Wednesday, November 5, 2014

Nature contents: 06 November 2014

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  journal cover  
Nature Volume 515 Issue 7525
 
This Week  
 
 
Editorials  
 
 
 
Journals unite for reproducibility
Consensus on reporting principles aims to improve quality control in biomedical research and encourage public trust in science.
On the mend
The scientific regeneration of central Europe is gathering pace, but needs further help to thrive.
Protect the parks
Balancing the needs of development and conservation is difficult — but urgent.
Advertising.
World View  
 
 
 
Metascience could rescue the ‘replication crisis’
Independent replication of studies before publication may reveal sources of unreliable results, says Jonathan W. Schooler.
Seven Days  
 
 
 
Seven days: 31 October–6 November 2014
The week in science: Lava flow invades Hawaiian town; Poland moves to join European Southern Observatory; and China completes round-trip lunar mission.
Research Highlights  
 
 
 
Zoology: Fish grind teeth to grunt | Virology: Improved mouse for Ebola research | Physiology: How baby bones self-repair | Materials: Device bends light from all angles | Climate change: Greenland's ice at mercy of ocean | Animal behaviour: Chimps plan for better breakfasts | Neuroscience: Nostalgia rewards the brain | Atmospheric science: Warming from soot overestimated | Chemistry: Vibrations yield new type of bond
Social Selection
Conference gender gap revealed
 
 
News in Focus
 
Fledgling space industry resolute after fatal crash
Virgin Galactic accident should not be allowed to stifle innovation, warn analysts.
Alexandra Witze
Future of Great Barrier Reef divides scientists
Marine-park management comes under scrutiny as conservationists descend on Australia.
Daniel Cressey
Ministers promise basket of gifts for German science
Politicians renew commitment to research and education progammes with €25 billion over six years.
Quirin Schiermeier
Models overestimate Ebola cases
Rate of infection in Liberia seems to plateau, raising questions over the usefulness of models in an outbreak.
Declan Butler
Lobbying sways NIH grants
Pressure on lawmakers from patient-advocacy groups has shaped agency spending on rare-disease research.
Sara Reardon
University sued by creationist
Microscopist’s wrongful-dismissal case faces long odds.
Christopher Kemp
Interactive notebooks: Sharing the code
The free IPython notebook makes data analysis easier to record, understand and reproduce.
Helen Shen
Features  
 
 
 
After the Berlin Wall: Central Europe up close
In the 25 years since the collapse of communism, the countries of central and Eastern Europe have each carved their own identity in science.
Alison Abbott, Quirin Schiermeier
Correction  
 
 
Correction
 
 
Comment
 
Working together: A call for inclusive conservation
Heather Tallis, Jane Lubchenco and 238 co-signatories petition for an end to the infighting that is stalling progress in protecting the planet.
Heather Tallis, Jane Lubchenco
Conservation: A to-do list for the world's parks
Experts share their priorities for what must be done to make protected areas more effective at conserving global biodiversity.
Economics: Account for depreciation of natural capital
Economic indicators that omit the depletion and degradation of natural resources and ecosystems are misleading, warns Edward B. Barbier.
Edward B. Barbier
Books and Arts  
 
 
 
History of science: Chemists behaving badly
Theodore Gray revels in the ego-ridden story of the elements that never were.
Theodore Gray
Books in brief
Barbara Kiser reviews five of the week's best science picks.
Barbara Kiser
Chemistry: A life in science and literature
Alison Abbott reviews the latest autobiography of Carl Djerassi, father of the Pill.
Alison Abbott
Correspondence  
 
 
 
Biodiversity: Reap the benefits of the Nagoya Protocol
David E. Schindel, Pierre du Plessis
India: Endangered species damned by dams
Pankaj Barah, Kaveri Bhuyan
Navigation Nobel: Soviet pioneer
Mihai Nadin
Navigation Nobel: Ways to help the lost
Raza M. Naqvi
 
 
Research
 
NEW ONLINE  
 
 
 
