Wednesday, July 29, 2015

Nature contents: 30 July 2015

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  journal cover  
Nature Volume 523 Issue 7562
 
This Week  
 
 
Editorials  
 
 
 
Tropical protection
After years of talk, the palm-oil industry is looking into adopting environmental standards. Such rules must be strong, and need to be implemented.
Secret service
Government labs should be subject to the same transparent oversight as academic facilities.
Realistic risks
The communication of risk in disease outbreaks is too often neglected; that must change.
 
Advertising.
World View  
 
 
 
Faith and science can find common ground
Pope Francis has found a meeting place for those with extreme religious and environmentalist stances, says David M. Lodge.
 
Seven Days  
 
 
 
The week in science: 24–30 July 2015
Warning about the dangers of AI weapons; Nigeria free of polio; and a hazy halo around Pluto.
Research Highlights  
 
 
 
Animal behaviour: How boa constrictors really kill | Quantum information: Qubit control in a 3D matrix | Stem cells: Stomach tissue made in a dish | Neurobiology: Marijuana's good without the bad | Astronomy: Telescope spies early galaxy's birth | Neurobiology: A critical period for brain health | Microbiology: Microbe war waged with biofilms | Engineering: Origami for thick materials | Metabolism: Reroute bile for better metabolism
Social Selection
Scientist criticizes media portrayal of research
 
 
News in Focus
 
Antibody drugs for Alzheimer's show glimmers of promise
After a string of failed trials, drugs that target protein build-up in the brain appear to slow disease progress.
Sara Reardon
  NASA launches mission to Greenland
Ship and planes will probe water–ice interface in fjords.
Jeff Tollefson
NASA spies Earth-sized exoplanet orbiting Sun-like star
Potentially rocky world spotted by Kepler spacecraft offers glimpse at Earth's future.
Alexandra Witze
  Neanderthals had outsize effect on human biology
From skin disorders to the immune system, sex with archaic species changed Homo sapiens.
Ewen Callaway
Budget showdown leaves US science agencies in limbo
Lawmakers face looming deadline to reach a deal — or risk government shutdown.
Chris Cesare
  'Half-pipe' telescope will probe dark energy in teen Universe
Canadian observatory aims to chart cosmic expansion rate between 10 billion and 8 billion years ago.
Davide Castelvecchi
Features  
 
 
 
Hospital checklists are meant to save lives — so why do they often fail?
An easy method that promised to cut complications in surgery may not be so simple after all.
Emily Anthes
The boom in mini stomachs, brains, breasts, kidneys and more
Biologists are building banks of 'organoids', and learning a lot about human development on the way.
Cassandra Willyard
Multimedia  
 
 
Podcast: 30 July 2015
This week, the ancient art of kirigami – paper cutting – applied to graphene. Plus, mini organs in dishes, and how mitochondria power our muscles.
Graphene Kirigami
Nature Video finds out how the Japanese art of paper cutting can give 'supermaterial' graphene even more incredible properties.
Correction  
 
 
Clarification
Correction
 
 
Comment
 
History: From blackboards to bombs
Seventy years after the destruction of Hiroshima and Nagasaki by nuclear weapons, David Kaiser investigates the legacy of 'the physicists' war'.
David Kaiser
Policy: Define biomass sustainability
The future of the bioeconomy requires global agreement on metrics and the creation of a dispute resolution centre, say Roeland Bosch, Mattheüs van de Pol and Jim Philp.
Roeland Bosch, Mattheüs van de Pol, Jim Philp
Summer Books  
 
 
 
Summer books
Plunge into a profusion of brilliant summer reads suggested by regular reviewers and editors, far away from the lab and lecture hall.
Nathaniel Comfort, Kevin Padian, Michael Harris et al.
Correspondence  
 
 
 
World Heritage Site: Many ways to access hominin fossil finds
Lee R. Berger
  Education: Initiatives to bridge faith and science
S. Joshua Swamidass
Forests: Tree rings track climate trade-offs
Pieter A. Zuidema, David Frank
  Europe: Universities aim for a sustainable future
Yves Fassin
Obituary  
 
 
 
Irwin Allan Rose (1926–2015)
Established role of ubiquitin in the destruction of cellular proteins.
Keith Wilkinson, Avram Hershko
 
 
Research
 
NEW ONLINE  
 
 
 
