Nature Communications - 15 October 2014

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Weekly Content Alert 15 October 2014  Featured image: Santos et al. determine the genetic basis of egg-spots found on the anal fins of male cichlid fishes Latest content: Articles Corrigendum Journal homepage Recommend to library Web feed   Advertisement Scientific Reports is now accepting submissions from all scientific fields. Online and open access, Scientific Reports is a primary research publication from the publishers of Nature, covering all areas of the natural and clinical sciences. The scope of the journal has been broadened to include all fields of medical research. Submit your manuscript now.        Latest Articles View all Articles     Carbonate-hosted methanotrophy represents an unrecognized methane sink in the deep sea Jeffrey J. Marlow, Joshua A. Steele, Wiebke Ziebis, Andrew R. Thurber, Lisa A. Levin and Victoria J. Orphan Methane is a significant contributor to greenhouse forcing, and determining its fluxes and reservoirs is important in understanding the methane cycle. Here, the authors investigate microbial methane oxidation in carbonates of the deep sea that represent a previously unrecognized biological sink for methane. 14 October 2014 | doi: 10.1038/ncomms6094 Earth Sciences  Biogeochemistry  Microbiology  Ultralow viscosity of carbonate melts at high pressures Yoshio Kono, Curtis Kenney-Benson, Daniel Hummer, Hiroaki Ohfuji, Changyong Park, Guoyin Shen, Yanbin Wang, Abby Kavner and Craig E. Manning Carbonate melt is one of the most important materials involved in the carbon cycle of the Earth’s interior; however, its mobility is poorly understood. Here, the authors suggest that carbonate melts possess much lower viscosities than previously thought, which in turn suggest very high mobility. 14 October 2014 | doi: 10.1038/ncomms6091 Earth Sciences  Geology and geophysics  Emulating weak localization using a solid-state quantum circuit Yu Chen, P. Roushan, D. Sank, C. Neill, Erik Lucero, Matteo Mariantoni, R. Barends, B. Chiaro, J. Kelly, A. Megrant, J. Y. Mutus, P. J. J. O'Malley, A. Vainsencher, J. Wenner, T. C. White, Yi Yin, A. N. Cleland and John M. Martinis Quantum simulators offer a test bed to emulate physical phenomena that are difficult to reproduce numerically. Using a multi-element superconducting quantum circuit, Chen et al. emulate weak localization for a mesoscopic system using a control sequence that lets them continuously tune the level of disorder. 14 October 2014 | doi: 10.1038/ncomms6184 Physical Sciences  Nanotechnology  Theoretical physics  A scaling law for random walks on networks OPEN Theodore J. Perkins, Eric Foxall, Leon Glass and Roderick Edwards Random walks on a network describe the dynamics of many natural and artificial systems. Here, Perkins et al. study the path distribution—characterizing how the walker moves—and find that it is either finite, stretched exponential or power law for any random walk on a finite network. 14 October 2014 | doi: 10.1038/ncomms6121 Physical Sciences  Applied physics  Biophysics  Prediction of extreme floods in the eastern Central Andes based on a complex networks approach N. Boers, B. Bookhagen, H. M. J. Barbosa, N. Marwan, J. Kurths and J. A. Marengo Extreme rainfall events in the eastern Central Andes can result in substantial economic and ecological damage, yet their prediction is difficult. Here, the authors introduce the concept of network divergence and propose a general framework for the prediction of extreme events. 14 October 2014 | doi: 10.1038/ncomms6199 Earth Sciences  Atmospheric science  Climate science  Stimuli-sensitive intrinsically disordered protein brushes Nithya Srinivasan, Maniraj Bhagawati, Badriprasad Ananthanarayanan and Sanjay Kumar Polymer brush surface coatings are important biomaterials for the reduction of biomolecule and cell adhesion. Here, the authors use a recombinantly expressed, intrinsically disordered protein to form a stimuli-responsive and enzyme-active polymer brush surface. 