Wednesday, May 4, 2016

Nature contents: 05 May 2016

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  journal cover  
Nature Volume 533 Issue 7601
 
This Week  
 
 
Editorials  
 
 
 
Lessons from the Ancient One
The final stages of a dispute over an ancient Native American skeleton signal the need for clearer oversight of such human remains.
The nuclear option
China is vigorously promoting nuclear energy, but its pursuit of reprocessing is misguided.
Fat lot of good
Humans’ exceptional ability to burn through calories fuels our evolution.
 

 
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World View  
 
 
 
Set up a public registry of competing interests
The problem of bias in published research must be tackled in a consistent and comprehensive fashion, says Adam G. Dunn.
 
Seven Days  
 
 
 
The week in science: 29 April–5 May 2016
New Mars missions shape up; Nobel laureate passes away; and a marten stops the world’s biggest science experiment.
Research Highlights  
 
 
 
Biomechanics: Peacocks maximize tail shimmer | Climate change: Knowledge alters public perception | Immunology: Why older people are prone to flu | Behavioural ecology: Single-celled life can learn | Microbiology: Gut microbes shape immunity | Planetary science: Martian water on the boil | Reproductive biology: Catching sperm for contraception | Ecology: Camera traps may aid conservation | Cancer biology: T cells team up with chemotherapy | Environmental science: UK food imports use scarce water
 
 
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News in Focus
 
Human embryos grown in lab for longer than ever before
Embryos cultured for up to 13 days after fertilization open a window into early development.
Sara Reardon
  Australia softens blow of climate job cuts
New research centre at national science agency CSIRO adds 40 jobs, amid hundreds of redundancies.
Myles Gough
Software error doomed Japanese Hitomi spacecraft
Space agency declares the astronomy satellite a loss.
Alexandra Witze
  US and China eye up European gravitational-wave mission
Space-based detector draws interest, but regulatory hurdles might complicate a partnership.
Elizabeth Gibney
Stem-cell plan aims to bring rhino back from brink of extinction
Ambitious effort depends on transformation of rhino tissue into sperm and egg cells.
Ewen Callaway
 
Features  
 
 
 
Can artificial intelligence create the next wonder material?
Some researchers believe that machine-learning techniques can revolutionize how materials science is done.
Nicola Nosengo
Nine years of censorship
Canadian scientists are now allowed to speak out about their work — and the government policy that had restricted communications.
Lesley Evans Ogden
Multimedia  
 
 
Nature Podcast: 5 May 2016
This week, the value of failed experiments, ketamine without side effects, and our brains’ energy demands.
 
 

BJC collections: Cancer Immunotherapy

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Comment
 
Policy: Security spending must cover disease outbreaks
Tadataka Yamada, V. Ayano Ogawa and Maria Freire call for research and development funding and coordination to counter global infectious-disease threats.
Tadataka Yamada, V. Ayano Ogawa, Maria Freire
Embryology policy: Revisit the 14-day rule
Studies of human development in vitro are on a collision course with an international policy that limits embryo research to the first two weeks of development, warn Insoo Hyun, Amy Wilkerson and Josephine Johnston.
Insoo Hyun, Amy Wilkerson, Josephine Johnston
Books and Arts  
 
 
 
Ethology: Intrepid translator of the hive
Mark L. Winston reviews a study of Karl von Frisch, the ethologist who unravelled bee communication.
Mark L. Winston
Books in brief
Barbara Kiser reviews five of the week's best science picks.
Barbara Kiser
Physics: Material to meaning
Robert P. Crease assesses Sean Carroll's attempt to construct morality out of quantum field theory.
Robert P. Crease
Correspondence  
 
 
 
Environment: Curb anchor scour for green shipping
Andrew R. Davis, Allison Broad
  Energy policy: Renewables targeted before Fukushima
Aleh Cherp, Jessica Jewell
Conservation: Debate over whale longevity is futile
P. J. Nico de Bruyn
  Industry: Shared goals score reproducible results
Eric Buenz
 
 
Specials
 
TOOLBOX  
 
 
 
The struggle with image glut
Experiments that generate millions of images have forced scientists to find new ways to store and share terabytes of experimental data.
Jeffrey M. Perkel
Outlook: Research commercialization  
 
 
 
Research commercialization
Herb Brody
  Cashing in on science
Alla Katsnelson
Start-ups: A sense of enterprise
Neil Savage
  Technology transfer: The leap to industry
Jessica Wapner
Assessment: Academic return
Michael Eisenstein
  Australia: Engagement upgrade
Bianca Nogrady
Q&A: Horst Domdey
Chelsea Wald
  China: Building an innovator
Nicky Phillips
Collaboration: The geography of discovery
Emily Sohn
  Funding: Donor drugs
Cassandra Willyard
Q&A: Helga Nowotny
Chelsea Wald
 