Developmental biology: Polarize to elongate
An analysis of fruit-fly embryos reveals that receptor proteins of the Toll family direct the oriented cell rearrangements required for the elongation of the head-to-tail axis during development.
Mammalian evolution: A beast of the southern wild
A newly discovered skull from the Cretaceous period belongs to a mammal that was big, strange and fast-moving. The fossil solves a long-standing mystery, and helps to resolve a controversy about mammalian evolution.
Biochemistry: Succinate strikes
The high levels of tissue-damaging reactive oxygen species that arise during a stroke or heart attack have been shown to be generated through the accumulation of the metabolic intermediate succinate.
First cranial remains of a gondwanatherian mammal reveal remarkable mosaicism
The gondwanatherians were mammals known only from teeth and some jaw fragments that lived in the southern continents alongside dinosaurs; here the entire cranium of a bizarre and badger-sized fossil mammal from the Cretaceous of Madagascar shows that gondwanatherians were related to the better-known multituberculates, a long-lived and successful group of now-extinct rodent-like mammals.
A positional Toll receptor code directs convergent extension in Drosophila
Body axis elongation from head to tail is essential for animal development, however, the spatial cues that direct cell rearrangements relative to the anterior–posterior axis were unknown; this Drosophila study of convergent extension reveals that three Toll family receptors, expressed in overlapping stripes, modulate the contractile properties of cells to generate the polarized cell rearrangements that lead to body axis elongation.
A relative shift in cloacal location repositions external genitalia in amniote evolution
It has been known for some time that limbs share at least some of their molecular patterning mechanism with external genitalia; here, this connection is examined in a variety of species, revealing that once-shared developmental trajectories could help to explain the observed patterning similarities.
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution
Cryo-electron tomography and subtomogram averaging methods reveal the structure of the capsid lattice within intact heterogeneous immature HIV-1 particles.
Approaching disorder-free transport in high-mobility conjugated polymers
Measurements and simulations of several high-mobility conjugated polymers show that their charge transport properties reflect an almost complete lack of disorder in the polymers, despite their amorphous microstructures, resulting from the resilience of the planar polymer backbone conformations to side-chain disorder.
A basal ichthyosauriform with a short snout from the Lower Triassic of China
The Ichthyopterygia appeared in the fossil record as fully evolved, aquatic creatures, with nothing known about their transition from land to water, but now some light is shed on this transition by a fossil from the Lower Triassic of southern China of a small, primitive and possibly amphibious ichthyosaur-like creature, close to the common ancestry of ichthyosaurs and the obscure Hupehsuchia, a group of extinct aquatic reptiles known only from southern China.
Formic-acid-induced depolymerization of oxidized lignin to aromatics
A method for the depolymerization of oxidized lignin under mild conditions in aqueous formic acid is described that results in more than 60 wt% yield of low-molecular-mass aromatics.
IgG1 protects against renal disease in a mouse model of cryoglobulinaemia
Here, the predominant murine immunoglobulin G subclass, IgG1, which is a poor activator of effector mechanisms, is shown to have a regulatory function, protecting against the development of IgG3 immune-complex-driven renal disease by competing with IgG3 for antigen and increasing immune complex solubility.
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.
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.
mTORC1-mediated translational elongation limits intestinal tumour initiation and growth
The mTORC1 complex has been implicated in tumorigenesis owing partially to its ability to increase protein translation; now, mTORC1 activity in the mouse intestine is shown not to be required for normal homeostasis but to be necessary for the triggering of tumorigenesis by APC mutations, suggesting that it could be a good target for the prevention of colorectal cancer in high-risk patients.
The participation of cortical amygdala in innate, odour-driven behaviour
The cortical amygdala is necessary and sufficient for processing odours that evoke aversive and attractive responses without learning.
The mutational landscapes of genetic and chemical models of Kras-driven lung cancer
Whole-exome sequencing is used to compare the mutational landscape of adenomas from three mouse models of non-small-cell lung cancer, induced either by exposure to carcinogens or by genetic mutation of Kras; the results reveal that the two types of tumour have different mutational profiles and adopt different routes to tumour development.
Ischaemic accumulation of succinate controls reperfusion injury through mitochondrial ROS
A metabolomics study on the ischaemic heart identifies succinate as a metabolite that drives the production of reactive oxygen species and contributes to ischaemia-reperfusion injury; pharmacological inhibition of succinate accumulation ameliorates ischaemia-reperfusion injury in a mouse model of heart attack and a rat model of stroke.
News and Views  
 
 
 
Accelerator physics: Surf's up at SLAC
Mike Downer, Rafal Zgadzaj
Developmental biology: Cells unite by trapping a signal
James Sharpe
50 & 100 Years Ago

Scientific Data

We will be attending the Society for Neuroscience conference on 16th - 19th November. Come and see us at booth 201.

