Wednesday, January 14, 2015

Nature contents: 15 January 2015

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  journal cover  
Nature Volume 517 Issue 7534
 
This Week  
 
 
Editorials  
 
 
 
Science and satire
The terrorist attacks in Paris were an assault on the fundamental values of free and democratic societies. Researchers, and humorists, must combat obscurantism everywhere.
Deep mysteries
Arguments among ocean scientists show how much remains to be discovered.
Out of the bag
The preference for either cats or dogs affects science more than you might think.
 
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World View  
 
 
 
The focus on bibliometrics makes papers less useful
Forcing research to fit the mould of high-impact journals weakens it. Hiring decisions should be based on merit, not impact factor, says Reinhard Werner.
 
Seven Days  
 
 
 
Seven days: 9–15 January 2015
The week in science: Trove of extinct animal bones found in underwater cave; influential leader of German science policy dies; and Japan approves massive stimulus package.
Research Highlights  
 
 
 
Animal behaviour: Monkey in the mirror | Microbiology: Gut microbes' survival tactics | Materials: Arsenic forms a semiconductor | Evolution: Lungs began with many chambers | Sustainability: Resource use peaks worldwide | Materials: Silicon buckles to form 3D shapes | Evolution: Mosquitoes gain resistance | Photonics: Few photons make 'ghost image' | Plant genetics: Maize's journey out of Mexico
Social Selection
Unveiling secret funding decisions
Social Selection
What would happen if grant reviews were made public?
 
 
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News in Focus
 
Political appointments spur concerns for Amazon
Environmentalists worried after Brazilian president picks ministers with ties to agriculture lobby.
Jeff Tollefson
  'I can haz genomes': cats claw their way into genetics
Canine dominance bows to tabby chic as cat sequencing takes off.
Ewen Callaway
First biosimilar drug set to enter US market
But such cheaper, generic versions of biological drugs face scientific, regulatory and patent hurdles.
Heidi Ledford
  Blown-up brains reveal nanoscale details
Material used in diaper absorbant can make brain tissue bigger and enable ordinary microscopes to resolve features down to 60 nanometres.
Ewen Callaway
Tropical paradise inspires virtual ecology lab
Digital version of Moorea will provide a way to experiment with an entire ecosystem.
Daniel Cressey
  Al Gore's dream spacecraft gears up for launch
Delayed DSCOVR probe will monitor conditions on Earth and solar storms in space.
Mark Zastrow
Features  
 
 
 
Agriculture: State-of-the-art soil
A charcoal-rich product called biochar could boost agricultural yields and control pollution. Scientists are putting the trendy substance to the test.
Rachel Cernansky
Microbiology: Here's looking at you, squid
Margaret McFall-Ngai has dissected the relationship between a beautiful squid and its live-in bacteria — and found lessons for microbiome research on the way.
Ed Yong
Correction  
 
 
Correction and clarification
 
 
Comment
 
Human adaptation: Manage climate-induced resettlement
Governments need research and guidelines to help them to move towns and villages threatened by global warming, argue David López-Carr and Jessica Marter-Kenyon.
David López-Carr, Jessica Marter-Kenyon
Books and Arts  
 
 
 
Science policy: From Brookhaven to Bush
Peter Gluckman finds US presidential science adviser John Marburger's posthumous collection enigmatic.
Peter Gluckman
History of chemistry: Words into gold
Philip Ball finds much wrestling with ideas in alchemists' scribbled-over texts.
Philip Ball
Correspondence  
 
 
 
Conservation: Giant tortoises hatch on Galapagos island
Washington Tapia Aguilera, Jeffreys Málaga, James P. Gibbs
  Natural history: save Italy's museums
Franco Andreone
Natural history: first museologist's legacy
Marco Romano, Richard L. Cifelli, Gian Battista Vai
  Developing world: Use mentoring to fix science inequality
Malgorzata Blicharska, Grzegorz Mikusiński
Pollinator assessment: IPBES responds on conflicts of interest
Anne Larigauderie
 
Obituary  
 
 
 
Alexander Grothendieck (1928–2014)
Mathematician who rebuilt algebraic geometry.
David Mumford, John Tate
 
 
Research
 
NEW ONLINE  
 
 
 
