COMMENT           Many eyes on Earth | Taxonomy: Call for ecosystem modelling data | Environment: Himalayas already have hazard network | This was no Antarctic pleasure cruise             More Earth & Environmental Sciences ▶                 NATURE REVIEWS CANCER & NATURE REVIEWS CLINICAL ONCOLOGY 2014 CALENDAR Download the calendar for FREE As well as plundering the Nature Reviews Cancer image bank for more clinically oriented figures for our 2014 calendar, we have chosen six images and figures from our sister journal, Nature Reviews Clinical Oncology. Our calendar is freely available thanks to support from  OriGene          Careers & Jobs ▲top               Equality: Standing out ▶     Welcoming lab environments and networking organizations help lesbian, gay, bisexual and transgender scientists to excel.                   Turning point: Eleni Antoniadou ▶     Enterprising bioengineering PhD student is motivated by helping people.             Careers related news & comment                   Risk management | Seven days: 3–9 January 2014 | Many eyes on Earth Declan Butler | China tops Europe in R&D intensity Richard Van Noorden | History: Shut up and calculate! David Kaiser | Publishing: Halt self-citation in impact measures Elissa Z. Cameron, Amy M. Edwards, Angela M. White | Particle-physics papers set free Richard Van Noorden               naturejobs.com Science jobs of the week       Post Doctoral Fellow     The Wistar Institute            Post-doctoral researcher     University of Patras            PhD posititon - Immunology     University Hospital Erlangen            Postdoctoral Scientist     University of Oxford          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.           • Natureevents Directory featured events           natureevents directory featured events         Next Generation Sequencing     13.04.14 Cambridge, UK         Natureevents Directory is the premier resource for scientists looking for the latest scientific conferences, courses, meetings and symposia. 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