 
 
Research
 
NEW ONLINE  
 
 
 
Human embryology: Implantation barrier overcome
The early stages of human development are normally hidden within the womb, but improved techniques for culturing embryos from the blastocyst stage promise to make these steps easier to investigate.
Celestial mechanics: Fresh solutions to the four-body problem
Describing the motion of three or more bodies under the influence of gravity is one of the toughest problems in astronomy. The report of solutions to a large subclass of the four-body problem is truly remarkable.
Depression: Ketamine steps out of the darkness
The way in which ketamine exerts its antidepressant effects has been perplexing. Evidence that a metabolite of the drug is responsible, and acts on a different target from ketamine, might be the key to an answer.
Neurobiology: Wired for sex
Analysis of a sensory neural circuit in the roundworm Caenorhabditis elegans reveals that its wiring is sex-specific, and arises through the elimination of connections that are originally formed in both sexes.
Landscape of somatic mutations in 560 breast cancer whole-genome sequences
Whole-genome sequencing of tumours from 560 breast cancer cases provides a comprehensive genome-wide view of recurrent somatic mutations and mutation frequencies across both protein coding and non-coding regions; several mutational signatures in these cancer genomes are associated with BRCA1 or BRCA2 function and defective homologous-recombination-based DNA repair.
Activation of NMDA receptors and the mechanism of inhibition by ifenprodil
X-ray crystallography, single-particle electron cryomicroscopy and electrophysiology were used to study the conformational changes that take place during the activation and inhibition of a mammalian GluN1b–GluN2B N-methyl-D-aspartate receptor.
Sex-specific pruning of neuronal synapses in Caenorhabditis elegans
How sex-specific neuronal circuits are generated during development is poorly understood; here, sensory neurons are identified in the round worm Caenorhabditis elegans, which initially connect in both male- and hermaphrodite-specific patterns, but a specific subset of these connections is pruned by each sex upon sexual maturation to produce sex-specific connectivity patterns and dimorphic behaviours.
The genetic history of Ice Age Europe
Analysis of ancient genomic data of 51 humans from Eurasia dating from 45,000 to 7,000 years ago provides insight into the population history of pre-Neolithic Europe and support for recurring migration and population turnover in Europe during this period.
NMDAR inhibition-independent antidepressant actions of ketamine metabolites
The metabolism of ketamine to (2S,6S;2R,6R)-hydroxynorketamine (HNK) is essential for its antidepressant effects, and the (2R,6R)-HNK enantiomer lacks ketamine-related side effects but exerts rapid and sustained antidepressant actions in mice; these antidepressant effects are independent of NMDAR inhibition but require AMPAR activity.
Continuous probing of cold complex molecules with infrared frequency comb spectroscopy
Combining cavity-enhanced direct frequency comb spectroscopy with buffer gas cooling enables rapid collection of well-resolved infrared spectra for molecules such as nitromethane, naphthalene and adamantane, confirming the value of the combined approach for studying much larger and more complex molecules than have been probed so far.
No Sun-like dynamo on the active star ζ Andromedae from starspot asymmetry
Infrared interferometry imaging of the old, magnetically active star ζ Andromedae reveals an asymmetric distribution of starspots, unlike the north–south starspot symmetry observed on the Sun, meaning the underlying dynamo mechanisms must be different.
Temperate Earth-sized planets transiting a nearby ultracool dwarf star
Three Earth-sized planets—receiving similar irradiation to Venus and Earth, and ideally suited for atmospheric study—have been found transiting a nearby ultracool dwarf star that has a mass of only eight per cent of that of the Sun.
Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals
Mutants of the C4-symmetric protein RhuA were designed to self-assemble into two-dimensional crystalline lattices with precise spatial arrangements and patterns; the lattices of one of the variants are auxetic and deform perpendicularly to an applied force in a way that is contrary to what is generally expected in typical materials.
Opponent and bidirectional control of movement velocity in the basal ganglia
Activity in the direct and indirect basal ganglia pathways can bidirectionally control the speed of movements that underlie reward-seeking actions in mice without affecting motivation.
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation OPEN
A novel approach is used to cultivate a substantial proportion of the human gut microbiota, representing an important step forward in characterizing the role of these bacteria in health and disease.
Metabolic acceleration and the evolution of human brain size and life history
Compared to other apes, humans live longer, reproduce faster and have larger brains; here, total energy expenditure is studied in humans and all species of great ape, and is shown to be significantly higher in humans, demonstrating that the human lineage has experienced an energy-boosting acceleration in metabolic rate.
Architecture of the mitochondrial calcium uniporter
The structure of the core region of the mitochondrial calcium uniporter (MCU) is determined by NMR and electron microscopy, revealing that MCU is a homo-pentamer with a specific transmembrane helix forming a hydrophilic pore across the membrane, and representing one of the largest membrane protein structures characterized by NMR spectroscopy.
Crystal structure of the human sterol transporter ABCG5/ABCG8
The X-ray structure of human ABCG5/ABCG8 heterodimer in a nucleotide-free state, being the first atomic model of an ABC sterol transporter.
Activation of the A2A adenosine G-protein-coupled receptor by conformational selection
The adenosine A2A receptor, a class A G-protein-coupled receptor, exists as an ensemble of two inactive and two active states in equilibrium and is activated by conformational selection rather than induced fit.
Self-organization of the in vitro attached human embryo
An in vitro model to study the early events that direct human embryo development after formation of the blastocyst and implantation in the uterine wall.
Maintenance and propagation of a deleterious mitochondrial genome by the mitochondrial unfolded protein response
In the context of mitochondrial genome heteroplasmy that causes defective oxidative phosphorylation in C. elegans, the ATFS-1-mediated mitochondrial unfolded protein response maintains the deleterious mitochondrial DNA in an attempt to recover oxidative phosphorylation activity and avoid cellular dysfunction.
Erratum: Universal resilience patterns in complex networks
Corrigendum: Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome
News and Views  
 
