Wednesday, January 27, 2016

Nature contents: 28 January 2016

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  journal cover  
Nature Volume 529 Issue 7587
 
This Week  
 
 
Editorials  
 
 
 
Digital intuition
A computer program that can outplay humans in the abstract game of Go will redefine our relationship with machines.
In praise of parks
Our affection for national parks is well founded, but many more areas need protection.
Found out
Self-doubt is a pernicious affliction that can overwhelm researchers.
 
World View  
 
 
 
India needs home-grown GM food to stop starvation
Indian scientists must develop domestic genetically modified crops rather than rely on unsuitable foreign technology, says Anurag Chaurasia.
 
Seven Days  
 
 
 
The week in science: 22–28 January 2016
The hottest year; a new frog genus; and the loss of Marvin Minsky.
Research Highlights  
 
 
 
Plant science: Plants count to five | Infectious disease: Antibody for range of ebolaviruses | Astronomy: Turbulence roils luminous galaxy | Bioengineering: Shielded cells treat diabetes | Oceanography: Rising seas differ by region | Materials: Add water for 3D-printed flowers | Chemistry: Polymers woven into stretchy web | Animal behaviour: Voles console stressed friends
Social Selection
Creepy-crawlies, cultural tales and clever canines: this week’s hot topics
 
 
Advertising.
 
 
News in Focus
 
Google AI algorithm masters ancient game of Go
Deep-learning software defeats human professional for first time.
Elizabeth Gibney
  Dog DNA probed for clues to human psychiatric ills
Pet project hunts genetic links to behaviour by polling owners on their companions’ quirks.
Heidi Ledford
Hawking’s latest black-hole paper splits physicists
Some welcome his latest report as a fresh way to solve a black-hole conundrum; others are unsure of its merits.
Davide Castelvecchi
  Monkeys genetically modified to show autism symptoms
But it is unclear how well the results match the condition in humans.
David Cyranoski
2015 declared the hottest year on record
Warming in the Pacific Ocean helps to shatter past records, and could bring even faster temperature rises.
Jeff Tollefson
  Paris climate deal hinges on better carbon accountancy
Local expertise is required to provide detailed emissions reports.
Jeff Tollefson
Features  
 
 
 
Slaughter of the song birds
Songbirds are a culinary delicacy in Cyprus — but catching and eating them is illegal. Even so, the practice is on the rise and could be threatening rare species.
Shaoni Bhattacharya
How quality control could save your science
It may not be sexy, but quality assurance is becoming a crucial part of lab life.
Monya Baker
Multimedia  
 
 
Nature: 28 January 2016
This week, the computer that can play Go, a general 'ageing' factor, and the stolen library of John Dee.
 
 
Comment
 
Research integrity: Don't let transparency damage science
Stephan Lewandowsky and Dorothy Bishop explain how the research community should protect its members from harassment, while encouraging the openness that has become essential to science.
Stephan Lewandowsky, Dorothy Bishop
Books and Arts  
 
 
 
In retrospect: The selfish gene
Matt Ridley reassesses Richard Dawkins's pivotal reframing of evolution, 40 years on.
Matt Ridley
History: Archive of wonders
Philip Ball browses remnants of the celebrated library of mathematician and occultist John Dee.
Philip Ball
Correspondence  
 
 
 
Government: Concern grows for Turkey's academics
Caghan Kizil
  Environmental management: Synthesize evidence to steer decisions
Anne-Christine Mupepele, Carsten F. Dormann
Climate adaptation: Hold atmosphere in trust for all
Robert Costanza
  Funding: What stops women getting more grants?
David McAllister, Jan Juillerat, Jackie Hunter
Renewables: Solar energy needs focus
Abu Bakar Munir, Firdaus Muhammad-Sukki, Nurul Aini Bani
 
 
 
Research
 
NEW ONLINE  
 
 
 