Neurodegeneration: Cold shock protects the brain
A protein released during hypothermia has been found to affect the progression of neurodegenerative disease in mice by sparing neurons from death and preserving the connections between them.
Ecology: Deep and complex ways to survive bleaching
Mass coral bleaching events can drive reefs from being the domains of corals to becoming dominated by seaweed. But longitudinal data show that more than half of the reefs studied rebound to their former glory.
Biochemistry: Elusive source of sulfur unravelled
The metabolic origin of the sulfur atom in the naturally occurring antibiotic lincomycin A has been obscure — until now. The biosynthetic steps involved reveal surprising roles for two sulfur-containing metabolites.
Mechanistic insights into the recycling machine of the SNARE complex
Using single-particle electron cryomicroscopy, several structures are reported which illuminate the mechanisms of action of the ATPase NSF that disassembles the SNARE complex into individual protein components.
Osteichthyan-like cranial conditions in an Early Devonian stem gnathostome
A new analysis of a 415-million-year-old fossil fish head originally described as from an early osteichthyan (bony fish) puts it instead as the sister group of the gnathosomes (jawed vertebrates), and suggests that the extinct acanthodians were relatives of cartilaginous fishes.
Probabilistic reanalysis of twentieth-century sea-level rise
A statistical reassessment of the tide gauge record concludes that sea level rose at a rate of about 1.2 millimetres per year from 1901 to 1990, slightly lower than prior estimates and now consistent with estimates based on individual contributions to sea-level change; the estimates reported here from 1990 onwards are consistent with other work, suggesting that the recent acceleration in sea-level rise is greater than previously thought.
Recognition determinants of broadly neutralizing human antibodies against dengue viruses
Human antibodies in complex with the soluble dimeric form of the dengue virus envelope protein E recognize a quaternary epitope and exhibit strong neutralizing activity against all four virus serotypes.
Metabolic coupling of two small-molecule thiols programs the biosynthesis of lincomycin A
Mycothiol and ergothioneine are shown to have important roles in the biosynthesis of lincomycin A, a sulfur-containing antibiotic that is used to treat severe Gram-positive bacterial infections in people who cannot receive penicillin antibiotics.
Predicting climate-driven regime shifts versus rebound potential in coral reefs
An analysis of 21 coral reefs in the Indian Ocean using data across 17 years that spanned a major climatic disturbance reveals factors that predispose a coral reef to recovery or regime shift from hard corals to macroalgae; these results could foreshadow the likely outcomes of tropical coral reefs to the effects of climate change, informing management and adaptation plans.
RBM3 mediates structural plasticity and protective effects of cooling in neurodegeneration
Structural synaptic plasticity and remodelling are features of the healthy adult brain and are seen during hibernation; a hibernation-inspired model of mouse cooling used to study synaptic regeneration has identified the 'cold-shock' RNA-binding protein, RBM3, as a regulator of synaptic assembly, deficiency of which contributes to synapse loss in neurodegenerative disease.
News and Views  
 
 
 
Biomechanics: Boxed up and ready to go
Stacy C. Farina, Adam P. Summers
Earth science: Mixing it up in the mantle
Jon Woodhead
Genomics: African dawn
Raj Ramesar
 
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Neuroscience: Dragonflies predict and plan their hunts
Stacey A. Combes
 
Physical chemistry: Hydrophobic interactions in context
Shekhar Garde
Organic chemistry: One catalyst, two reactions
Emmanuelle Schulz
 
HIV: Seeking ultimate victory
Louis J. Picker, Jeffrey D. Lifson
Insight  
 
 
 
Frontiers in biology
Alex Eccleston, Noah Gray, Sadaf Shadan et al.
From circuits to behaviour in the amygdala
Patricia H. Janak, Kay M. Tye
The biology of innate lymphoid cells
David Artis, Hergen Spits
Nutrient-sensing mechanisms and pathways
Alejo Efeyan, William C. Comb, David M. Sabatini
Necroptosis and its role in inflammation
Manolis Pasparakis, Peter Vandenabeele
Function and information content of DNA methylation
Dirk Schübeler
Articles  
 
 
 
The African Genome Variation Project shapes medical genetics in Africa
The African Genome Variation Project contains the whole-genome sequences of 320 individuals and dense genotypes on 1,481 individuals from sub-Saharan Africa; it enables the design and interpretation of genomic studies, with implications for finding disease loci and clues to human origins.
Deepti Gurdasani, Tommy Carstensen, Fasil Tekola-Ayele et al.
Internal models direct dragonfly interception steering
This study tracks dragonfly head and body movements during high-velocity and high-precision prey-capture flights, and shows that the dragonfly uses predictive internal models and reactive control to build an interception trajectory that complies with biomechanical constraints.
Matteo Mischiati, Huai-Ti Lin, Paul Herold et al.
Letters  
 
 
 