 
 
Parkinson's disease: Guilt by genetic association
Asa Abeliovich, Herve Rhinn
Cell biology: Ubiquitination without E1 and E2 enzymes
Sagar Bhogaraju, Ivan Dikic
Materials science: Clockwork at the atomic scale
Marjana Ležaić
 
 

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Bioengineering: Evolved to overcome Bt-toxin resistance
Daniel Dovrat, Amir Aharoni
 
Immunology: Mum's microbes boost baby's immunity
Mihir Pendse, Lora V. Hooper
Nuclear physics: Elusive transition spotted in thorium
Marianna Safronova
 
Articles  
 
 
 
Direct detection of the 229Th nuclear clock transition
Direct detection of the 229Th nuclear clock transition has been achieved, placing direct constraints on transition energy and half-life; these results are a step towards a nuclear clock, nuclear quantum optics and a nuclear laser.
Lars von der Wense, Benedict Seiferle, Mustapha Laatiaoui et al.
Principles underlying sensory map topography in primary visual cortex
Recordings from cat visual cortex show that the cortical maps for stimulus orientation, direction and retinal disparity depend on an organization in which thalamic axons with similar retinotopy and light/dark responses are clustered together in the cortex.
Jens Kremkow, Jianzhong Jin, Yushi Wang et al.
Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance
Phage-assisted continuous evolution (PACE) rapidly evolves Bacillus thuringiensis toxins through more than 500 generations of mutation, selection, and replication to bind a receptor expressed on the surface of insect-pest midgut cells.
Ahmed H. Badran, Victor M. Guzov, Qing Huai et al.
Letters  
 
 
 
