Nature contents: 28 November 2013

Can't view this email? Click here to view in your browser.     Volume 503 Number 7477      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.               Speed. Resolution. Clarity. Accuracy. The Hamamatsu NanoZoomer Series delivers all of this and more. The ultimate digital whole-slide scanner and virtual microscopy tool, the NanoZoomer delivers reliable, robust scanning 24/7/365 at the touch of a button. Outstanding features include high sensitivity, fast scanning, flexible fluorescence capabilities, and a Z-stack feature to accommodate thicker tissue samples.       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 ▼   Potential for spin-based information processing in a thin-film molecular semiconductor   Spintronics devices, which exploit the intrinsic spin of electrons as well as their charge, require precise control and read-out of electron spins. For organic semiconductors to find use in spintronic applications, it is desirable to find molecules with long spin relaxation times. This study identifies copper phthalocyanine, a blue dye used in paints and dyes, as one such molecule. It is inexpensive and can be easily processed into a thin-film form of the type used for device fabrication, making it a candidate for spin-based quantum information processing and other spintronic applications.       Earth & Environmental Sciences More Earth & Environmental sciences ▼   Origin and age of the earliest Martian crust from meteorite NWA7533   The NWA 7533 meteorite from Northwest Africa has been identified as the first sample of Martian highlands rock in the meteorite collection. Munir Humayun and co-authors show that NWA 7533 has a composition indicative of a highlands breccia. It also contains zircons more than 4.4 billion years old, implying that early crustal differentiation on Mars occurred in the first 100 million years of its history, at the same time as crust formation on the Moon and the Earth.       Biological Sciences More Biological sciences ▼   Self-reinforcing impacts of plant invasions   Invasive plants can transform ecosystem function to the detriment of species originally in place. But what happens if the invasive species is eradicated — can ousted plants carry on as if nothing has heppened? Stephanie Yelenik and Carla D'Antonio returned to grass-invaded fields in Hawai'i Volcanoes National Park to study invader impacts replicated more that two decades on. The invasive grass had altered nitrogen mineralization levels but decades later the ecosystem had returned to a pre-invasion state. But the new conditions did not allow native re-establishment. Instead, a new invader thrived — the nitrogen-fixing tree Morella faya.           Eppendorf Award Winner 2013 In 2013 the prize was awarded to Ben Lehner, ICREA Research Professor, EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation, Barcelona, Spain. More about his research at http://corporate.eppendorf.com/en/company/scientific-awards/european-award/2013-award-winner/ If you want to apply for the Eppendorf Award 2014, click here           Podcast & Video     In this week's podcast: how the mind talks to the body, a new way to explore the structure of complex molecules, and the Collider exhibition at London's Science Museum.         News & Comment Read daily news coverage▶ ▲top               THIS WEEK           Editorials                   Nailing fingerprints in the stars ▶     Laboratory-based experiments are sorely needed to complement the rapidly proliferating spectral data originating from observations by the latest space telescopes.             The DIY dilemma ▶     Misconceptions about do-it-yourself biology mean that opportunities are being missed.             Enemy of the good ▶     Universities need to counter pressures that undermine support for younger researchers.             World View                   Football fever could be a dose of dengue ▶     Fans at next year's World Cup in Brazil may be exposed to a nasty and incurable tropical disease, warns Simon Hay.             Seven Days                   Seven days: 22–28 November 2013 ▶     The week in science: Two-time Nobel winner Frederick Sanger dies, volcano creates Japanese island, and Iran agrees to uranium limits.             NEWS IN FOCUS           China aims for the Moon ▶     Planned launch of lunar rover follows a string of triumphs for the country's space programme.             LHC plans for open data future ▶     Researchers share results to keep them accessible.             Project ranks billions of drug interactions ▶     Drugable.com predicts mechanisms through computation.             China battles army of invaders ▶     Raft of control measures slows the march of alien species.             Nations fight back on ivory ▶     Politicians take action on poaching in Africa as tusk seizures approach record numbers.             Features                   Research ethics: 3 ways to blow the whistle ▶     Reporting suspicions of scientific fraud is rarely easy, but some paths are more effective than others.             Immunology: The pursuit of happiness ▶     Researchers have struggled to identify how certain states of mind influence physical health. One biologist thinks he has an answer.             