Wednesday, December 16, 2015

Nature contents: 17 December 2015

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  journal cover  
Nature Volume 528 Issue 7582
 
This Week  
 
 
Editorials  
 
 
 
A seismic shift
After 25 years of divisive debate, the governments of the world unite in Paris to fight global warming. But the hard work must start now.
Crop conundrum
The EU should decide definitively whether gene-edited plants are covered by GM laws.
Science for peace
The German research community can benefit from the influx of migrants.
 
 
AIMResearch - Highlighting research from the Advanced Institute for Materials Research (AIMR) in Japan, which promotes mathematics-materials science collaboration
Latest highlight: Metallic glasses: Thermal cycling is the secret to eternal youth
In the spotlight: International workshop: Taking spintronics for a spin
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World View  
 
 
 
Use data to challenge mental-health stigma
Web surveys of attitudes towards mental illness reveal the size of the problem — and offer a way to find fixes, says Neil Seeman.
 
Seven Days  
 
 
 
The week in science: 11–17 December 2015
Fusion machine fires up; chemicals mega-merger; and AIDS funding is cut.
Research Highlights  
 
 
 
Environmental science: Ocean plastic piling up fast | Astrophysics: Cosmic boost reveals dim galaxy | Genomics: Missed mutations in cancer genomes | Geophysics: Rising sea levels alter Earth's spin | Astronomy: Galaxies caught in cosmic web | Ocean science: Possible pause in Arctic sea-ice loss | Evolution: How birds spread around the globe | Materials: Electrons dance in pulled graphene | Developmental biology: Mini Fallopian tubes in a dish
Social Selection
What's in a journal name?
 
 

Nature Genetics and Nature Reviews Cancer present:

NUCLEAR REPROGRAMMING AND THE CANCER GENOME 2016
Sponsored by CapitalBio Corporation

February 21-23, 2016 | La Jolla, CA, USA
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News in Focus
 
Nations approve historic global climate accord
Agreement forged in Paris aims to hold warming 'well below' 2 °C.
Jeff Tollefson, Kenneth R. Weiss
  Cancer studies clash over mechanisms of malignancy
Debate surrounds relative importance of environmental and intrinsic factors.
Heidi Ledford
Yellow Sea talks raise hopes for marine science
Negotiations between South Korea and China to demarcate boundary could aid research.
Mark Zastrow
  Europe's genetically edited plants stuck in legal limbo
Scientists frustrated at delay in deciding if GM regulations apply to precision gene editing.
Alison Abbott
German researchers pledge help in refugee crisis
Social scientists launch integration studies and warn of need to counter rising xenophobia.
Quirin Schiermeier
 
Features  
 
 
 
The science myths that will not die
False beliefs and wishful thinking about the human experience are common. They are hurting people — and holding back science.
Megan Scudellari
Correction  
 
 
Correction
 
 
Comment
 
Chemistry: Why synthesize?
Philip Ball ponders the many reasons that chemists make molecules, and weighs what is lost, and gained, when they don't.
Philip Ball
Books and Arts  
 
 
 
Urban studies: Blueprint for a cooperative city
Colin Ellard examines a study of the new urban paradigm that fosters 'deep sharing'.
Colin Ellard
Books in brief
Barbara Kiser reviews five of the week's best science picks.
Barbara Kiser
Science communication: In the cross hairs of controversy
Nancy Baron reviews a handbook for scientists keen to influence policy.
Nancy Baron
Correspondence  
 
 
 
Authorship: Archives and citation miss equal authors
Brian D. Brown, Miriam Merad
  Disaster management: Design buildings for rapid evacuation
Enrico Ronchi
Training: Common doctorates across Europe
Stefan U. Hardt, Jannis Papazoglou, Benedikt W. Pelzer
  Innovation: Clean energy enters virtuous cycle
Jessika E. Trancik
Clinical trials: Crowdfunded trials doubly scrutinized
David Hawkes, Melanie Thomson
 
 
 
Specials
 
Outlook: Prostate Cancer  
 
 
 
Prostate cancer
Herb Brody
  Small organ, big reach
Richard Hodson
Screening: Diagnostic dilemma
Emily Sohn
  Perspective: Enforce the clinical guidelines
Monique Roobol
Prognosis: Proportionate response
Sarah Deweerdt
  Treatment: When less is more
Meredith Wadman
Metastasis: Resistance fighters
Neil Savage
  Microbiology: Inflammatory evidence
Kirsten Weir
Q&A: Declan Murphy
Bianca Nogrady
  Therapy: An immune one–two punch
Katherine Bourzac
Prostate cancer: 4 big questions
Richard Hodson
 
Sponsor

Produced with support from Ferring Pharmaceuticals and a grant from Astellas Pharma Global Development, Inc. and Medivation, Inc.

