nature

THIS WEEK

Editorials

All together now ▶

Proposals to bring hydrofluorocarbons under the auspices of the Montreal Protocol provide a simple test of the international community’s commitment to tackling climate change.

Time to talk ▶

Online discussion is an essential aspect of the post-publication review of findings.

Playful paradoxes ▶

A half-century of Doctor Who has shown the dramatic possibilities of science in the arts.

World View

Science’s rightful place is in service of society ▶

Science policy must concentrate less on how much money is spent, and more on how to translate investments into public good, says Daniel Sarewitz.

Seven Days

Seven days: 25–31 October 2013 ▶

The week in science: PubMed pilots online commenting, NASA laser communications set speed record, and Greenland lifts ban on uranium mining.

NEWS IN FOCUS

Polio risk looms over Europe ▶

Cases in Syria highlight vulnerability of nearby countries to the viral disease.

Root of maths genius sought ▶

Entrepreneur’s ‘Project Einstein’ taps 400 top academics for their DNA.

Black holes shrink but endure ▶

Theorist’s idea takes on information-preservation problem.

Lightning network tested out in Guinea ▶

Project to forecast African storms provides cheap alternative to radar-based weather services.

Astronomers revisit dwarf stars’ promise ▶

Kepler data spur searches for habitable planets around small, low-temperature stars.

Farmers dig into soil quality ▶

Analytical technique promises to match fertilizers to soil in bid to boost yields in Africa.

Feature

Astronomy: Southern star ▶

Can the Southern African Large Telescope live up to its potential?

Ecology: Lady of the lakes ▶

Diane Orihel set her PhD aside to lead a massive protest when Canada tried to shut down its unique Experimental Lakes Area.

COMMENT

Environment: Waste production must peak this century ▶

Without drastic action, population growth and urbanization will outpace waste reduction, warn Daniel Hoornweg, Perinaz Bhada-Tata and Chris Kennedy.

Climate change: Melting glaciers bring energy uncertainty ▶

Countries should work together to understand how the Himalayan thaw will affect hydroelectric energy, says Javaid R. Laghari.

Books and Arts

Physics: The time lord and fellow travellers ▶

As television's time-bending Doctor Who turns 50, Andrew Jaffe explores time travel in fiction and science.

Books in brief ▶

Psychology: The appetite for right ▶

John Whitfield explores two studies that take us from infant ethics to moral choices faced by adults in society.

Space science: Zero-gravity hero ▶

John Gilbey is gripped by the memoir of Chris Hadfield, a former International Space Station commander.

Correspondence

Anthropocene: keep the guard up Tim Caro | Anthropocene: action makes sense Daniel Simberloff, Piero Genovesi | IPCC: Climate panel is ripe for examination Mike Hulme, Martin Mahony | City trees: Urban greening needs better data Diane E. Pataki | Visual acuity: Bird vision offers sharp insight Damian Scarf

Obituary

David Hunter Hubel (1926–2013) ▶

Neuroscientist who helped to reveal how the brain processes visual information.

Correction

Correction ▶

RESEARCH

Latest Online

Evolutionary ecology: Novelty makes the heart grow fonder ▶

Jeffrey S. McKinnon, Maria R. Servedio

HIV: Antibodies advance the search for a cure ▶

Louis J. Picker, Steven G. Deeks

Psychology: Good and bad news on the adolescent brain ▶

Valerie F. Reyna

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.

Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys ▶

Dan H. Barouch, James B. Whitney, Brian Moldt et al.

Treatment of SHIV-infected monkeys with potent broadly neutralizing anti-HIV-1 monoclonal antibodies resulted in rapid control of viral replication in both peripheral blood and tissues; viral rebound was linked to decreasing antibody concentrations and not the generation of escape mutations, and setpoint viral load following viral rebound remained lower than the initial baseline viral load.

Dendritic spikes enhance stimulus selectivity in cortical neurons in vivo  ▶

Spencer L. Smith, Ikuko T. Smith, Tiago Branco et al.