Genomics: From sea to sea
The genome sequence of the marine flowering plant eelgrass (Zostera marina) sheds light on how marine algae evolved into land plants before moving back to the sea.
Parkinson's disease: Disorder in the court
The native structure of the protein α-synuclein, which is implicated in Parkinson's disease, is controversial. In-cell nuclear magnetic resonance now shows that it remains disordered when loaded into living cells.
Ageing: A stretch in time
Plots of survival against time for nematode worms in different conditions can be superimposed by rescaling the time axis. This observation has far-reaching implications for our understanding of the nature of ageing.
Schizophrenia: From genetics to physiology at last
The identification of a set of genetic variations that are strongly associated with the risk of developing schizophrenia provides insights into the neurobiology of this destructive disease.
Structural disorder of monomeric α-synuclein persists in mammalian cells
Atomic resolution in-cell NMR and EPR spectroscopy show that the human amyloid protein α-synuclein remains disordered within all mammalian cells tested, including neurons, and identifies which parts of the protein dynamically interact or remain shielded from the cytoplasm, thus counteracting aggregation under physiological cell conditions.
Active medulloblastoma enhancers reveal subgroup-specific cellular origins
Genomic studies of the paediatric brain tumour medulloblastoma have revealed four clinically distinct molecular subgroups; here active gene regulatory elements in 28 primary medulloblastoma tissues are mapped to reveal differentially regulated enhancers across the different subgroups, allowing insights into the transcription factors that characterize subgroup divergence and the cellular origin of the poorly characterized Group 3 and 4 subgroups.
Schizophrenia risk from complex variation of complement component 4
Schizophrenia is associated with genetic variation at the major histocompatibility complex locus; this study reveals that alleles at this locus associate with schizophrenia in proportion to their tendency to generate greater expression of complement component 4 (C4A) genes and that C4 promotes the elimination of synapses.
Persistent HIV-1 replication maintains the tissue reservoir during therapy
By examining viral sequences in lymphoid tissue from three HIV-1-infected individuals receiving drug therapy, the authors find phylogenetic evidence for ongoing virus replication, suggesting that the antiretroviral drug concentration in the lymphoid tissue is insufficient to fully suppress the virus; using a mathematical model, they further explain why drug resistance does not necessarily arise as a result.
Observation of polar vortices in oxide superlattices
In material systems with several interacting degrees of freedom, the complex interplay between these factors can give rise to exotic phases; now superlattices consisting of alternating layers of PbTiO3 and SrTiO3 are found to exhibit an unusual form of ferroelectric ordering in the PbTiO3 layers, in which the electric dipoles arrange themselves into regular, ordered arrays of vortex–antivortex structures.
An essential receptor for adeno-associated virus infection
An adeno-associated virus (AAV) receptor protein essential for AAV2 entry into cells is identified; AAV receptor binds directly to the virus, and its ablation renders a diverse range of mammalian cell types and mice resistant to infection by AAV of multiple serotypes.
Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells
Genome-wide binding profiles for eight different chromatin remodellers in mouse embryonic stem (ES) cells are determined at single nucleosome resolution; each remodeller binds at specific nucleosome positions relative to the start of genes, and the same remodeller acts as a positive or negative regulator of transcription depending on the promoter chromatin organization and epigenetic marking of the gene it binds.
Uranium-mediated electrocatalytic dihydrogen production from water
Homogenous electrocatalytic water reduction with formation of dihydrogen is demonstrated with a trisaryloxide U(iii) complex, for which the catalytic cycle was elucidated and found to involve rare terminal U(iv)–OH and U(v)=O complexes.
Autism-like behaviours and germline transmission in transgenic monkeys overexpressing MeCP2
Lentivirus-based transgenic Macaca fascicularis monkeys are generated expressing the human MECP2 transgene in the brain, and they display behavioural alterations including changes in social interaction and increased anxiety; germline transmission of the transgene to the F1 offspring is shown, and these monkeys also had an altered social interaction phenotype.
The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea OPEN
Whole-genome sequencing of the seagrass Zostera, representing the first marine angiosperm genome to be fully sequenced, provides insight into the evolutionary changes associated with a transition to a marine environment in this angiosperm lineage.
The temporal scaling of Caenorhabditis elegans ageing
A diverse range of molecular and genetic manipulations all alter lifespan distributions of Caenorhabditis elegans by an apparent stretching or shrinking of time.
NEK7 is an essential mediator of NLRP3 activation downstream of potassium efflux
NEK7, a member of the NIMA-related kinase family, is identified as a regulator of NLRP3 inflammasome oligomerization and activation; NEK7 functions downstream of potassium efflux in a manner that is independent of its kinase activity.
Corrigendum: Essential roles of PI(3)K–p110β in cell growth, metabolism and tumorigenesis
News and Views  
 
