Nature contents: 08 August 2013

Can't view this email? Click here to view in your browser.     Volume 500 Number 7461      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.               See what nature is hiding BD Horizon™ Brilliant Violet™ polymer conjugates are brighter than traditional dyes and can help identify cell populations with lower receptor density than previously possible. Learn how to resolve rare and dim cell populations with our expanded set of tools and information and request a free sample at bdbiosciences.com/go/brilliant.       Jump to the content that matters to you View Table of Contents ▶ ▼ News & Comment   ▼ Biological Sciences   ▼ Chemical Sciences   ▼ Physical Sciences   ▼ Earth & Environmental Sciences   ▼ Careers & Jobs       This week's highlights     Physical Sciences More Physical sciences ▼   Squeezed light from a silicon micromechanical resonator   Light falling on a mechanical object exerts a small force that alters the object's motion. The motion of the object itself exerts back-action on the light, resulting in 'squeezed' light with non-classical behaviour. The use of such squeezed light was proposed nearly three decades ago as a way of overcoming the standard quantum limits in precision force measurements. Oskar Painter and colleagues demonstrate squeezed-light generation in a silicon micromechanical system. With further development the technology could be used to make integrated microscale devices for precision metrology applications.       Earth & Environmental Sciences More Earth & Environmental sciences ▼   Insolation-driven 100,000-year glacial cycles and hysteresis of ice-sheet volume   An explanation for the 100,000-year glacial cycles observed in Northern Hemisphere ice sheets over the past one million years is provided in Nature this week. Earth's climate is dominated by a 100,000-year cycle of ice ages. Variations in insolation - the solar radiation reaching Earth's surface - caused by constant changes in Earth's orbit and orientation to the Sun are closely associated with glaciations, but the physical mechanisms driving the cycle have remained unclear. Now Ayako Abe-Ouchi and colleagues demonstrate that insolation variations interact with the size of the ice sheets and the solid Earth to control the 100,000-year cycles.       Biological Sciences More Biological sciences ▼   The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line   The first genomic characterization of the HeLa cancer cell line, the longest-serving and arguably most commonly used human cell line in biomedical research, reveals a genome that is surprisingly stable with respect to both point mutation and copy number alterations. The point mutation rate may be no higher than the somatic mutation rate of normal tissue, and very few copy number alterations distinguish the genomes of different HeLa strains that were split from one another in the mid-1950s. The authors examine the relationship between gene dosage and expression by integrating several datasets, including those from the ENCODE project, and find strong activation of the MYC proto-oncogene by the human papilloma virus type 18 (HPV-18) integration at chromosome 8q24.21.           Only 7.5% of the Brazilian Caatinga is protected Semiarid biome is the most susceptible to human interference and climate change, warn researchers Melatonin helps to fight breast cancer, according to a study  Sign up for FAPESP's free weekly newsletter to know the latest developments of Brazilian science           Podcast & Video     In this week's podcast: famous cells and genetic privacy, what the 'love hormone' oxytocin does in the brain, smart uses for metamaterials, and the 'personalities' of NASA's rovers. In our latest video feature 3D maps show the brain at its most detailed and messy. The maps - or connectomes - provide new insights into how the brain processes visual information.         News & Comment Read daily news coverage▶ ▲top               THIS WEEK           Editorials                   Handle with care ▶     The possibility that H7N9 avian influenza may evolve sufficiently to cause a pandemic has scientists turning again to controversial research —they must be careful how they justify the risks taken.             Blood ties ▶     Scientists should give donors more information about how their biospecimens are used.             World View                   Balancing privacy with public benefit ▶     Maximizing access to research data will greatly benefit science, and users can help to establish universal principles on how to do it, says Martin Bobrow.             