COMMENT           Security: Expand nuclear forensics ▶     Characterizing nuclear materials deters illicit trafficking and terrorism, but more scientists, techniques and collaborations are needed, says Klaus Mayer.             Technology: Sharing data in materials science ▶     Two years on from the launch of the US Materials Genome Initiative, five experts highlight how materials scientists still need to work differently.             Books and Arts                   Forensic science: Bringing out the dead ▶     Alison Abbott reviews the story of how a DNA forensics team cracked a grisly puzzle.             Physics: Overhearing Heisenberg ▶     Ann Finkbeiner ponders a script inspired by the 1945 internment of eminent German physicists in England.             Books in brief ▶             Particle physics: Smashing spectacle ▶     Zeeya Merali weighs up a simulated tour of the Large Hadron Collider.             Correspondence                   Mitigate damage risk from bush fires Katharine Haynes, Deanne Bird, John McAneney | Russian universities need change of tack Renad Zhdanov | Definition of maths genius is elusive Hutan Ashrafian | Greece's high CT scanning record Ioannis Seimenis, Stelios Argentos, Stathis Efstathopoulos | TB vaccine failure was predictable Peter Beverley             Obituary                   George Herbig (1920–2013) ▶     Astronomer who pioneered studies of young stars.             Correction                   Correction ▶               Biological Sciences ▲top             RESEARCH           Latest Online                   Stem cells: Dual response to Ras mutation ▶     S. Haihua Chu, Scott A. Armstrong             Cancer: Discrepancies in drug sensitivity ▶     John N. Weinstein, Philip L. Lorenzi             Structural basis for Ca2+ selectivity of a voltage-gated calcium channel ▶     Lin Tang, Tamer M. Gamal El-Din, Jian Payandeh et al.     X-ray crystal structures of a voltage-gated Na+ channel mutated to be highly Ca2+ selective provide a framework for understanding the mechanisms of ion selectivity and conductance in vertebrate voltage-gated Ca2+ channels.             Astrocytes mediate synapse elimination through MEGF10 and MERTK pathways ▶     Won-Suk Chung, Laura E. Clarke, Gordon X. Wang et al.     This study describes comprehensive synaptic engulfment by astrocytes, mediating synapse elimination in an activity-dependent manner; this elimination process involves the MEGF10 and MERTK phagocytic pathways and persists into adulthood, with mutant mice that lack these pathways in astrocytes exhibiting a failure to refine retinogeniculate connections during development.             Targeting Plasmodium PI(4)K to eliminate malaria ▶     Case W. McNamara, Marcus C. S. Lee, Chek Shik Lim et al.     The lipid kinase phosphatidylinositol-4-OH kinase (PI(4)K) is identified as a target of the imidazopyrazines, a new antimalarial compound class that can inhibit several Plasmodium species at each stage of the parasite life cycle; the imidazopyrazines exert their inhibitory action by interacting with the ATP-binding pocket of PI(4)K.             N6-methyladenosine-dependent regulation of messenger RNA stability ▶     Xiao Wang, Zhike Lu, Adrian Gomez et al.     The mRNAs of higher eukaryotes are extensively modified internally with N6-methyladenosine, but the specific functional role of this modification has been unclear; here this modification on mRNA is shown to be recognized by several proteins, the modification and its recognition serve to regulate the RNA's lifetime.             High-content genome-wide RNAi screens identify regulators of parkin upstream of mitophagy ▶     Samuel A. Hasson, Lesley A. Kane, Koji Yamano et al.     Mitophagy is the elimination of damaged mitochondria by the autophagosome regulated by the ubiquitin ligase, parkin and the kinase PINK1; a genome-wide RNAi screen with high-content microscopy has identified new genes that have an upstream role in parkin translocation to the mitochondria.             In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features ▶     Yiliang Ding, Yin Tang, Chun Kit Kwok et al.     RNA adopts vast and complicated secondary structures in the living cell; reported here is a new approach, structure-seq, that characterises RNA structure in vivo on a genome-wide scale at nucleotide resolution and should be applicable to any organism.             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.             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.             Oncogenic Nras has bimodal effects on stem cells that sustainably increase competitiveness ▶     Qing Li, Natacha Bohin, Tiffany Wen et al.     Oncogenic Nras in mouse haematopoietic stem cells can increase the probability of cell division in some cells and decrease it in others; this bimodal activity explains how this single pre-leukaemic mutation can increase proliferation without reducing competitiveness by clonally expanding the rapidly dividing cell population and also promoting long-term self-renewal of stem cells.             