Impact jetting as the origin of chondrules
The origin of most chondrules (small, previously molten spherules inside meteorites) is shown to be impact jetting; chondrules form from the shock-melted material ejected from a protoplanet on impact, making meteorites a byproduct of planet formation.
Brandon C. Johnson, David A. Minton, H. J. Melosh et al.
Direct observation of electron propagation and dielectric screening on the atomic length scale
Attosecond light pulses are now available experimentally, enabling ultrafast processes on the atomic scale to be probed; here the free-electron-like propagation of electrons through ultrathin layers of magnesium is observed in real time.
S. Neppl, R. Ernstorfer, A. L. Cavalieri et al.
Non-stabilized nucleophiles in Cu-catalysed dynamic kinetic asymmetric allylic alkylation
A copper-catalysed dynamic kinetic asymmetric transformation using racemic substrates and alkyl nucleophiles is reported; organometallic reagents are generated in situ from alkenes by hydrometallation, and give highly enantioenriched products under mild reaction conditions.
Hengzhi You, Emeline Rideau, Mireia Sidera et al.
The terrestrial uranium isotope cycle
Examination of the global uranium cycle — whereby uranium from the Earth's crust is first transported to the oceans and then returned, by subduction, to the mantle — shows that the subducted uranium is isotopically distinct from the Earth as a whole and that this signature has been stirred throughout upper mantle, arguably within the past 600 million years.
Morten B. Andersen, Tim Elliott, Heye Freymuth et al.
Promoterless gene targeting without nucleases ameliorates haemophilia B in mice
Promoterless recombinant adeno-associated virus is used without nucleases to target the human coagulation factor IX gene to the liver-expressed albumin locus in haemophilia B mice, with an on-target integration into ∼0.5% of the albumin alleles in hepatocytes; stable F9 plasma levels at 7–20% of normal were obtained, leading to normal coagulation times in treated factor-IX-deficient mice.
A. Barzel, N. K. Paulk, Y. Shi et al.
Productivity limits and potentials of the principles of conservation agriculture
A global meta-analysis of conservation agriculture principles indicates that the potential contribution of no-till to the sustainable intensification of agriculture is more limited than often assumed.
Cameron M. Pittelkow, Xinqiang Liang, Bruce A. Linquist et al.
Long-term phenotypic evolution of bacteria
A comparative analysis of bacterial growth and genetic phenotypes using hundreds of genome-scale metabolic models reveals a two-stage evolutionary process that consists of a rapid initial phenotypic diversification followed by a slow long-term divergence.
Germán Plata, Christopher S. Henry, Dennis Vitkup
The neural representation of taste quality at the periphery
Using two-photon microendoscopy and genetically encoded calcium indicators the tuning properties of the first neural station of the gustatory system are explored; results reveal that ganglion neurons are matched to specific taste receptor cells, supporting a labelled line model of information transfer in the taste system.
Robert P. J. Barretto, Sarah Gillis-Smith, Jayaram Chandrashekar et al.
Control of plant stem cell function by conserved interacting transcriptional regulators
Here, plant HAM proteins are shown to physically interact with the transcription factor WUSCHEL and the related WOX proteins, with this interaction driving downstream transcriptional programs and determining the activities of stem cells.
Yun Zhou, Xing Liu, Eric M. Engstrom et al.
Modulation of hydrophobic interactions by proximally immobilized ions
Chemical force microscopy measurements show that the immobilization of specific cationic groups near non-polar domains produces pronounced changes in the domains' hydrophobic interaction strengths: charged ammonium groups double interaction strengths, whereas guanidinium groups eliminate measurable interactions.
C. Derek Ma, Chenxuan Wang, Claribel Acevedo-Vélez et al.
Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations
Despite receiving antiretroviral therapy, most patients with HIV still have latent reservoirs of the virus; here, these reservoirs are shown to be dominated by viruses with cytotoxic T lymphocyte escape mutations, with potential implications for the development of therapeutic vaccines.
Kai Deng, Mihaela Pertea, Anthony Rongvaux et al.
CEACAM1 regulates TIM-3-mediated tolerance and exhaustion
CEACAM1 functions as a novel heterophilic ligand for TIM-3 and is necessary for TIM-3-mediated tolerance, which has marked consequences for inflammation, infection and cancer.
Yu-Hwa Huang, Chen Zhu, Yasuyuki Kondo et al.
An ERK/Cdk5 axis controls the diabetogenic actions of PPARγ
Blocking ERK/MAP kinases improves insulin sensitivity thorough a mechanism similar to the actions of the anti-diabetic thiazolidinediones drugs on PPARγ.
Alexander S. Banks, Fiona E. McAllister, João Paulo G. Camporez et al.
Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter
The subnanometre-resolution electron cryomicroscopy structure of TmrAB, a heterodimeric ABC transport protein, in a nucleotide-free, inward-facing conformation, is determined.
JungMin Kim, Shenping Wu, Thomas M. Tomasiak et al.
 
 
Careers & Jobs
 
Feature  
 
 
 
Work–life balance: Lab life with kids
Kendall Powell
Career Briefs  
 
 
 
Career progression: Consider all options
Futures  
 
 
The left hands of lovers
Strong connection.
Emily Eckart
 
 
 
 
 

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