Nature Index 2015 China  
 
 
 
Nature Index 2015 China
Karen McGhee, Nicky Phillips
Building a powerhouse
Larissa Kogleck
The rapid rise of a research nation
China's economic boom is mirrored by its similarly meteoric rise in high-quality science.
Yingying Zhou
Three giants tighten their grip
The benefits of economics and history converge with the demands of population growth and sustainability issues in China's most productive research and technology centres.
Peng Tian
At the very heart of progress
The ambition driving China's astonishing progress in the output of high-quality science is particularly strong in some cities, whose growth far outstrips expectation.
Sarah O'Meara
The changing face of industry
Amid fierce international competitiveness, governments at all levels are responding by orchestrating collaborations between industry and academic institutions.
David Cyranoski
Alliances for scientific success
The diverse histories of China's cities strongly influence their collaboration patterns.
Hepeng Jia
A guide to the Nature Index
A description of the terminology and methodology used in this supplement, and a guide to the functionality available free online at natureindex.com.
Nature Index China tables
China's leading institutions for high-quality science, ordered by weighted fractional count (WFC) for 2014. Also shown are the total number of articles, and the change in WFC from 2013.
 
 
Research
 
NEW ONLINE  
 
 
 
Ecology: Different worlds
Patterns of species association reveal that terrestrial plant and animal communities today are structured differently from communities spanning the 300 million years that preceded large-scale human activity.
Substantial contribution of extrinsic risk factors to cancer development
Recent analyses have suggested that the intrinsic behaviour of tissue stem cells may be responsible for malignant transformation and cancer progression, raising questions regarding the influence of extrinsic factors on tumorigenesis; here, both data-driven and model-driven evidence show that such intrinsic risk factors contribute only marginally to cancer development, indicating that cancer risk is heavily influenced by extrinsic factors.
DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions
The ability of the DEAD-box RNA helicase DDX5 to interact with master transcription factor RORγt is dependent on binding of the long noncoding RNA Rmrp; the DDX5–RORγt complex coordinates transcription of selective TH17 genes and is required for the pathogenicity of TH17 cells.
Network-analysis-guided synthesis of weisaconitine D and liljestrandinine
Network analysis to determine the maximally bridged ring (or rings) of molecules is used as part of a strategy for the syntheses of architecturally complex natural chemicals; this strategy is demonstrated via the synthesis of the diterpenoid alkaloids weisaconitine D and liljestrandinine.
A continuum from clear to cloudy hot-Jupiter exoplanets without primordial water depletion
A spectroscopic comparison of ten hot-Jupiter exoplanets reveals that the difference between the planetary radius measured at optical and infrared wavelengths allows atmosphere types ranging from clear to cloudy to be distinguished; the difference in radius at a given wavelength correlates with the spectral strength of water at that wavelength, suggesting that haze obscures the signal from water.
Tuft-cell-derived IL-25 regulates an intestinal ILC2–epithelial response circuit
Epithelial tuft cells are shown to be the source of intestinal interleukin (IL)-25 that is required for activation of type 2 innate lymphoid cells (ILC2s), ILC2-regulated tuft and goblet cell expansion, and control of parasite infection.
Exploring the repeat protein universe through computational protein design
In this study, 83 proteins containing helix–loop–helix–loop repeats were designed—with sequences unrelated to known repeat proteins—and experimentally characterized; 43 solution X-ray scattering spectra and 15 structures of the designed proteins show that these non-natural repeat proteins have a broad range of curvatures and that their overall structures are in close agreement with design models.
Rational design of α-helical tandem repeat proteins with closed architectures
The development and validation of computational methods for geometry-guided de novo design of tandem repeat protein architectures.
Exceptional preservation of tiny embryos documents seed dormancy in early angiosperms
The discovery of embryos and their associated nutrient storage tissues in exceptionally well-preserved angiosperm seeds from the Early Cretaceous period.
Holocene shifts in the assembly of plant and animal communities implicate human impacts
Plant and animal assemblage co-occurrence patterns have remained relatively consistent for 300 million years but have changed over the Holocene epoch as the impact of humans has dramatically increased.
Germline variant FGFR4  p.G388R exposes a membrane-proximal STAT3 binding site
A gain-of-function effect of the cancer-associated rs351855 single-nucleotide polymorphism encoding the FGFR4 Arg388 allele in humans.
Competition between DNA methylation and transcription factors determines binding of NRF1
The relationship between DNA methylation and transcription factor binding was studied across the genome in mouse embryonic stem cells-the study reveals that the transcription factor NRF1 is methylation-sensitive and how physiological binding of NRF1 relies on local removal of DNA methylation.
The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators
The FOXO transcription factor, DAF-16, is required for the long-life phenotype of daf-2 mutant nematode worms; here the authors find that daf-2 mutant worms maintain neuronal functions and behaviours with age by using a set of transcriptional targets that are distinct from previously identified canonical FOXO/DAF-16-regulated targets.
Corrigendum: Mapping tree density at a global scale
Corrigendum: Hallmarks of pluripotency
Corrigendum: Failure to replicate the STAP cell phenomenon
Corrigendum: Gigantism and comparative life-history parameters of tyrannosaurid dinosaurs
Corrigendum: Dinosaurian growth patterns and rapid avian growth rates
News and Views  
 