Astrophysics: Monster star found hiding in plain sight
Donald F. Figer
Ecology: Diversity breeds complementarity
David Tilman, Emilie C. Snell-Rood
Organic chemistry: Shape control in reactions with light
Kazimer L. Skubi, Tehshik P. Yoon
Cancer: Metastasis risk after anti-macrophage therapy
Ioanna Keklikoglou, Michele De Palma
Insight  
 
 
 
Sustainable ecosystems and society
Patrick Goymer
Implications of agricultural transitions and urbanization for ecosystem services
Graeme S. Cumming, Andreas Buerkert, Ellen M. Hoffmann et al.
Learning to coexist with wildfire
Max A. Moritz, Enric Batllori, Ross A. Bradstock et al.
The performance and potential of protected areas
James E. M. Watson, Nigel Dudley, Daniel B. Segan et al.
Articles  
 
 
 
Life cycles, fitness decoupling and the evolution of multicellularity
Simple cooperating groups of bacteria reproduced either by embracing or purging cheating types; those that embraced cheats adopted a life cycle of alternating phenotypic states, underpinned by a developmental switch that allowed the fitness of collectives to decouple from the fitness of constituent cells.
Katrin Hammerschmidt, Caroline J. Rose, Benjamin Kerr et al.
Architecture of mammalian respiratory complex I
Complex I is the first enzyme of the mitochondrial electron transport chain and it is essential for oxidative phosphorylation in mammalian mitochondria; here the electron cryo-microscopy structure of complex I from bovine heart mitochondria is reported, advancing knowledge of its structure in mammals.
Kutti R. Vinothkumar, Jiapeng Zhu, Judy Hirst
Letters  
 
 
 