Resolved atomic lines reveal outflows in two ultraluminous X-ray sources
Ultraluminous X-ray sources are thought to be powered by accretion onto a compact object; now the discovery of X-ray emission lines and blueshifted absorption lines in the high-resolution spectra of ultraluminous X-ray sources NGC 1313 X-1 and NGC 5408 X-1 shows that in each case the compact object is surrounded by powerful winds with an outflow velocity of about 0.2 times that of light.
Ciro Pinto, Matthew J. Middleton, Andrew C. Fabian
Scalable and sustainable electrochemical allylic C–H oxidation
An electrochemical C–H oxidation strategy that exhibits broad substrate scope, operational simplicity and high chemoselectivity is described; it uses inexpensive and readily available materials and represents a scalable allylic C–H oxidation that could be adopted in large-scale industrial settings without substantial environmental impact.
Evan J. Horn, Brandon R. Rosen, Yong Chen et al.
Polar metals by geometric design
Ab initio calculations are used to identify the structural conditions under which a polar state in metals might be stabilized; this information is used to guide the experimental realization of new room-temperature polar metals.
T. H. Kim, D. Puggioni, Y. Yuan et al.
Machine-learning-assisted materials discovery using failed experiments
Failed chemical reactions are rarely reported, even though they could still provide information about the bounds on the reaction conditions needed for product formation; here data from such reactions are used to train a machine-learning algorithm, which is subsequently able to predict reaction outcomes with greater accuracy than human intuition.
Paul Raccuglia, Katherine C. Elbert, Philip D. F. Adler et al.
Chondritic xenon in the Earth’s mantle
High-precision analysis of magmatic gas from the Eifel volcanic area in Germany suggests that the light xenon isotopes reflect a chondritic primordial component that differs from the precursor of atmospheric xenon, consistent with an asteroidal origin for the volatile elements in the Earth’s mantle.
Antonio Caracausi, Guillaume Avice, Peter G. Burnard et al.
The genetic program for cartilage development has deep homology within Bilateria
Vertebrate and invertebrate cartilage share structural and biochemical properties, and their development is controlled by a highly conserved genetic circuit, suggesting that a deeply homologous mechanism underlies the parallel evolution of cartilage in Bilateria.
Oscar A. Tarazona, Leslie A. Slota, Davys H. Lopez et al.
Topology of ON and OFF inputs in visual cortex enables an invariant columnar architecture
Two-photon imaging of calcium signals in the tree shrew visual cortex shows that light-responsive and dark-responsive inputs have distinct arrangements that allow the cortex to map the orientation, visual location and spatial phase of visual stimuli.
Kuo-Sheng Lee, Xiaoying Huang, David Fitzpatrick
Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression
A CRISPR/Cas9 system is used to dissect the role of allelic risk variants on the expression of the α-synuclein gene SNCA, which has been linked to Parkinson’s disease development.
Frank Soldner, Yonatan Stelzer, Chikdu S. Shivalila et al.
Unique human immune signature of Ebola virus disease in Guinea
Fatal Ebola virus disease is characterized by a high proportion of CD4+ and CD8+ T cells expressing the inhibitory molecules CTLA-4 and PD-1, correlating with high virus load; individuals who survive the infection exhibit lower expression of these inhibitory molecules and generate Ebola-specific CD8+ T cells, suggesting that dysregulation of the T cell response is a key component of Ebola virus disease pathophysiology.
Paula Ruibal, Lisa Oestereich, Anja Lüdtke et al.
A single injection of anti-HIV-1 antibodies protects against repeated SHIV challenges
A single injection of four anti-HIV-1-neutralizing monoclonal antibodies blocks repeated weekly low-dose virus challenges of simian/human immunodeficiency virus.
Rajeev Gautam, Yoshiaki Nishimura, Amarendra Pegu et al.
EBI2 augments Tfh cell fate by promoting interaction with IL-2-quenching dendritic cells
The differentiation of T follicular helper cells requires the G-protein-coupled receptor Ebi2 as well as the interaction with CD25-producing dendritic cells that quench T-cell-derived interleukin-2.
Jianhua Li, Erick Lu, Tangsheng Yi et al.
Noncanonical autophagy inhibits the autoinflammatory, lupus-like response to dying cells
Defects in LC3-associated phagocytosis in mice are shown to result in systemic lupus erythematosus-like disease; dying cells are engulfed but not degraded in LAP-deficient mice, resulting in increased serum levels of autoantibodies and inflammatory cytokines, and evidence of kidney disease.
Jennifer Martinez, Larissa D. Cunha, Sunmin Park et al.
Ubiquitination independent of E1 and E2 enzymes by bacterial effectors
An unprecedented mechanism of ubiquitination that is independent of E1 and E2 enzymes, instead relying on activation of ubiquitin by ADP-ribosylation, and which is mediated by members of the SidE effector family encoded by the bacterial pathogen Legionella pneumophila, establishes that ubiquitination can be carried out by a single enzyme.
Jiazhang Qiu, Michael J. Sheedlo, Kaiwen Yu et al.
Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9
A CRISPR/Cas9 genome editing framework has been developed that allows controlled introduction of mono- and bi-allelic sequence changes, and is used to generate induced human pluripotent stem cells with heterozygous and homozygous dominant mutations in amyloid precursor protein and presenilin 1 that have been associated with early onset Alzheimer’s disease.
Dominik Paquet, Dylan Kwart, Antonia Chen et al.
Corrigenda  
 
 
 
Corrigendum: Dissecting a circuit for olfactory behaviour in Caenorhabditis elegans
Sreekanth H. Chalasani, Nikos Chronis, Makoto Tsunozaki et al.
Corrigendum: Discovery of Atg5/Atg7-independent alternative macroautophagy
Yuya Nishida, Satoko Arakawa, Kenji Fujitani et al.
Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions
Wendy Huang, Benjamin Thomas, Ryan A. Flynn et al.
 
 
 
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Careers & Jobs
 
Feature  
 
 
 
Relationships: Scions of science
Amber Dance
Career Briefs  
 
 
 
Faculty positions: Tenure figures tumble
Academies: Diversity drive
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The Museum of Nothing
But is it art?
Anna Zumbro
 
 
 
 
 

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