Neuronal dendrites are not passive cables, but whether their excitability contributes to computation at the cell’s soma has been uncertain; by observing and interfering with dendritic ‘spikes’ during sensory stimulation, it is now shown that active dendritic processing enhances somatic orientation selectivity, a fundamental brain computation.

A directional switch of integrin signalling and a new anti-thrombotic strategy ▶

Bo Shen, Xiaojuan Zhao, Kelly A. O’Brien et al.

The direction of integrin signalling is found to be determined by the coordinated and opposing binding waves of talin and Gα₁₃ to the same region of the integrin β₃ cytoplasmic domain at mutually exclusive but distinct sites, and a potent new anti-thrombotic drug that does not cause bleeding is designed on the basis of these findings.

The nuclear receptor Rev-erbα controls circadian thermogenic plasticity ▶

Zachary Gerhart-Hines, Dan Feng, Matthew J. Emmett et al.

The nuclear receptor Rev-erbα, a powerful repressor of transcription, is shown to link circadian and thermogenic networks by regulating the function of brown adipose tissue.

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.

Structural basis for the modular recognition of single-stranded RNA by PPR proteins ▶

Ping Yin, Quanxiu Li, Chuangye Yan et al.

Although the roles of pentatricopeptide repeat (PPR) proteins in RNA metabolism are well characterised, the mechanism by which they recognise specific single-stranded (ss)RNAs remains ill-understood; here X-ray crystal structures of maize PPR10 in the presence and absence of ssRNA provide details of the PPR10–ssRNA interaction.

Staphylococcus δ-toxin induces allergic skin disease by activating mast cells ▶

Yuumi Nakamura, Jon Oscherwitz, Kemp B. Cease et al.

Staphylococcus aureus δ-toxin is an inducer of mast cell degranulation in mice and is important for promoting inflammatory skin disease.

Structure of LIMP-2 provides functional insights with implications for SR-BI and CD36 ▶

Dante Neculai, Michael Schwake, Mani Ravichandran et al.

These results reveal the first high-resolution structural analysis of LIMP-2 and, by homology modelling, the structure of SR-BI and CD36, members of the CD36 superfamily of scavenger receptor proteins.

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.

Mating advantage for rare males in wild guppy populations ▶

Kimberly A. Hughes, Anne E. Houde, Anna C. Price et al.

Manipulation of the frequency of naturally occurring colour patterns within replicate pools of fish at three sites shows that males with rare colour patterns have higher reproductive fitness, demonstrating negative frequency-dependent selection mediated by sexual selection.

High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation ▶

Matthew D. Simon, Stefan F. Pinter, Rui Fang et al.

During mammalian X-chromosome inactivation, the Xist long noncoding RNA coats the future inactive X chromosome and recruits polycomb repressive complex 2 to a nucleation site, but how Xist spreads silencing across the entire X chromosome is unclear; here high-resolution maps of Xist binding sites across the X chromosome are generated and show that Xist does not spread across the inactive X chromosome uniformly but in two steps, initially targeting gene-rich islands before later spreading to intervening gene-poor domains.

Derivation of novel human ground state naive pluripotent stem cells ▶

Ohad Gafni, Leehee Weinberger, Abed AlFatah Mansour et al.

It is known that human embryonic stem (ES) cells are more similar to mouse primed epiblast stem cells than to naive mouse ES cells; here culture conditions are determined that allow human ES and induced pluripotent stem cells to acquire a pluripotent state that retains growth characteristics highly similar to mouse naive ES cells, and competence in generating cross-species human-mouse embryonic chimaerism.

Antibody-mediated immunotherapy of macaques chronically infected with SHIV suppresses viraemia ▶

Masashi Shingai, Yoshiaki Nishimura, Florian Klein et al.

A new generation of broad and potent anti-HIV-1 monoclonal antibodies has recently been isolated; co-administration of two such antibodies is shown here to result in rapid and potent suppression of plasma viraemia in five chronically SHIV-infected macaques that lasts for several weeks.