Seven Days                   Seven days: 2–8 August 2013 ▶     The week in science: Archaeologists open double coffin at Grey Friars, tissue engineers serve up lab-grown hamburger, and MIT releases report on Aaron Swartz case.             NEWS IN FOCUS           Scientists swept up in terrorism trials ▶     Turkish government ignores calls that trials are unfair.             Best way to kill lab animals sought ▶     Researchers debate most humane methods of dispatch.             Squeezed light mutes quantum noise ▶     Silicon zip reduces energy fluctuations in laser beams to improve sensitivity of optical motion sensors.             Deal done over HeLa cell line ▶     Family of Henrietta Lacks agrees to release of genomic data.             Spin rate of black holes pinned down ▶     Calculation offers way to probe galactic evolution.             Features                   Climate science: A line in the sands ▶     The scientific community is sharply divided over the proposed Keystone XL pipeline from Canada's tar sands.             Exotic optics: Metamaterial world ▶     Engineered structures with bizarre optical properties are set to migrate out of the laboratory and into the marketplace.             COMMENT           Biospecimen policy: Family matters ▶     Kathy L. Hudson and Francis S. Collins discuss how and why the US National Institutes of Health worked with the family of Henrietta Lacks, the unwitting source of the HeLa cell line, to craft an agreement for access to HeLa genome data.             Energy policy: A low-carbon road map for China ▶     Recycling, renewables and a reinvigorated domestic energy market will allow China to lead the world in low-carbon development, say Zhu Liu and colleagues.             Books and Arts                   Social psychology: The gloat factor ▶     Dan Jones mulls over a study of why we enjoy the misfortunes of others.             Development: Starved for solutions ▶     Calestous Juma weighs up a call for a revolution to end world hunger.             Science and religion: Godless chronicles ▶     Glenn Branch goes for a dip in the antitheologic.             Correspondence                   Avian flu: Gain-of-function experiments on H7N9 Ron A. M. Fouchier, Yoshihiro Kawaoka & 20 co-authors | Avian flu: Extra oversight for H7N9 experiments Harold W. Jaffe, Amy P. Patterson, Nicole Lurie | US sequester: Follow Obama's lead and take a pay cut Peter Foukal | Sustainability: Three reasons for eco-label failure Ralf Buckley                 Frontiers reviews are fair, constructive and transparent. Authors will meet an innovative referee process that brings authors and referees in close and positive contact. "The cross-talk between authors and reviewers speeds up the publication process, and provides a terrific forum for reaching consensus." Frontiers Author Be a part of the future of research publication         Biological Sciences ▲top             RESEARCH           Latest Online                   Systems biology: Metabolite turns master regulator ▶     Joshua D. Rabinowitz, Thomas J. Silhavy             Microbiology: A weapon for bacterial warfare ▶     Alain Filloux             Coordination of bacterial proteome with metabolism by cyclic AMP signalling ▶     Conghui You, Hiroyuki Okano, Sheng Hui et al.     Cyclic AMP, one of the earliest discovered and most intensely studied signalling molecules in molecular biology, is widely believed to signal the carbon status in mediating catabolite repression in bacteria; here a quantitative approach reveals a much broader physiological role for cAMP signalling, whereby it coordinates the allocation of proteomic resources with the global metabolic needs of the cell, including, for example, nitrogen or sulphur.             Oxytocin enhances hippocampal spike transmission by modulating fast-spiking interneurons ▶     Scott F. Owen, Sebnem N. Tuncdemir, Patrick L. Bader et al.     Oxytocin is shown to sharpen neuronal network activity by increasing fast-spiking interneuron activity.             A gustatory receptor paralogue controls rapid warmth avoidance in Drosophila ▶     Lina Ni, Peter Bronk, Elaine C. Chang et al.     After previously discovering that the ion channel TRPA1 is used as an internal temperature sensor in Drosophila to control the slow response of flies to shallow thermal gradients, the authors show here that the rapid response of flies to steep warming gradients relies on a different protein, GR28B, providing the first example of a thermosensory role for a gustatory receptor.             Induction of mouse germ-cell fate by transcription factors in vitro  ▶     Fumio Nakaki, Katsuhiko Hayashi, Hiroshi Ohta et al.     