Mutational and fitness landscapes of an RNA virus revealed through population sequencing ▶     Ashley Acevedo, Leonid Brodsky, Raul Andino     A new approach to accurately determine mutation frequencies with RNA virus populations called circular sequencing (CirSeq) has been developed; a study of the genetic composition of populations of poliovirus shows the fitness landscape for each nucleotide variant in an evolving RNA virus.             Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity ▶     John W. Schoggins, Donna A. MacDuff, Naoko Imanaka et al.     The specificity of interferon effectors across an expanded range of viruses is studied, with results indicating that positive-sense single-stranded RNA viruses are more susceptible to interferon-stimulated gene activity than negative-sense RNA or DNA viruses; in addition, the DNA sensor cGAS is shown to have an unappreciated role in RNA virus inhibition.             Inconsistency in large pharmacogenomic studies ▶     Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai Juul Birkbak et al.     This Analysis compares two large-scale pharmacogenomic data sets that catalogued the sensitivity of a large number of cancer cell lines to approved and potential drugs, and finds that whereas the gene expression data are largely concordant between the two studies, the reported drug sensitivity measures and subsequently their association with genomic features are highly discordant.             Articles and Letters                   Memory and modularity in cell-fate decision making ▶     Thomas M. Norman, Nathan D. Lord, Johan Paulsson et al.     This study shows that Bacillus subtilis switches from a solitary, motile lifestyle to a multicellular, sessile state in a random, memoryless fashion, but that the underlying gene network is buffered against its own stochastic variation to tightly time the reverse transition; thus bacteria keep track of time to force their progeny to cooperate during the earliest stage of multicellular growth.             Effect of natural genetic variation on enhancer selection and function ▶     S. Heinz, C. E. Romanoski, C. Benner et al.     Naturally occurring genetic variation between inbred mouse strains is used as a mutagenesis strategy to investigate mechanisms responsible for the selection and function of cis-regulatory elements in macrophages; lineage-determining transcription factors are proposed to select enhancer-like regions in the genome in a collaborative fashion and facilitate the binding of signal-dependent factors.             A small-molecule AdipoR agonist for type 2 diabetes and short life in obesity ▶     Miki Okada-Iwabu, Toshimasa Yamauchi, Masato Iwabu et al.     An orally active small molecule, AdipRon, that binds to and activates both adiponectin receptors (AdipoR1 and AdipoR2) is identified; it ameliorates diabetes in mice on a high-fat diet and in genetically obese db/db mice, and if this can be extrapolated to humans, orally active agonists such as AdipoRon are a promising new approach to treat obesity-related diseases such as type 2 diabetes.             Self-reinforcing impacts of plant invasions change over time ▶     Stephanie G. Yelenik, Carla M. D'Antonio     Plant invasions are thought to alter the ecosystem in a way that disadvantages the native species, making re-establishment after eradication difficult; here, on returning to a site at which an invasive plant altered nitrogen-mineralization levels several decades ago, mineralization is found to have returned to pre-invasion levels, although these new conditions favour new invaders over the natives.             Cortical interneurons that specialize in disinhibitory control ▶     Hyun-Jae Pi, Balázs Hangya, Duda Kvitsiani et al.     Cortical inhibitory interneurons expressing vasoactive intestinal polypeptide (VIP) are shown to specialize in suppressing the activity of other inhibitory interneurons and are activated by reinforcement signals, thus increasing the activity of excitatory neurons by releasing them from inhibition; these results reveal a cell-type-specific microcircuit that tunes cortical activity under certain behavioural conditions.             Differential L1 regulation in pluripotent stem cells of humans and apes ▶     Maria C. N. Marchetto, Iñigo Narvaiza, Ahmet M. Denli et al.     Induced pluripotent stem-cell characterization reveals phenotypical differences between humans and non-human primates (NHPs): gene expression analysis shows differences in the regulation of long interspersed element-1 (L1) transposons, and in the expression of L1-restricting genes APOBEC3B and PIWIL2, correlating with higher L1 mobility in NHPs; this indicates that L1 mobility differences may have differentially shaped the human and NHP genomes.             Cell intrinsic immunity spreads to bystander cells via the intercellular transfer of cGAMP ▶     Andrea Ablasser, Jonathan L. Schmid-Burgk, Inga Hemmerling et al.     The cytoplasmic DNA receptor cGAS catalyses the synthesis of the second messenger cGAMP, which in turn activates type I interferon via STING; this study shows that cGAMP is transmitted to neighbouring cells via gap junction channels and activates STING, thus inducing an antiviral state in these bystander cells independent of paracrine interferon signalling.             Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor ▶     Xing-Yi Ge, Jia-Lu Li, Xing-Lou Yang et al.     