Articles and Letters

Arteriolar niches maintain haematopoietic stem cell quiescence ▶

Yuya Kunisaki, Ingmar Bruns, Christoph Scheiermann et al.

Immunofluorescence imaging and computational modelling are used to study the spatial distribution of different cell types within the haematopoietic stem cell (HSC) niche; findings show that quiescent HSCs associate specifically with small arterioles that are preferentially found in the endosteal bone marrow and are essential in maintaining this quiescence.

Crystal structure of the 14-subunit RNA polymerase I ▶

Carlos Fernández-Tornero, María Moreno-Morcillo, Umar J. Rashid et al.

RNA polymerase (Pol) I transcribes ribosomal RNA that is critically required for ribosome assembly, and the enzyme is a major determinant of protein biosynthesis and cell growth; here the crystal structure of the complete 14-subunit Pol I from yeast is determined, providing insights into its unique architecture and the possible functional roles of its components.

RNA polymerase I structure and transcription regulation ▶

Christoph Engel, Sarah Sainsbury, Alan C. Cheung et al.

The crystal structure of the complete 14-subunit RNA polymerase (Pol) I from yeast is determined, providing insights into its unique architecture and the possible functional roles of its components.

Decoupling of soil nutrient cycles as a function of aridity in global drylands ▶

Manuel Delgado-Baquerizo, Fernando T. Maestre, Antonio Gallardo et al.

Soil samples collected from 224 dryland sites around the world show that aridity affects the concentration of organic carbon and total nitrogen differently from the concentration of inorganic phosphorus, suggesting that any predicted increase in aridity with climate change could uncouple the carbon, nitrogen and phosphorus cycles in drylands and negatively affect the services provided by these ecosystems.

DMSP biosynthesis by an animal and its role in coral thermal stress response ▶

Jean-Baptiste Raina, Dianne M. Tapiolas, Sylvain Forêt et al.

Until now, dimethylsulphoniopropionate (DMSP), an important component in the sulphur cycle, has been thought to be produced solely by algae and some plants; however, this study shows that the coral animal also produces DMSP, in addition to that produced by the coral’s algal symbiont, with potential implications for the sulphur cycle and its climatic consequences as corals and their symbionts are affected by global change.

Structural insight into magnetochrome-mediated magnetite biomineralization ▶

Marina I. Siponen, Pierre Legrand, Marc Widdrat et al.

The magnetosome-associated protein mamP is an iron oxidase that reveals a unique arrangement of a self-plugged PDZ domain fused to two magnetochrome domains, defining a new class of c-type cytochrome exclusively found in magnetotactic bacteria.

Single-molecule fluorescence probes dynamics of barrier crossing ▶

Hoi Sung Chung, William A. Eaton

Here the Kramers diffusion coefficient and free-energy barrier are characterized for the first time through single-molecule fluorescence measurements of the temperature- and viscosity-dependence of the transition path time for protein folding.

Photosynthetic entrainment of the Arabidopsis thaliana circadian clock ▶

Michael J. Haydon, Olga Mielczarek, Fiona C. Robertson et al.

In Arabidopsis thaliana, the rhythm of sugar production by photosynthesis sets the timing of the circadian clock, by regulating the expression of circadian clock genes.

Synthetic non-oxidative glycolysis enables complete carbon conservation ▶

Igor W. Bogorad, Tzu-Shyang Lin, James C. Liao

A non-oxidative, cyclic pathway—termed non-oxidative glycolysis—is designed and constructed that enables complete carbon conservation in sugar catabolism to acetyl-coenzyme A, and can be used to achieve a 100% carbon yield to fuels and chemicals.

Discovery of new enzymes and metabolic pathways by using structure and genome context ▶

Suwen Zhao, Ritesh Kumar, Ayano Sakai et al.