Expression of the three transcription factors BLIMP1, PRDM14 and TFAP2C, or of PRDM14 alone, converts epiblast-like cells into primordial germ cell (PGC)-like cells; the transcription-factor-induced PGC-like cells acquire key transcriptome and epigenetic reprogramming in PGCs, and contribute to spermatogenesis and fertile offspring.             Vesicular and non-vesicular transport feed distinct glycosylation pathways in the Golgi ▶     Giovanni D'Angelo, Takefumi Uemura, Chia-Chen Chuang et al.     Glucosylceramide (GlcCer), a common precursor of different glycosphingolipids, is shown to be channelled to two distinct pathways in the Golgi; non-vesicular transport from the cis- to trans-Golgi network results in the synthesis of the globo series of glycosphingolipids, whereas vesicular transport is the main source of GlcCer for ganglioside synthesis in the Golgi cisternae.             Stability and function of regulatory T cells is maintained by a neuropilin-1–semaphorin-4a axis ▶     Greg M. Delgoffe, Seng-Ryong Woo, Meghan E. Turnis et al.     Neuropilin-1 (Nrp1) on regulatory T (Treg) cells is shown to interact with semaphorin-4a (Sema4a) to promote a program of Treg-cell stability and survival, in part through PTEN-mediated modulation of Akt signalling; Nrp1-deficient Treg cells can maintain immune homeostasis but fail to suppress in inflammatory sites, such as tumours, providing an attractive immunotherapeutic target for the treatment of cancers.             Charting a dynamic DNA methylation landscape of the human genome ▶     Michael J. Ziller, Hongcang Gu, Fabian Müller et al.     Whole-genome bisulphite sequencing data from diverse human cell and tissue types shows that only about 22% of CpGs change their methylation state across these cell types; most of these CpGs are located at gene regulatory elements, particularly enhancers and transcription-factor-binding sites, and these selected regions with dynamic DNA methylation patterns could help to define putative regulatory elements further.             PAAR-repeat proteins sharpen and diversify the type VI secretion system spike ▶     Mikhail M. Shneider, Sergey A. Buth, Brian T. Ho et al.     An X-ray structure of bacterial type VI secretion system components reveals that PAAR family proteins bind at the tip of the VgrG spike, providing new insights into the mechanisms of type VI secretion; experiments using bacteria confirmed the importance of PAAR proteins.             The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device ▶     Jason N. Busby, Santosh Panjikar, Michael J. Landsberg et al.     The crystal structure of the complex formed by the B and C toxin complex proteins is reported, revealing how toxin complexes are processed and protected; the proteins assemble to form a large hollow structure that sequesters the cytotoxic portion of the C protein, and a β-propeller domain mediates attachment to the A protein in the native ABC complex.             Prolonged dopamine signalling in striatum signals proximity and value of distant rewards ▶     Mark W. Howe, Patrick L. Tierney, Stefan G. Sandberg et al.     Cyclic voltammetry reveals an extended mode of reward-predictive dopamine signalling in the striatum as rats navigate; signals increase as the rats approach distant rewards, instead of showing phasic or steady tonic activity, and the increases scale flexibly with the distance and size of the rewards.             Limited airborne transmission of H7N9 influenza A virus between ferrets ▶     Mathilde Richard, Eefje J. A. Schrauwen, Miranda de Graaf et al.     An investigation into the transmissibility of the H7N9 influenza A virus in ferrets finds that although the virus has some determinants associated with human adaptation and transmissibility between mammals, the airborne transmission between ferrets is limited.             Articles and Letters                   A Jurassic mammaliaform and the earliest mammalian evolutionary adaptations ▶     Chang-Fu Zhou, Shaoyuan Wu, Thomas Martin et al.     Haramiyids were Mesozoic era animals that until now have been identified only from their distinctive teeth, and are thought to be related to the better-known multituberculates: here the authors describe a haramiyid that is very primitive in terms of its jaw and ankle characteristics, suggesting a lack of relationship to the multituberculates.             Connectomic reconstruction of the inner plexiform layer in the mouse retina ▶     Moritz Helmstaedter, Kevin L. Briggman, Srinivas C. Turaga et al.     