Whole-genome sequences of two novel SARS-CoV-related bat coronaviruses, in addition to a live isolate of a bat SARS-like coronavirus, are reported; the live isolate can infect human cells using ACE2, providing the strongest evidence to date that Chinese horseshoe bats are natural reservoirs of SARS-CoV.             Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit ▶     Yaser Hashem, Amedee des Georges, Vidya Dhote et al.     A sub-nanometre reconstruction of a 40S complex containing eIF3 and a hepatitis C virus (HCV)-like internal ribosome entry site (IRES) shows that the IRES displaces eIF3 from the 40S and sequesters it to gain access to the 40S subunit.             Accelerated growth in the absence of DNA replication origins ▶     Michelle Hawkins, Sunir Malla, Martin J. Blythe et al.     When all origins of replication are deleted from the archaeon Haloferax volcanii, homologous recombination is used to initiate DNA replication and the growth rate is accelerated.             K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions ▶     Jonathan M. Ostrem, Ulf Peters, Martin L. Sos et al.     Small molecules are developed that irreversibly bind to the common G12C mutant of K-Ras but not the wild-type protein; crystallographic studies reveal the formation of an allosteric pocket that is not apparent in previous Ras studies, and the small molecules shift the affinity of K-Ras to favour GDP over GTP.             Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement ▶     Robin Teufel, Akimasa Miyanaga, Quentin Michaudel et al.     Structural and functional studies reveal how the bacterial flavoenzyme EncM catalyses the oxygenation–dehydrogenation dual oxidation of a highly reactive substrate, and show that EncM maintains a stable flavin oxygenating species that promotes substrate oxidation and triggers a rarely seen Favorskii-type rearrangement.             News & Views                   Ecology: A leak in the loop ▶     Katharine N. Suding             Drug discovery: Pocket of opportunity ▶     Gideon Bollag, Chao Zhang             Systems biology: How bacteria choose a lifestyle ▶     James C. W. Locke             Molecular biology: Antibiotic re-frames decoding ▶     John F. Atkins, Pavel V. Baranov             Stem cells: Dual response to Ras mutation ▶     S. Haihua Chu, Scott A. Armstrong             Cancer: Discrepancies in drug sensitivity ▶     John N. Weinstein, Philip L. Lorenzi             Corrigendum                   Corrigendum: Membrane potential dynamics of grid cells ▶     Cristina Domnisoru, Amina A. Kinkhabwala, David W. Tank             Retraction                   Retraction: Dance reveals symmetry especially in young men ▶     William M. Brown, Lee Cronk, Keith Grochow et al.             Research Highlights                   Pharmacology: Painkiller kills the bad effects of pot | Palaeoecology: Dung reveals goats' last days | Neuroscience: Satiety signal from the mouth | Virology: A more predictable flu | Ecology: Mother frogs arm their tadpoles | Physiology: Smells maintain blood cells         NEWS & COMMENT           Football fever could be a dose of dengue | China battles army of invaders | Immunology: The pursuit of happiness | Forensic science: Bringing out the dead | Books in brief | Definition of maths genius is elusive | Greece's high CT scanning record | TB vaccine failure was predictable | The DIY dilemma | Project ranks billions of drug interactions | Nations fight back on ivory             More Biological Sciences ▶                 Nature Medicine and Eli Lilly and Company present: Shifting Paradigms on Alzheimer's Disease December 3, 2013 Lilly Corporate Center, Indianapolis, IN, USA   Click here to register for this symposium today!         Chemical Sciences ▲top             RESEARCH           Latest Online                   DNA-mediated nanoparticle crystallization into Wulff polyhedra ▶     Evelyn Auyeung, Ting I. N. G. Li, Andrew J. Senesi et al.     Very slow cooling, over several days, of solutions of complementary-DNA-modified nanoparticles through the melting temperature of the system produces nanoparticle assemblies with the Wulff equilibrium crystal structure, thus showing that DNA hybridization can direct nanoparticle assembly along a pathway that mimics atomic crystallization.             Research Highlights                   Organic chemistry: Fast and easy fluorine fix         NEWS & COMMENT           Security: Expand nuclear forensics             More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   DNA-mediated nanoparticle crystallization into Wulff polyhedra ▶     Evelyn Auyeung, Ting I. N. G. Li, Andrew J. Senesi et al.     Very slow cooling, over several days, of solutions of complementary-DNA-modified nanoparticles through the melting temperature of the system produces nanoparticle assemblies with the Wulff equilibrium crystal structure, thus showing that DNA hybridization can direct nanoparticle assembly along a pathway that mimics atomic crystallization.             Dissipative production of a maximally entangled steady state of two quantum bits ▶     Y. Lin, J. P. Gaebler, F. Reiter et al.     