Microbiology: Cyanate fuels the nitrogen cycle
Cyanate, a degradation product of urea and cyanide, has been found to be a sufficient single substrate for the growth and reciprocal feeding of microorganisms that are essential to the global nitrogen cycle.
Synthetic biology: Ribosomal ties that bind
The ribosome is the cellular complex of proteins and RNA molecules that synthesizes proteins. An artificial ribosome in which the two main subunits are tethered together creates opportunities for engineering this process.
DNA replication: Strand separation unravelled
The DNA double helix must be separated into single strands to be duplicated. A structure of the Mcm2–7 helicase enzyme responsible for this activity yields unprecedented insight into how the process is initiated.
HipBA–promoter structures reveal the basis of heritable multidrug tolerance
The molecular basis of multidrug tolerance in chronic urinary tract infections is mediated by mutations in the N-subdomain-1 of the Escherichia coli HipA protein kinase.
Structure of the eukaryotic MCM complex at 3.8 Å
Cryo-electron microscopy is used to visualize the double hexamer of the eukaryotic minichromosome maintenance complex (MCM), which is assembled during the G1 phase of DNA replication; two interdigitated hexamers have a central channel that tightly fits a DNA duplex, and the orientation of the tilted single hexamers sheds light on many functional aspects, particularly in the initial origin DNA melting.
RNA degradation paths in a 12-subunit nuclear exosome complex
Solving the crystal structure of an exosome complex from yeast, bound to different RNA substrates, offers insights into how the exosome can be utilized for precise processing of some 3′ ends, such as that of the 5.8S rRNA, while other RNAs are degraded to completion.
Graphene kirigami
The ratio of in-plane stiffness to out-of-plane bending stiffness of graphene is shown to be similar to that of a piece of paper, which allows ideas from kirigami (a variation of origami that allows cutting) to be applied to micrometre-scale graphene sheets to build mechanically stretchable yet robust electrodes, springs and hinges.
Regulation of mitochondrial morphology and function by stearoylation of TFR1
Mitochondria have essential functions within cells, and their dysfunction is linked to various disorders; here, the fatty acid stearic acid (C18:0), which is a dietary component, and the transferrin receptor (TFR1) are shown to regulate mitochondrial function.
A self-organized biomechanical network drives shape changes during tissue morphogenesis
Feedbacks between the dissociation and advection of myosin II result in self-organized behaviour of actomyosin networks that drives shape changes during tissue morphogenesis.
Cyanate as an energy source for nitrifiers
The ammonia-oxidizing archaeon Nitrososphaera gargensis can utilize cyanate as the only source of energy for growth due to the presence of a cyanase enzyme, and cyanase-encoding nitrite-oxidizing bacteria can work together with cyanase-negative ammonia oxidizers to collectively grow on cyanate via reciprocal feeding; cyanases are widespread in the environment according to metagenomic data sets, pointing to the potential importance of cyanate in the nitrogen cycle.
Protein synthesis by ribosomes with tethered subunits
A ribosome with tethered subunits, 'Ribo-T', is engineered by making a hybrid RNA composed of ribosomal RNA of large and small subunits; Ribo-T can support cell growth in vivo in the absence of wild-type ribosomes, and is used to establish a fully orthogonal ribosome–mRNA system.
Corrigendum: Eocene primates of South America and the African origins of New World monkeys
News and Views  
 
 
 
Sustainability: Bypassing the methane cycle
Paul L. E. Bodelier
Inorganic chemistry: Movies of a growth mechanism
Krista S. Walton
Materials science: Composite for energy storage takes the heat
Harry J. Ploehn
 

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Structural biology: Arresting developments in receptor signalling
Jeffrey L. Benovic
 
Genetics of disease: Associations with depression
Patrick F. Sullivan
Ophthalmology: Cataracts dissolved
J. Fielding Hejtmancik
 
Strong-field physics: Harmonic radiation from crystals
Peter Hommelhoff, Takuya Higuchi
Articles  
 
 
 
Timing and climate forcing of volcanic eruptions for the past 2,500 years
Ice-core and tree-ring data show that large volcanic eruptions in the tropics and high latitudes were primary drivers of temperature variability in the Northern Hemisphere during the past 2,500 years, firmly implicating such eruptions as catalysts in major sixth-century pandemics, famines, and socioeconomic disruptions.
M. Sigl, M. Winstrup, J. R. McConnell et al.
Metabolic co-dependence gives rise to collective oscillations within biofilms
The emergence of long-range metabolic co-dependence within a biofilm drives oscillations in growth that resolve a social conflict between cooperation and competition, thereby increasing community-level fitness against chemical attack.
Jintao Liu, Arthur Prindle, Jacqueline Humphries et al.
Biogenesis and structure of a type VI secretion membrane core complex
The assembly, architecture and role of the bacterial type VI secretion system (T6SS) membrane core complex is presented.
Eric Durand, Van Son Nguyen, Abdelrahim Zoued et al.
Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser
G protein-coupled receptors are a large family of signalling proteins that mediate cellular responses primarily via G proteins or arrestins, and they are targets of one-third of the current clinically used drugs; here, an active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin-1 is determined, revealing unique structural features that may constitute essential elements for arrestin-biased signalling.
Yanyong Kang, X. Edward Zhou, Xiang Gao et al.
Letters  
 
 
 