Improved electron microscopy methods are used to map a mammalian retinal circuit of close to 1,000 neurons; the work reveals a new type of retinal bipolar neuron and suggests functional mechanisms for known visual computations.             A visual motion detection circuit suggested by Drosophila connectomics ▶     Shin-ya Takemura, Arjun Bharioke, Zhiyuan Lu et al.     Reconstruction of a connectome within the fruitfly visual medulla, containing more than 300 neurons and over 8,000 chemical synapses, reveals a candidate motion detection circuit; such a circuit operates by combining displaced visual inputs, an operation consistent with correlation based motion detection.             Nitrogen losses in anoxic marine sediments driven by Thioploca–anammox bacterial consortia ▶     M. G. Prokopenko, M. B. Hirst, L. De Brabandere et al.     A novel symbiotic consortium is described between two chemolithotrophic bacteria — anaerobic ammonium-oxidizing (anammox) bacteria and the nitrate-sequestering sulphur-oxidizing Thioploca species — in anoxic sediments of the Soledad basin at the Mexican Pacific margin.             A new arboreal haramiyid shows the diversity of crown mammals in the Jurassic period ▶     Xiaoting Zheng, Shundong Bi, Xiaoli Wang et al.     Suggestions that haramiyids were related to multituberculates are substantiated with the first discovery of a haramiyid skeleton from the Jurassic period of China; recalibrating evolutionary relationships, this finding means that the lineage leading to placentals and marsupial mammals was distinct in the Triassic period, more than 200 million years ago.             A latent capacity for evolutionary innovation through exaptation in metabolic systems ▶     Aditya Barve, Andreas Wagner     A computational analysis of the ability of a metabolic reaction network to synthesize all biomass from a single source of carbon and energy shows that when such networks are required to be viable on one particular carbon source, they are typically also viable on multiple other carbon sources that were not targets of selection.             The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line ▶     Andrew Adey, Joshua N. Burton, Jacob O. Kitzman et al.     Haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain shows that HeLa is relatively stable in terms of point variation; integration of several data sets reveals strong, haplotype-specific activation of the proto-oncogene MYC by the human papilloma virus type 18 genome, and enables the relationship between gene dosage and expression to be examined.             A directional tuning map of Drosophila elementary motion detectors ▶     Matthew S. Maisak, Juergen Haag, Georg Ammer et al.     This study uses calcium imaging to show that T4 and T5 neurons are divided in specific subpopulations responding to motion in four cardinal directions, and are specific to ON versus OFF edges, respectively; when either T4 or T5 neurons were genetically blocked, tethered flies walking on air-suspended beads failed to respond to the corresponding visual stimuli.             Generation of inner ear sensory epithelia from pluripotent stem cells in 3D culture ▶     Karl R. Koehler, Andrew M. Mikosz, Andrei I. Molosh et al.     A new approach has been developed in order to achieve the stepwise differentiation of inner ear sensory epithelia from mouse embryonic stem cells in a three-dimensional culture: this process, which mimics normal development and produces cells that have functional characteristics of mechanosensitive hair cells, is hoped to provide further insights into inner ear development and disorder.             Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells ▶     Kathryn Blaschke, Kevin T. Ebata, Mohammad M. Karimi et al.     Vitamin C is a direct regulator of Tet enzyme activity and DNA methylation fidelity in mouse ES cells; addition of vitamin C promotes Tet activity, increases 5-hydroxymethlycytosine (5hmC) and DNA demethylation of many gene promoters, upregulates demethylated germline genes, and induces a state that more closely approximates that of the inner cell mass of the blastocyst.             Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 ▶     Guangwen Lu, Yawei Hu, Qihui Wang et al.     MERS-CoV is a newly emerged coronavirus that is related to SARS-CoV and has proven fatal in half of the people it has infected to date: here the crystal structure of the MERS-CoV receptor binding domain is presented in complex with its receptor on human cells, CD26.             Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota ▶     Koji Atarashi, Takeshi Tanoue, Kenshiro Oshima et al.     