 
 
Neuroscience: A mechanism for myelin injury
Aiman S. Saab, Klaus-Armin Nave
Genome editing: The domestication of Cas9
Fyodor Urnov
Neuroscience: Fluorescent boost for voltage sensors
Viviana Gradinaru, Nicholas C. Flytzanis
 

Nature Index 2015 China

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Evolution: A lizard that generates heat
Colleen G. Farmer
 
Stellar astrophysics: The mystery of globular clusters
Antonella Nota, Corinne Charbonnel
Infection biology: Small RNA with a large impact
Matthias P. Machner, Gisela Storz
 
Bioanalytical devices: Technological leap for sweat sensing
Jason Heikenfeld
Perspectives  
 
 
 
Allowable CO2 emissions based on regional and impact-related climate targets
Targets for reducing atmospheric carbon dioxide are related to regional changes in climate extremes rather than to changes in global mean temperature, in order to convey their urgency better to individual countries.
Sonia I. Seneviratne, Markus G. Donat, Andy J. Pitman et al.
Articles  
 
 
 
Mastering the game of Go with deep neural networks and tree search
A computer Go program based on deep neural networks defeats a human professional player to achieve one of the grand challenges of artificial intelligence.
David Silver, Aja Huang, Chris J. Maddison et al.
High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects
A high-fidelity variant of Streptococcus pyogenes CRISPR–Cas9 is reported that lacks detectable off-target events as assessed by genome-wide break capture and targeted sequencing methods.
Benjamin P. Kleinstiver, Vikram Pattanayak, Michelle S. Prew et al.
Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions
Using dual RNA-seq technology to profile RNA expression simultaneously in the bacterial pathogen Salmonella and its host during infection reveals molecular phenotypes of small noncoding RNAs in the infection process.
Alexander J. Westermann, Konrad U. Förstner, Fabian Amman et al.
Letters  
 
 
 