Lanosterol reverses protein aggregation in cataracts
Exploring the genetic basis of congenital cataracts in two families identifies a molecule, lanosterol, which prevents intracellular protein aggregation of various cataract-causing mutant crystallins, and which can reduce cataract severity and increase lens transparency in vivo in dogs.
Ling Zhao, Xiang-Jun Chen, Jie Zhu et al.
Real-time observation of interfering crystal electrons in high-harmonic generation
The generation of high harmonics in the solid phase is studied with time-resolved measurements and a quantum many-body theory; the underlying motion of electrons is found to differ from that observed during high-harmonic generation in atomic gases, and involves quantum interference between electrons from multiple valence bands.
M. Hohenleutner, F. Langer, O. Schubert et al.
A Middle Triassic stem-turtle and the evolution of the turtle body plan
A new Middle Triassic stem-turtle from Germany sheds new light on the evolutionary transition of turtles and their long-contentious relationships to other amniotes.
Rainer R. Schoch, Hans-Dieter Sues
Sparse whole-genome sequencing identifies two loci for major depressive disorder
Genomic analysis of 5,303 Chinese women with recurrent major depressive disorder (MDD) enables the identification and replication of two genome-wide significant loci contributing to risk of MDD on chromosome 10: one near the SIRT1 gene; the other in an intron of the LHPP gene.
CONVERGE consortium, Na Cai, Tim B. Bigdeli et al.
Impermanence of dendritic spines in live adult CA1 hippocampus
A new microendoscopic method reveals that hippocampal dendritic spines in the CA1 region undergo a complete turnover in less than six weeks in adult mice; this contrasts with the much greater stability of synapses in the neocortex and provides a physical basis for the fact that episodic memories are only retained by the mouse hippocampus for a few weeks.
Alessio Attardo, James E. Fitzgerald, Mark J. Schnitzer
Magnetospherically driven optical and radio aurorae at the end of the stellar main sequence
Radio and optical spectroscopic observations of a brown dwarf reveal auroral emissions powered by magnetospheric currents, showing that aurorae may be a signature of magnetospheres much larger than those observed in our Solar System.
G. Hallinan, S. P. Littlefair, G. Cotter et al.
Flexible high-temperature dielectric materials from polymer nanocomposites
The addition of boron nitride nanosheets to polymer nanocomposites creates dielectric materials that operate at much higher working temperatures than previous polymer dielectrics, as well as being flexible, lightweight, photopatternable, scalable and robust, which now makes them more attractive for electronic device applications than ceramic dielectrics.
Qi Li, Lei Chen, Matthew R. Gadinski et al.
Onset of Antarctic Circumpolar Current 30 million years ago as Tasmanian Gateway aligned with westerlies
Neodymium isotopes from fossil fish teeth and tectonic reconstructions show that the deep Tasmanian Gateway opened up about 33 million years ago and that the Antarctic Circumpolar Current arose 30 million years ago, when the gateway probably moved into the latitudes of the strong westerly winds.
Howie D. Scher, Joanne M. Whittaker, Simon E. Williams et al.
Parent stem cells can serve as niches for their daughter cells
Little is known about how the relative proportions of stem cells and differentiated cells are regulated; basal stem/progenitor cells of the mouse airway epithelium self renew and differentiate into secretory and ciliated cells, and basal stem cells continuously send daughter cells a forward niche signal necessary for daughter cell fate maintenance.
Ana Pardo-Saganta, Purushothama Rao Tata, Brandon M. Law et al.
Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice
Expression of a barley transcription factor SUSIBA2 in rice generates a plant with high-starch content and low-methane emissions by conferring a shift in the carbon flux that favours the allocation of photosynthates to aboveground biomass rather than to the roots.
J. Su, C. Hu, X. Yan et al.
T-cell exhaustion, co-stimulation and clinical outcome in autoimmunity and infection
CD8 T-cell exhaustion, although a negative prognostic indicator during persistent infections, is shown to be associated with a good outcome in autoimmune and inflammatory diseases.
Eoin F. McKinney, James C. Lee, David R. W. Jayne et al.
Mitochondrial reticulum for cellular energy distribution in muscle
Mitochondria are shown to form a conductive pathway throughout the cell in the form of a proton motive force, and throughout this network, mitochondrial protein localization seems to be varied, allowing optimized generation and utilization of the mitochondrial membrane potential; the rapid energy distribution network, which depends on conduction rather than diffusion, could explain how the muscle can rapidly respond to energy demands.
Brian Glancy, Lisa M. Hartnell, Daniela Malide et al.
Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex
Structural and biochemical studies of RNA polymerase II (Pol II) assembled on DNA containing 5-carboxycytosine reveals that Pol II can sense the oxidized methylation state of DNA and transiently slows down during transcription.
Lanfeng Wang, Yu Zhou, Liang Xu et al.
Corrigenda  
 
 
 
Corrigendum: Genome-wide characterization of the routes to pluripotency
Samer M. I. Hussein, Mira C. Puri, Peter D. Tonge et al.
Corrigendum: Divergent reprogramming routes lead to alternative stem-cell states
Peter D. Tonge, Andrew J. Corso, Claudio Monetti et al.
Retraction  
 
 
 
Retraction: Integrative genomics identifies APOE ε4 effectors in Alzheimer's disease
Herve Rhinn, Ryousuke Fujita, Liang Qiang et al.
 
 

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Careers & Jobs
 
Feature  
 
 
 
Extramural work: To serve or not to serve
Roberta Kwok
Q&AS  
 
 
 
Turning point: Heather Schneider
Virginia Gewin
Futures  
 
 
The shoulder of Orion
A life-changing experience.
Eric Garside
 
 
 
 
 

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