 
 
Biodiversity: Recovery as nitrogen declines
David Tilman, Forest Isbell
Quantum physics: Entanglement beyond identical ions
Tobias Schaetz
Reproducibility: Experimental mismatch in neural circuits
Thomas C. Südhof
 
Microbiomes: Curating communities from plants
Gwyn A. Beattie
 
Climate science: A history of Greenland's ice loss
Beata M. Csatho
50 & 100 Years Ago
 
In retrospect: Twenty-five years of thesex-determining gene
Jennifer A. Marshall Graves
Reviews  
 
 
 
Rarity in mass extinctions and the future of ecosystems
The fossil record provides a nuanced view of ecosystem collapse over intervals of mass extinction, with abundant, biomineralizing and widespread species preferentially preserved; here the authors collate evidence for 'mass rarity' during these intervals, and suggest that the increasing rarity of modern species, rather than their outright extinction, may be a better metric for comparing the current biodiversity crisis to the 'Big Five' mass extinctions in the Earth's history.
Pincelli M. Hull, Simon A. F. Darroch, Douglas H. Erwin
Articles  
 
 
 
Growth and splitting of neural sequences in songbird vocal development
Neural sequences recorded from the vocal premotor area HVC in juvenile birds learning song 'syllables' show 'prototype' syllables forming early, with multiple new highly divergent neural sequences emerging from this precursor syllable as learning progresses.
Tatsuo S. Okubo, Emily L. Mackevicius, Hannah L. Payne et al.
Acute off-target effects of neural circuit manipulations
Transient manipulation of neural activity is widely used to probe the function of specific circuits, yet such targeted perturbations could also have indirect effects on downstream circuits that implement separate and independent functions; a study to test this reveals that transient perturbations of specific circuits in mammals and songbirds severely impair learned skills that recover spontaneously after permanent lesions of the same brain areas.
Timothy M. Otchy, Steffen B. E. Wolff, Juliana Y. Rhee et al.
Functional overlap of the Arabidopsis leaf and root microbiota
The microbiota of the rhizosphere (roots) and phyllosphere (leaves) of healthy plants consist of taxonomically structured bacterial communities; here the majority of species representing the main bacterial phyla from these two organs were isolated and genomes of about 400 representative bacteria were sequenced; the resources of cultured bacteria, corresponding genomes and a gnotobiotic plant system enabled an examination of the taxonomic overlap and functional specialization between the rhizosphere and phyllosphere bacterial microbiota.
Yang Bai, Daniel B. Müller, Girish Srinivas et al.
Phosphorylation and linear ubiquitin direct A20 inhibition of inflammation
The authors define molecular mechanisms by which distinct domains of the ubiquitin editing enzyme A20 contribute to the regulation of inflammation and cell death.
Ingrid E. Wertz, Kim Newton, Dhaya Seshasayee et al.
Letters  
 
 
 