This study identifies 17 strains of human-derived Clostridia capable of inducing the accumulation and functional maturation of regulatory T cells; it is suggested that these strains may be useful candidates for the future development of oral bacterial therapeutics to treat human inflammatory disorders.             Pyrimidine homeostasis is accomplished by directed overflow metabolism ▶     Marshall Louis Reaves, Brian D. Young, Aaron M. Hosios et al.     Here, the authors identify a previously unknown regulatory strategy used by Escherichia coli to control end-product levels of the pyrimidine biosynthetic pathway: this involves feedback regulation of the near-terminal pathway enzyme UMP kinase, with accumulation of UMP prevented by its degradation to uridine through UmpH, a phosphatase with a previously unknown function.             News & Views                   Neuroscience: Accurate maps of visual circuitry ▶     Richard H. Masland             50 & 100 Years Ago ▶             Biochemistry: Curbing the excesses of low demand ▶     Athel Cornish-Bowden             Evolutionary biology: The handiwork of tinkering ▶     Paul Flicek             Palaeontology: Jurassic fossils and mammalian antiquity ▶     Richard L. Cifelli, Brian M. Davis             Systems biology: Metabolite turns master regulator ▶     Joshua D. Rabinowitz, Thomas J. Silhavy             Microbiology: A weapon for bacterial warfare ▶     Alain Filloux             Corrigenda                   Corrigendum: Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions ▶     Lars Guelen, Ludo Pagie, Emilie Brasset, Wouter Meuleman, Marius B. Faza et al.             Corrigendum: Immune surveillance by CD8αα+ skin-resident T cells in human herpes virus infection ▶     Jia Zhu, Tao Peng, Christine Johnston, Khamsone Phasouk, Angela S. Kask et al.             Corrigendum: Sema3A regulates bone-mass accrual through sensory innervations ▶     Toru Fukuda, Shu Takeda, Ren Xu et al.             Erratum                   Erratum: Integrated genomic characterization of endometrial carcinoma ▶     The Cancer Genome Atlas Research Network             Retraction                   Retraction: Bird-like fossil footprints from the Late Triassic ▶     Ricardo N. Melchor, Silvina de Valais, Jorge F. Genise             Research Highlights                   Animal behaviour: Travelling zebras forecast the weather | Infectious disease: Flu makes bacteria go bad | Molecular biology: Molecular switches in RNA | Social biology: Insects show savvy mob mentality | Evolution: Mammals and monogamy | Molecular psychiatry: A factor for autism and schizophrenia | Plant biology: Cheating orchids turn over new leaf         NEWS & COMMENT           Handle with care | Deal done over HeLa cell line | Biospecimen policy: Family matters | Social psychology: The gloat factor | Avian flu: Gain-of-function experiments on H7N9 | Avian flu: Extra oversight for H7N9 experiments | Sustainability: Three reasons for eco-label failure | Best way to kill lab animals sought             More Biological Sciences ▶                 2013 Nature Awards for Mentoring in Science   Nominations are now open. This year Nature invites nominations of outstanding scientific mentors in Italy. Two prizes of €10,000 will be awarded, one for mid-career and one for lifetime achievement. Nominations close on Tuesday 20 August 2013.   Nominate your mentor!          Chemical Sciences ▲top             RESEARCH           Latest Online                   The role of spin in the kinetic control of recombination in organic photovoltaics ▶     Akshay Rao, Philip C. Y. Chow, Simon Gélinas et al.     The interplay of spin, energetics and delocalization of the electronic excitations are shown to create a spin blockade of electron–hole recombination in organic photovoltaic cells, resulting in high quantum efficiencies.             News & Views                   Biochemistry: Curbing the excesses of low demand ▶     Athel Cornish-Bowden             More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   The role of spin in the kinetic control of recombination in organic photovoltaics ▶     Akshay Rao, Philip C. Y. Chow, Simon Gélinas et al.     The interplay of spin, energetics and delocalization of the electronic excitations are shown to create a spin blockade of electron–hole recombination in organic photovoltaic cells, resulting in high quantum efficiencies.             A 'kilonova' associated with the short-duration γ-ray burst GRB 130603B ▶     N. R. Tanvir, A. J. Levan, A. S. Fruchter et al.     