Pathway docking (in silico docking of metabolites to several enzymes and binding proteins in a metabolic pathway) enables the discovery of a catabolic pathway for the osmolyte trans-4-hydroxy-l-proline betaine.

Meiotic chromosome structures constrain and respond to designation of crossover sites ▶

Diana E. Libuda, Satoru Uzawa, Barbara J. Meyer et al.

Meiotic crossover regulation is proposed to operate as a self-limiting system in which meiotic chromosome structures create an environment that promotes crossovers, which in turn modify chromosome structures to inhibit crossover formation at additional neighbouring sites.

Visualizing virus assembly intermediates inside marine cyanobacteria ▶

Wei Dai, Caroline Fu, Desislava Raytcheva et al.

This study reports the first application of Zernike phase contrast (ZPC) electron cryo-tomography to examine cellular processes without the need for labelling or sectioning; the technique is used to visualize the maturation of the cyanophage Syn5 inside its host cell, identifying subcellular compartments and five distinct Syn5 assembly intermediates.

News & Views

Structural biology: Pivotal findings for a transcription machine ▶

Joost Zomerdijk

50 & 100 Years Ago ▶

Biophysics: Rough passage across a barrier ▶

Benjamin Schuler, Jane Clarke

Marine biology: Coral animals combat stress with sulphur ▶

Graham Jones

Evolutionary ecology: Novelty makes the heart grow fonder ▶

Jeffrey S. McKinnon, Maria R. Servedio

HIV: Antibodies advance the search for a cure ▶

Louis J. Picker, Steven G. Deeks

Psychology: Good and bad news on the adolescent brain ▶

Valerie F. Reyna

Research Highlights

Ecology: Hunting leads to a leap in lizards | Remote Sensing: Illicit gold rush in Peruvian Amazon | Cancer: Antibody creeps up on cancer | Neuroscience: Rats propelled by electric pulses | Evolution: Human ancestor had small thumbs | Virology: Not all dormant HIV is defective | Alzheimer's disease: Tau tangles exposed

NEWS & COMMENT

Books in brief | Psychology: The appetite for right | Anthropocene: keep the guard up | Anthropocene: action makes sense | David Hunter Hubel (1926–2013) | Polio risk looms over Europe | Root of maths genius sought | Ecology: Lady of the lakes

More Biological Sciences ▶

RESEARCH

Latest Online

Structural basis for the modular recognition of single-stranded RNA by PPR proteins ▶

Ping Yin, Quanxiu Li, Chuangye Yan et al.

Although the roles of pentatricopeptide repeat (PPR) proteins in RNA metabolism are well characterised, the mechanism by which they recognise specific single-stranded (ss)RNAs remains ill-understood; here X-ray crystal structures of maize PPR10 in the presence and absence of ssRNA provide details of the PPR10–ssRNA interaction.

Articles and Letters

Structural insight into magnetochrome-mediated magnetite biomineralization ▶

Marina I. Siponen, Pierre Legrand, Marc Widdrat et al.

The magnetosome-associated protein mamP is an iron oxidase that reveals a unique arrangement of a self-plugged PDZ domain fused to two magnetochrome domains, defining a new class of c-type cytochrome exclusively found in magnetotactic bacteria.

Single-molecule fluorescence probes dynamics of barrier crossing ▶

Hoi Sung Chung, William A. Eaton

Here the Kramers diffusion coefficient and free-energy barrier are characterized for the first time through single-molecule fluorescence measurements of the temperature- and viscosity-dependence of the transition path time for protein folding.

News & Views

Biophysics: Rough passage across a barrier ▶

Benjamin Schuler, Jane Clarke

NEWS & COMMENT

Climate change: Melting glaciers bring energy uncertainty

More Chemical Sciences ▶

RESEARCH

Latest Online

Extrasolar planets: An infernal Earth ▶

Drake Deming

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.

Structural basis for the modular recognition of single-stranded RNA by PPR proteins ▶

Ping Yin, Quanxiu Li, Chuangye Yan et al.