Formation of new stellar populations from gas accreted by massive young star clusters
Three massive star clusters in the Magellanic Clouds show clear evidence of burst-like star formation that occurred a few hundred million years after their initial formation era; such clusters could have accreted sufficient gas to form new stars while orbiting in their host galaxies’ gaseous disks throughout the period between their initial and more recent bursts of star formation.
Chengyuan Li, Richard de Grijs, Licai Deng et al.
A mechanism of viral immune evasion revealed by cryo-EM analysis of the TAP transporter
The cryo-electron microscopy structure of human TAP transporter, a peptide transporter central to MHC class I antigen presentation and cellular immunity, in complex with the herpes simplex virus protein ICP47.
Michael L. Oldham, Richard K. Hite, Alanna M. Steffen et al.
Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation
The first structure of fully active HOIP of the RBR family of RING-type E3 ligases in its transfer complex with an E2~ubiquitin conjugate provides insights into its mechanism of action, including the ideal alignment of the E2 and E3 catalytic centres for ubiquitin transfer and the allosteric regulation of the RBR family.
Bernhard C. Lechtenberg, Akhil Rajput, Ruslan Sanishvili et al.
Structure of transcribing mammalian RNA polymerase II
The first high-resolution, cryo-electron microscopy structure of mammalian RNA polymerase II, in the form of a transcribing complex comprising DNA template and RNA transcript.
Carrie Bernecky, Franz Herzog, Wolfgang Baumeister et al.
Measurement noise 100 times lower than the quantum-projection limit using entangled atoms
Quantum entanglement is thought to offer great promise for improving measurement precision; now a spin-squeezing implementation with cold atoms offers levels of sensitivity unavailable with any competing conventional method, sensing microwave induced rotations a factor of 70 beyond the standard quantum limit.
Onur Hosten, Nils J. Engelsen, Rajiv Krishnakumar et al.
Proton-gated Ca2+-permeable TRP channels damage myelin in conditions mimicking ischaemia
Ischaemia damages nerve myelin by depriving neurons and their myelinating oligodendrocytes of oxygen and glucose; here it is shown that ischaemic damage is caused through the H+-dependent activation of TRPA1 channels, and not via glutamate receptors of the NMDA type, as previously thought, providing a new mechanism and promising therapeutic targets for diseases as diverse and prevalent as cerebral palsy, spinal cord injury, stroke and multiple sclerosis.
Nicola B. Hamilton, Karolina Kolodziejczyk, Eleni Kougioumtzidou et al.
Graded Foxo1 activity in Treg cells differentiates tumour immunity from spontaneous autoimmunity
The transcription factor Foxo1 is shown to be involved in the determination of distinct subsets of regulatory T (Treg) cells, and the differentiation of activated phenotype Treg cells is associated with the repression of the Foxo1-dependent transcriptional program; constitutively active Foxo1 expression triggers depletion of activated Treg cells in peripheral tissues and leads to CD8 T-cell-mediated autoimmunity and anti-tumour immunity.
Chong T. Luo, Will Liao, Saida Dadi et al.
Fully integrated wearable sensor arrays for multiplexed in situ perspiration analysis
By merging plastic-based skin sensors with silicon integrated circuits, a flexible, wearable perspiration analysis system is presented that measures skin temperature and the metabolites and electrolytes in human sweat and analyses the information in situ.
Wei Gao, Sam Emaminejad, Hnin Yin Yin Nyein et al.
Lithium-ion battery structure that self-heats at low temperatures
Here we report a lithium-ion all-climate battery that very efficiently heats itself up in extremely cold environments by diverting current through a strip of metal foil to generate heat of resistance and then reverts to normal high-power operation.
Chao-Yang Wang, Guangsheng Zhang, Shanhai Ge et al.
No iron fertilization in the equatorial Pacific Ocean during the last ice age
Core isotope measurements in the equatorial Pacific Ocean reveal that although atmospheric dust deposition during the last ice age was higher than today’s, the productivity of the equatorial Pacific Ocean did not increase; this may have been because iron-enabled greater nutrient consumption, mainly in the Southern Ocean, reduced the nutrients available in the equatorial Pacific Ocean, and hence also productivity there.
K. M. Costa, J. F. McManus, R. F. Anderson et al.
Mitofusin 2 maintains haematopoietic stem cells with extensive lymphoid potential
The role of mitochondria in haematopoietic stem-cell maintenance has not been examined in detail; here mitofusin 2, which modulates mitochondrial fusion and tethering of endoplasmic reticulum to the mitochondria, is shown to be necessary for the maintenance of haematopoietic stem cells with extensive lymphoid potential.
Larry L. Luchsinger, Mariana Justino de Almeida, David J. Corrigan et al.
Structure of the E6/E6AP/p53 complex required for HPV-mediated degradation of p53
Structural details of how oncogenic human papilloma viruses induce cancer by targeting the tumour suppressor p53 for ubiquitin-mediated degradation.
Denise Martinez-Zapien, Francesc Xavier Ruiz, Juline Poirson et al.
 
 

Infectious disease control and elimination

The Diagnostics Modelling Consortium was established in 2013 to facilitate the integration of diagnostic data into models of disease transmission dynamics. In this supplement, the Consortium and its partners report on the latest research outcomes across several major diseases. 

Available free online.

Financial support for publication has been provided by the Bill & Melinda Gates Foundation 
 
 
Careers & Jobs
 
Feature  
 
 
 
Psychology: Faking it
Chris Woolston
Q&AS  
 
 
 
Turning point: Louis Picker
Virginia Gewin
Futures  
 
 
Robot burial
A moment to reflect.
H. E. Roulo
 
 
 
 
 

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