Strong evidence that a kilonova — an event similar to a faint, short-lived supernova — accompanied the short-duration γ-ray burst GRB 130603B provides support for the hypothesis that such bursts are produced by the merger of two compact stellar objects.             Articles and Letters                   Squeezed light from a silicon micromechanical resonator ▶     Amir H. Safavi-Naeini, Simon Gröblacher, Jeff T. Hill et al.     Quantum fluctuations of a laser are transferred onto the motion of a mechanical resonator and interfere with the fluctuations of the light reflected from the resonator, leading to 'squeezed' light with optical noise suppressed below the standard quantum limit.             Insolation-driven 100,000-year glacial cycles and hysteresis of ice-sheet volume ▶     Ayako Abe-Ouchi, Fuyuki Saito, Kenji Kawamura et al.     Comprehensive climate and ice-sheet models show that insolation and internal feedbacks between the climate, the ice sheets and the lithosphere–asthenosphere system explain the 100,000-year period on which the Northern Hemisphere ice sheets grow and shrink.             News & Views                   Solar system: Saturn's tides control Enceladus' plume ▶     John Spencer             Research Highlights                   Astronomy: Heavy-metal stars make lead clouds         NEWS & COMMENT           Squeezed light mutes quantum noise | Exotic optics: Metamaterial world | Spin rate of black holes pinned down             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Articles and Letters                   An observed correlation between plume activity and tidal stresses on Enceladus ▶     M. M. Hedman, C. M. Gosmeyer, P. D. Nicholson et al.     The plume at the south pole of Enceladus is several times brighter when that moon is near the apocentre of its eccentric orbit around Saturn than when it is near its orbital pericentre, showing that more material appears to be escaping from beneath Enceladus' surface at times when models predict its fissures should be under tension.             Insolation-driven 100,000-year glacial cycles and hysteresis of ice-sheet volume ▶     Ayako Abe-Ouchi, Fuyuki Saito, Kenji Kawamura et al.     Comprehensive climate and ice-sheet models show that insolation and internal feedbacks between the climate, the ice sheets and the lithosphere–asthenosphere system explain the 100,000-year period on which the Northern Hemisphere ice sheets grow and shrink.             Nitrogen losses in anoxic marine sediments driven by Thioploca–anammox bacterial consortia ▶     M. G. Prokopenko, M. B. Hirst, L. De Brabandere et al.     A novel symbiotic consortium is described between two chemolithotrophic bacteria — anaerobic ammonium-oxidizing (anammox) bacteria and the nitrate-sequestering sulphur-oxidizing Thioploca species — in anoxic sediments of the Soledad basin at the Mexican Pacific margin.             News & Views                   Solar system: Saturn's tides control Enceladus' plume ▶     John Spencer             Climate science: Solution proposed for ice-age mystery ▶     Shawn J. Marshall             Research Highlights                   Environmental sciences: Ships acidify oceans         NEWS & COMMENT           Climate science: A line in the sands | Energy policy: A low-carbon road map for China             More Earth & Environmental Sciences ▶                 Nature proudly sponsors the Imagine Science Film Awards Where science meets cinema   Submit your film and compete for the $2,500 Nature Scientific Merit Award and the $1,000 Nature Audience Award www.imaginesciencefilms.org/festival/submit-your-film/         Careers & Jobs ▲top               Data-sharing: Everything on display ▶     Researchers can get visibility and connections by putting their data online — if they go about it in the right way.                   Turning point: Kevin Gurney ▶     Researcher's interest in climate change gets him into international policy negotiation.             Careers related news & comment                   Handle with care | Balancing privacy with public benefit Martin Bobrow | Seven days: 2–8 August 2013 | Deal done over HeLa cell line Ewen Callaway | Climate science: A line in the sands Jeff Tollefson | Best way to kill lab animals sought Daniel Cressey               naturejobs.com Science jobs of the week       Postdoctoral Research Fellow     Tulane University Health Sciences Center            Postdoctoral Research Associate     University of Oxford (Department of Biochemistry)            PhD Position     Heidelberg University, Institute of Physiology and Pathophysiology            Biostatistician     Medical Research Council          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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