Although the roles of pentatricopeptide repeat (PPR) proteins in RNA metabolism are well characterised, the mechanism by which they recognise specific single-stranded (ss)RNAs remains ill-understood; here X-ray crystal structures of maize PPR10 in the presence and absence of ssRNA provide details of the PPR10–ssRNA interaction.

A rocky composition for an Earth-sized exoplanet ▶

Andrew W. Howard, Roberto Sanchis-Ojeda, Geoffrey W. Marcy et al.

Doppler spectroscopic measurements of the mass of the Earth-sized planet Kepler-78b reveal that its mean density is similar to Earth’s, suggesting a composition of rock and iron.

An Earth-sized planet with an Earth-like density ▶

Francesco Pepe, Andrew Collier Cameron, David W. Latham et al.

Data from the Kepler spacecraft and the HARPS-N ground-based spectrograph indicate that the extrasolar planet Kepler-78b has a mean density similar to that of Earth and imply that it is composed of rock and iron.

Articles and Letters

A uniform metal distribution in the intergalactic medium of the Perseus cluster of galaxies ▶

Norbert Werner, Ondrej Urban, Aurora Simionescu et al.

A uniform iron abundance in the intracluster gas of the Perseus cluster suggests that the metal enrichment of the intergalactic medium occurred before the cluster formed, probably more than ten billion years ago, rather than after the cluster formed.

Minimal-excitation states for electron quantum optics using levitons ▶

J. Dubois, T. Jullien, F. Portier et al.

Minimal-excitation fermionic quasiparticles are created by applying a potential with Lorentzian time dependence to the contact of a narrow constriction in a two-dimensional electron gas.

Coupling a single electron to a Bose–Einstein condensate ▶

Jonathan B. Balewski, Alexander T. Krupp, Anita Gaj et al.

A single electron in a defined orbital is found to interact with a quantum many-body system through electron–phonon coupling.

Structural insight into magnetochrome-mediated magnetite biomineralization ▶

Marina I. Siponen, Pierre Legrand, Marc Widdrat et al.

The magnetosome-associated protein mamP is an iron oxidase that reveals a unique arrangement of a self-plugged PDZ domain fused to two magnetochrome domains, defining a new class of c-type cytochrome exclusively found in magnetotactic bacteria.

Single-molecule fluorescence probes dynamics of barrier crossing ▶

Hoi Sung Chung, William A. Eaton

Here the Kramers diffusion coefficient and free-energy barrier are characterized for the first time through single-molecule fluorescence measurements of the temperature- and viscosity-dependence of the transition path time for protein folding.

News & Views

Quantum physics: Single electrons pop out of the Fermi sea ▶

Christian Flindt

50 & 100 Years Ago ▶

Biophysics: Rough passage across a barrier ▶

Benjamin Schuler, Jane Clarke

Extrasolar planets: An infernal Earth ▶

Drake Deming

Research Highlights

Materials science: Water sculptures crafted in oil

NEWS & COMMENT

Climate change: Melting glaciers bring energy uncertainty | Astronomy: Southern star | Physics: The time lord and fellow travellers | Books in brief | Space science: Zero-gravity hero | Visual acuity: Bird vision offers sharp insight | Root of maths genius sought | Black holes shrink but endure | Astronomers revisit dwarf stars’ promise

More Physical Sciences ▶

RESEARCH

Latest Online

Extrasolar planets: An infernal Earth ▶

Drake Deming

Articles and Letters

Gradual demise of a thin southern Laurentide ice sheet recorded by Mississippi drainage ▶

Andrew D. Wickert, Jerry X. Mitrovica, Carlie Williams et al.

Four reconstructions of North American ice-sheet history are tested using oxygen isotope records from the Gulf of Mexico in a water-mixing model; the one based on ice physics is the best match to the isotopic data and to the observed Last Glacial Maximum fall in sea level due to melting of the Laurentide ice sheet.

Decoupling of soil nutrient cycles as a function of aridity in global drylands ▶

Manuel Delgado-Baquerizo, Fernando T. Maestre, Antonio Gallardo et al.