Turbulent heating in galaxy clusters brightest in X-rays
Analysis of X-ray data of galaxy clusters shows that turbulent heating of the intracluster medium is sufficient to counteract the radiative energy losses from the medium.
I. Zhuravleva, E. Churazov, A. A. Schekochihin et al.
Suppression of cooling by strong magnetic fields in white dwarf stars
Cool white dwarf stars often have mysteriously strong magnetic fields (because their coolness suggests that they are old, and magnetic fields should decline in strength with age) and unexplained brightness variations; here the magnetic field is shown to suppress atmospheric convection, inhibiting cooling evolution and causing dark spots.
G. Valyavin, D. Shulyak, G. A. Wade et al.
Recent Northern Hemisphere stratospheric HCl increase due to atmospheric circulation changes
Policies have been in place since 1987 to reduce the release of chlorine atoms in the stratosphere, where they deplete ozone; here observations show that since 2007 hydrogen chloride has been increasing in the lower stratosphere of the Northern Hemisphere, an increase that is attributed to a slowdown in atmospheric circulation.
E. Mahieu, M. P. Chipperfield, J. Notholt et al.
Selection for niche differentiation in plant communities increases biodiversity effects
Here, new ecological communities are established using plants from mixed-species communities or monocultures; ecosystem functioning and morphological trait diversity are shown to be greater in plants from mixed-species communities, suggesting that biodiversity effects in natural communities strengthen over time.
Debra Zuppinger-Dingley, Bernhard Schmid, Jana S. Petermann et al.
Nodal signalling determines biradial asymmetry in Hydra
A Nodal-related gene is uncovered in Hydra and is involved in setting up the body axis, and a β-Catenin–Nodal–Pitx signalling cassette is shown to have existed before the divergence of cnidarians, including Hydra, and bilaterians.
Hiroshi Watanabe, Heiko A. Schmidt, Anne Kuhn et al.
High-efficiency acceleration of an electron beam in a plasma wakefield accelerator
To develop plasma wakefield acceleration into a compact and affordable replacement for conventional accelerators, beams of charged particles must be accelerated at high efficiency in a high electric field; here this is demonstrated for a bunch of charged electrons ‘surfing’ on a previously excited plasma wave.
M. Litos, E. Adli, W. An et al.
Solution-processed, high-performance light-emitting diodes based on quantum dots
The insertion of an insulating layer into a multilayer light-emitting diode (LED) based on quantum dots and produced by depositing the layers from solution increases the performance of the LEDs to levels comparable to those of state-of-the-art organic LEDs produced by vacuum deposition, while retaining the advantages of solution processing.
Xingliang Dai, Zhenxing Zhang, Yizheng Jin et al.
Asymmetric photoredox transition-metal catalysis activated by visible light
A chiral iridium complex serves as a sensitizer for photoredox catalysis and at the same time provides very effective asymmetric induction for the enantioselective alkylation of 2-acyl imidazoles; the metal centre simultaneously serves as the exclusive source of chirality, the catalytically active Lewis acid centre, and the photoredox centre.
Haohua Huo, Xiaodong Shen, Chuanyong Wang et al.
Sensory-evoked LTP driven by dendritic plateau potentials in vivo
Whole-cell recordings in mouse somatosensory cortex in vivo show that rhythmic sensory-whisker stimulation induces long-term synaptic potentiation (LTP) in layer 2/3 (L2/3) pyramidal cells, in the absence of somatic spikes, through long-lasting NMDAR-mediated depolarizations that are generated by synaptic networks originating from the posteromedial complex of the thalamus.
Frédéric Gambino, Stéphane Pagès, Vassilis Kehayas et al.
Luminal signalling links cell communication to tissue architecture during organogenesis
Groups of cells within a migrating collective assemble shared luminal cavities that trap and concentrate the signalling molecule fibroblast growth factor, providing a self-organising mechanism to focus and coordinate cell communication within tissues.
Sevi Durdu, Murat Iskar, Celine Revenu et al.
PLETHORA gradient formation mechanism separates auxin responses
Through a combination of experimental and computational approaches, the interplay between the plant hormone auxin and the auxin-induced PLETHORA transcription factors is shown to control zonation and gravity-prompted growth movements in plants.
Ari Pekka Mähönen, Kirsten ten Tusscher, Riccardo Siligato et al.
Cessation of CCL2 inhibition accelerates breast cancer metastasis by promoting angiogenesis
In mouse models of breast cancer, anti-CCL2 therapy—thought to be potentially useful in treating cancer—is shown to accelerate the growth of lung metastases on discontinuation due to a surge of recruitment of bone marrow monocytes and increased interleukin-6-dependent vascularization of the lung metastatic environment.
Laura Bonapace, Marie-May Coissieux, Jeffrey Wyckoff et al.
Tumour-infiltrating Gr-1+ myeloid cells antagonize senescence in cancer
Senescence in cancer can be antagonized by a subset of immune cells acting in a non-cell-autonomous manner.
Diletta Di Mitri, Alberto Toso, Jing Jing Chen et al.
Broad and potent HIV-1 neutralization by a human antibody that binds the gp41–gp120 interface
Molecular and structural characterization is reported for a new broad and potent monoclonal antibody against HIV that binds to an epitope bridging the gp41 and gp120 subunits — the antibody affects a step in virus entry after binding to CD4 and before engagement of CCR5.
Jinghe Huang, Byong H. Kang, Marie Pancera et al.
Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells
The modification of uridine to pseudouridine is widespread in transfer and ribosomal RNAs but not observed so far in a coding RNA; here a new technique is used to detect this modification on a genome-wide scale, leading to the identification of pseudouridylation in messenger RNAs as well as almost 100 new sites in non-coding RNAs.
Thomas M. Carlile, Maria F. Rojas-Duran, Boris Zinshteyn et al.
Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli
The CRISPR/Cas system is an RNA-guided bacterial protection system against foreign nucleic acids of bacterial and archaeal origin; here a high-resolution crystal structure of the CRIPSR RNA–Cas complex shows that the CRIPSR RNA plays an essential role not only in target recognition but also in complex assembly.
Hongtu Zhao, Gang Sheng, Jiuyu Wang et al.
 
 
Nature Autumn Books
What book are you planning on reading next? Discover Nature's selection of the latest must read books to help you make your choice. Find out more
 
 
Careers & Jobs
 
Column  
 
 
 
Column: It takes time and a team to win grants
Ingrid Eisenstadter
Futures  
 
 
Boundary waters
Dive in.
Marissa Lingen
 
 
 
 
 

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