14 October 2014 | doi: 10.1038/ncomms6145 Physical Sciences  Bioengineering  Materials science  Drosophila Strip serves as a platform for early endosome organization during axon elongation Chisako Sakuma, Takeshi Kawauchi, Shuka Haraguchi, Mima Shikanai, Yoshifumi Yamaguchi, Vladimir I. Gelfand, Liqun Luo, Masayuki Miura and Takahiro Chihara Endosomes are critical for regulating the amount and localization of cell surface molecules. Here the authors performed a genetic screen in Drosophila and identified the protein, Strip, as a molecular linker between retrograde transport and fusion of early endosomes, which is required for axonal growth. 14 October 2014 | doi: 10.1038/ncomms6180 Biological Sciences  Cell biology  Neuroscience  Manganese hexacyanomanganate open framework as a high-capacity positive electrode material for sodium-ion batteries Hyun-Wook Lee, Richard Y. Wang, Mauro Pasta, Seok Woo Lee, Nian Liu and Yi Cui Sodium-ion batteries are considered an alternative to lithium-ion batteries because of easy availability and low cost of sodium. Here, Lee et al. report a manganese hexacyanomanganate material as a sodium-ion battery cathode, which exhibits high discharge capacity. 14 October 2014 | doi: 10.1038/ncomms6280 Chemical Sciences  Materials science  Physical chemistry  Implementation of a quantum metamaterial using superconducting qubits Pascal Macha, Gregor Oelsner, Jan-Michael Reiner, Michael Marthaler, Stephan André, Gerd Schön, Uwe Hübner, Hans-Georg Meyer, Evgeni Il’ichev and Alexey V. Ustinov Superconducting flux qubits operating as two-level systems can act as artificial atoms, and so represent a potential metamaterial building block. Macha et al. assemble 20 such qubits into a metamaterial in which the ‘atoms’ are collectively coupled to the quantized mode of a microwave photon field. 14 October 2014 | doi: 10.1038/ncomms6146 Physical Sciences  Condensed matter  Materials science  Nanotechnology  Host–parasite network structure is associated with community-level immunogenetic diversity Shai Pilosof, Miguel A. Fortuna, Jean-François Cosson, Maxime Galan, Chaisiri Kittipong, Alexis Ribas, Eran Segal, Boris R. Krasnov, Serge Morand and Jordi Bascompte Genes of the major histocompatibility complex (MHC) are crucial for immune response, yet it is unclear what shapes their diversity at a community level. Here, the authors show that indirect effects among rodent hosts and their helminth parasites can play a crucial role in shaping host MHC diversity. 14 October 2014 | doi: 10.1038/ncomms6172 Biological Sciences  Ecology  Evolution  Missing driver in the Sun–Earth connection from energetic electron precipitation impacts mesospheric ozone OPEN M. E. Andersson, P. T. Verronen, C. J. Rodger, M. A. Clilverd and A. Seppälä Energetic electron precipitation (EEP) from the Earth's outer radiation belt can lead to ozone loss in the mesosphere, yet long-term variability has not been quantified. Here, the authors present satellite observations and show that on solar cycle timescales EEP causes ozone to vary by up to 34%. 14 October 2014 | doi: 10.1038/ncomms6197 Earth Sciences  Atmospheric science  Climate science  Optical control of insulin release using a photoswitchable sulfonylurea OPEN Johannes Broichhagen, Matthias Schönberger, Simon C. Cork, James A. Frank, Piero Marchetti, Marco Bugliani, A. M. James Shapiro, Stefan Trapp, Guy A. Rutter, David J. Hodson and Dirk Trauner Sulfonylureas are widely used anti-diabetic drugs, which promote insulin release by blocking a pancreatic ion channel. Here the authors create a photoswitchable sulfonylurea derivative and use it to control insulin release from cultured cells and isolated pancreatic islets by illumination with blue light. 14 October 2014 | doi: 10.1038/ncomms6116 Biological Sciences  Chemical biology  The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration Sung-Hoon Jun, Akira Hirata, Tamotsu Kanai, Thomas J. Santangelo, Tadayuki Imanaka and Katsuhiko S. Murakami Archaeal and eukaryotic RNA polymerases (RNAP) have conserved functional and structural similarities. Here, Jun et al. solve the first structure of a euryarchaeal RNAP in the open clamp conformation and identify insertions that may have evolved in eukaryotic Pol II to bind unique transcription factors. 14 October 2014 | doi: 10.1038/ncomms6132 Biological Sciences  Biochemistry  Microbiology  mGlu5 receptors regulate synaptic sumoylation via a transient PKC-dependent diffusional trapping of Ubc9 into spines Céline Loriol, Frédéric Cassé, Anouar Khayachi, Gwénola Poupon, Magda Chafai, Emmanuel Deval, Carole Gwizdek and Stéphane Martin Sumoylation plays key roles in neurotransmission but the mechanisms regulating this post-translational system in neurons remain unclear. Here the authors show that synaptic diffusion of the sole SUMO-conjugating enzyme Ubc9 is regulated by synaptic activity via an mGlu5R-dependent signalling pathway. 