Engineered dissipation is used to deterministically produce and stabilize entanglement between two trapped-ion quantum bits, independently of their initial states; the entanglement is stabilized even in the presence of experimental noise and decoherence.             Autonomously stabilized entanglement between two superconducting quantum bits ▶     S. Shankar, M. Hatridge, Z. Leghtas et al.     An entangled Bell state of two superconducting quantum bits can be stabilized for an arbitrary time using an autonomous feedback scheme, that is, one that does not require a complicated external error-correcting feedback loop.             Articles and Letters                   Puzzling accretion onto a black hole in the ultraluminous X-ray source M 101 ULX-1 ▶     Ji-Feng Liu, Joel N. Bregman, Yu Bai et al.     The ultraluminous X-ray source M 101 ULX-1 consists of a black hole orbiting a Wolf-Rayet star; optical spectroscopy now shows that the orbital period is 8.2 days, suggesting that the black hole has a mass in the range 5 to 30 solar masses, though the X-ray spectra are unlike what is expected from accretion onto a stellar-mass black hole—accretion must occur from captured stellar wind, which has hitherto been thought to be so inefficient that it could not power an ultraluminous source.             Potential for spin-based information processing in a thin-film molecular semiconductor ▶     Marc Warner, Salahud Din, Igor S. Tupitsyn et al.     The characteristic relaxation and dephasing times of the electronic spins in thin-film copper phthalocyanine are long enough that this common, low-cost organic semiconductor has potential for both quantum and classical information processing.             Perovskite oxides for visible-light-absorbing ferroelectric and photovoltaic materials ▶     Ilya Grinberg, D. Vincent West, Maria Torres et al.     Most known ferroelectric photovoltaic materials have very wide electronic bandgaps (that is, they absorb only high-energy photons) but here a family of perovskite oxides is described that have tunable bandgaps, allowing their use across the whole visible-light spectrum.             News & Views                   Astrophysics: Exception tests the rules ▶     K. D. Kuntz             Research Highlights                   Organic chemistry: Fast and easy fluorine fix | Physics: Pinch of salt makes for bumpy icicles         NEWS & COMMENT           Nailing fingerprints in the stars | Security: Expand nuclear forensics | Technology: Sharing data in materials science | George Herbig (1920–2013) | Physics: Overhearing Heisenberg | Books in brief | Particle physics: Smashing spectacle | Definition of maths genius is elusive | LHC plans for open data future             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Articles and Letters                   Origin and age of the earliest Martian crust from meteorite NWA 7533 ▶     M. Humayun, A. Nemchin, B. Zanda et al.     Chemical analysis of the meteorite NWA 7533 indicates that it may be a Martian regolith breccia and, if so, that the crust of Mars may have formed in the first 100 million years of the planet's history.             News & Views                   Ecology: A leak in the loop ▶     Katharine N. Suding             Planetary science: A chunk of ancient Mars ▶     Harry Y. McSween             Brief Communications Arising                   Does quadrupole stability imply LLSVP fixity? ▶     Maxwell L. Rudolph, Shijie Zhong             Conrad et al. reply ▶     Clinton P. Conrad, Bernhard Steinberger, Trond H. Torsvik             Research Highlights                   Climate sciences: Crusty alga uncovers sea-ice loss | Glaciology: Anatomy of an ice shelf's demise         NEWS & COMMENT           Mitigate damage risk from bush fires | China aims for the Moon | Nations fight back on ivory             More Earth & Environmental Sciences ▶                 Subscribe to Nature this Holiday season for only $50, £50 or €50   Enjoy 51 issues in print, online and multimedia content, and access via the nature.com app for iPhone, iPod touch and the new issue-based NatureJournals iPad app with enhanced features.   Subscribe today!          Careers & Jobs ▲top               Technology: Tools from scratch ▶     Three-dimensional printing can help researchers to design and build devices without breaking the bank.                   Awards: Guidance in adversity ▶     The Italian winners of this year's Nature mentoring awards found a way to inspire in a sometimes difficult funding environment.             Careers related news & comment                   Enemy of the good | Seven days: 22–28 November 2013 | Research ethics: 3 ways to blow the whistle Ed Yong, Heidi Ledford, Richard Van Noorden | Russian universities need change of tack Renad Zhdanov               naturejobs.com Science jobs of the week       Post Doctoral Research Assistant     University of Bristol            Research Associate     Loma Linda University (LLU)            PhD position     Molecular Oncology Department, University of Goettingen            Postdoctoral Researchers     International Institute for Applied Systems Analysis (IIASA)          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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