Soil samples collected from 224 dryland sites around the world show that aridity affects the concentration of organic carbon and total nitrogen differently from the concentration of inorganic phosphorus, suggesting that any predicted increase in aridity with climate change could uncouple the carbon, nitrogen and phosphorus cycles in drylands and negatively affect the services provided by these ecosystems.

DMSP biosynthesis by an animal and its role in coral thermal stress response ▶

Jean-Baptiste Raina, Dianne M. Tapiolas, Sylvain Forêt et al.

Until now, dimethylsulphoniopropionate (DMSP), an important component in the sulphur cycle, has been thought to be produced solely by algae and some plants; however, this study shows that the coral animal also produces DMSP, in addition to that produced by the coral’s algal symbiont, with potential implications for the sulphur cycle and its climatic consequences as corals and their symbionts are affected by global change.

News & Views

Ecology: Drivers of decoupling in drylands ▶

David A. Wardle

Water management: The data gap ▶

Blanca Jiménez Cisneros

Marine biology: Coral animals combat stress with sulphur ▶

Graham Jones

Extrasolar planets: An infernal Earth ▶

Drake Deming

Research Highlights

Remote Sensing: Illicit gold rush in Peruvian Amazon | Climate science: Meandering winds precede heat spells | Planetary science: Why Martian craters are flat

NEWS & COMMENT

All together now | Environment: Waste production must peak this century | Climate change: Melting glaciers bring energy uncertainty | Astronomy: Southern star | Ecology: Lady of the lakes | Anthropocene: keep the guard up | Anthropocene: action makes sense | IPCC: Climate panel is ripe for examination | City trees: Urban greening needs better data | Lightning network tested out in Guinea

More Earth & Environmental Sciences ▶

Medical imaging ▶

Herb Brody

Scans: Enhanced medical vision ▶

The ability to look inside the human body without using a scalpel has revolutionized how we diagnose and treat illness and injury. By Brian Owens.

Alzheimer's disease: Mapping the brain's decline ▶

Imaging the brains of Alzheimer's patients provides insights into the way this insidious disease progresses.

Inflammation: A complex problem ▶

Multi-protein inflammasomes are being implicated in a surprising number of diseases, and researchers are keen to find out why.

Surgery: The eyes of the operation ▶

Real-time imaging of a patient's body is guiding surgeons and radiologists past healthy tissue to the diseased cells.

Technology: Multiple exposure ▶

Combining imaging techniques can provide a wealth of information about disease.

Software: The computer will see you now ▶

From image-analysis software to lens-free microscopes that fit on a mobile phone, new tools are providing pathologists with clearer and more informative images.

Perspective: The big picture ▶

Many medical images are used once then filed away. This trove of clinical data should be made available to biomedical researchers, says Alan Moody.

Next-generation scans: Seeing into the future ▶

From magnetically tagged sugar to smoke-sensing surgical knives and beams of high-energy protons, the next wave of imaging technologies will provide a clearer view of the body.

Sponsors

Europe: Swedish success story ▶

Institutions shake off rivalries to build scientific collaborations and hire world-class talent.

Turning point: Mark Matthews ▶

Former English teacher pursues app development to help patients with mental illness.

Mobility disincentive ▶

Switching institutions or research groups can delay tenure.

Inaccurate predictions ▶

Peer review fails at predicting success.

Real-time online advice ▶

Online portal coaches prospective postgraduates on study programmes in Europe.

Careers related news & comment

Time to talk | Science’s rightful place is in service of society Daniel Sarewitz | Seven days: 25–31 October 2013 | Space science: Zero-gravity hero John Gilbey

Research Technician

University of Essex 

Postdoctoral Scholar

University of California, Irvine 

PhD or Postdoc position

TU Dresden 

Post Doctoral Position

Institut Pasteur, Paris 

Diet, gut microbiology and human health

11.12.13 London, UK