Multi-element logic gates for trapped-ion qubits
Harnessing the entanglement of different ionic species could bring new flexibility in quantum computing, and now two groups independently demonstrate entanglement between different atomic species; Tan et al. achieve entanglement between different elements, whereas the related paper by Ballance et al. shows entanglement between different atomic isotopes, together demonstrating a first step towards mixed-species quantum logic.
T. R. Tan, J. P. Gaebler, Y. Lin et al.
Self-shaping of oil droplets via the formation of intermediate rotator phases upon cooling
A mechanism for the repression of homologous recombination in G1, the stage of the cell cycle preceding replication, is determined; the critical aspects are the interaction between BRCA1 and PALB2–BRCA2, and suppression of DNA-end resection.
Nikolai Denkov, Slavka Tcholakova, Ivan Lesov et al.
A large-scale dynamo and magnetoturbulence in rapidly rotating core-collapse supernovae
Global, three-dimensional simulations of rapidly rotating massive stars show that turbulence driven by magnetohydrodynamic instability is a promising mechanism for the formation of pulsars and magnetars, the latter potentially powering hyperenergetic and superluminous supernovae.
Philipp Mösta, Christian D. Ott, David Radice et al.
Hybrid quantum logic and a test of Bell's inequality using two different atomic isotopes
Harnessing the entanglement of different ionic species could bring new flexibility in quantum computing, and now two groups independently demonstrate entanglement between different atomic species; Ballance et al. achieve entanglement between different atomic isotopes, whereas the related paper by Tan et al. shows entanglement between different elements, together demonstrating a first step towards mixed-species quantum logic.
C. J. Ballance, V. M. Schäfer, J. P. Home et al.
Radiative heat transfer in the extreme near field
Nanoscale radiative heat transfer between both dielectric and metal surfaces separated by gaps as small as two nanometres is characterized by large gap-dependent heat transfer enhancements that are accurately modelled by the theoretical framework of fluctuational electrodynamics and has important implications for technological design.
Kyeongtae Kim, Bai Song, Víctor Fernández-Hurtado et al.
Spatial and temporal distribution of mass loss from the Greenland Ice Sheet since AD 1900
Aerial imagery from the 1980s is used to calculate ice mass loss around the entire Greenland Ice Sheet from 1900 to the present; during the twentieth century the Greenland Ice Sheet contributed at least 25.0 ± 9.4 millimetres of global-mean sea level rise.
Kristian K. Kjeldsen, Niels J. Korsgaard, Anders A. Bjørk et al.
Grassland biodiversity bounces back from long-term nitrogen addition
Data from the long-running Park Grass Experiment is used to show that grassland biodiversity is recovering since UK atmospheric nitrogen levels started to decline 25 years ago in all but the most acidic soils.
J. Storkey, A. J. Macdonald, P. R. Poulton et al.
Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon
Age at maturity in Atlantic salmon (Salmo salar) is governed to a substantial extent by a locus showing dominance reversal, providing a resolution for sexual conflict in this trait, for which selection favours different ages in the two sexes.
Nicola J. Barson, Tutku Aykanat, Kjetil Hindar et al.
Repairing oxidized proteins in the bacterial envelope using respiratory chain electrons
The identification of an enzymatic system repairing proteins containing oxidized methionine in the bacterial cell envelope, a compartment particularly susceptible to oxidative damage by host defence mechanisms.
Alexandra Gennaris, Benjamin Ezraty, Camille Henry et al.
Neutrophils support lung colonization of metastasis-initiating breast cancer cells
Neutrophils are shown to have a role in driving the metastasis of breast cancer cells to the lung, with neutrophil-derived leukotrienes promoting metastatic initiation in the lung by expanding the sub-pool of cancer cells with high tumorigenic potential.
Stefanie K. Wculek, Ilaria Malanchi
Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism
A causal variant is identified at the LMO1 oncogene locus that drives the genetic association of LMO1 with neuroblastoma susceptibility; the causal SNP disrupts a GATA transcription factor binding site within a tissue-specific super-enhancer element in the first intron of LMO1, thereby affecting LMO1 expression.
Derek A. Oldridge, Andrew C. Wood, Nina Weichert-Leahey et al.
A mechanism for the suppression of homologous recombination in G1 cells
A mechanism for the repression of homologous recombination in G1, the stage of the cell cycle preceding replication, is determined; the critical aspects are the interaction between BRCA1 and PALB2–BRCA2, and suppression of DNA-end resection.
Alexandre Orthwein, Sylvie M. Noordermeer, Marcus D. Wilson et al.
 
 
Careers & Jobs
 
Feature  
 
 
 
Mentorship: Stewards of China's future
Ed Gerstner
Futures  
 
 
Citadel
How to survive the solstice.
John Gilbey
 
 
 
 
 

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