14 October 2014 | doi: 10.1038/ncomms6113 Biological Sciences  Cell biology  Neuroscience  Quantum mechanical limit to plasmonic enhancement as observed by surface-enhanced Raman scattering Wenqi Zhu and Kenneth B. Crozier Plasmonic nanostructures concentrate light into sub-wavelength volumes, enhancing its electric field. In a series of surface-enhanced Raman measurements, Zhu and Crozier show that as the structure size shrinks, quantum-mechanical electron tunnelling places a limit on the achievable enhancement. 14 October 2014 | doi: 10.1038/ncomms6228 Physical Sciences  Nanotechnology  Optical physics  Highly modular bow-tie gene circuits with programmable dynamic behaviour Laura Prochazka, Bartolomeo Angelici, Benjamin Haefliger and Yaakov Benenson Engineering gene expression systems that can be programmed to respond to specific environmental conditions is challenging. Here, the authors develop a synthetic bow-tie circuit that is able to sense signals from microRNA molecules and affect a change in protein dynamics in mammalian cells. 14 October 2014 | doi: 10.1038/ncomms5729 Biological Sciences  Bioengineering  Systems biology  Thermally robust and porous noncovalent organic framework with high affinity for fluorocarbons and CFCs Teng-Hao Chen, Ilya Popov, Watchareeya Kaveevivitchai, Yu-Chun Chuang, Yu-Sheng Chen, Olafs Daugulis, Allan J. Jacobson and Ognjen Š. Miljanić There is significant research into using metal-organic frameworks for gas storage and separation, however, discrete molecule-based systems are rarer. Here, the authors report a small organic molecule that organizes into a relatively stable noncovalent organic framework, capable of adsorbing greenhouse species. 13 October 2014 | doi: 10.1038/ncomms6131 Chemical Sciences  Materials science  Nanotechnology  Organic chemistry  Vanadium dioxide nanowire-based microthermometer for quantitative evaluation of electron beam heating H. Guo, M. I. Khan, C. Cheng, W. Fan, C. Dames, J. Wu and A. M. Minor Understanding localized heating of a material by a beam of electrons is important in electron microscopy, but measuring temperature at the nanoscale is difficult. Here, the authors show that a vanadium dioxide nanowire can act as a microthermometer and measure electron beam heating in silicon nanowires. 13 October 2014 | doi: 10.1038/ncomms5986 Physical Sciences  Applied physics  Nanotechnology  Small palladium islands embedded in palladium–tungsten bimetallic nanoparticles form catalytic hotspots for oxygen reduction Guangzhi Hu, Florian Nitze, Eduardo Gracia-Espino, Jingyuan Ma, Hamid Reza Barzegar, Tiva Sharifi, Xueen Jia, Andrey Shchukarev, Lu Lu, Chuansheng Ma, Guang Yang and Thomas Wågberg Bimetallic nanoparticles are extensively investigated as electrocatalysts for fuel cell applications. Here, the authors demonstrate that palladium–tungsten nanoparticles are very active for the oxygen reduction reaction, attributed to the formation of small palladium islands embedded in the nanoparticles. 13 October 2014 | doi: 10.1038/ncomms6253 Chemical Sciences  Catalysis  Materials science  Integrated control of hepatic lipogenesis versus glucose production requires FoxO transcription factors Rebecca A. Haeusler, Kirsten Hartil, Bhavapriya Vaitheesvaran, Isabel Arrieta-Cruz, Colette M. Knight, Joshua R. Cook, Helene L. Kammoun, Mark A. Febbraio, Roger Gutierrez-Juarez, Irwin J. Kurland and Domenico Accili The transcription factors FoxoO1 and Srebp-1 control hepatic glucose and lipid production, respectively. Here, Haeusler et al. propose a model that integrates glucose and lipid regulation in the normal and diabetic liver under the unifying control of FoxO transcription factors. 13 October 2014 | doi: 10.1038/ncomms6190 Biological Sciences  Medical research  Germline variants in the SEMA4A gene predispose to familial colorectal cancer type X OPEN Eduard Schulz, Petra Klampfl, Stefanie Holzapfel, Andreas R. Janecke, Peter Ulz, Wilfried Renner, Karl Kashofer, Satoshi Nojima, Anita Leitner, Armin Zebisch, Albert Wölfler, Sybille Hofer, Armin Gerger, Sigurd Lax, Christine Beham-Schmid, Verena Steinke, Ellen Heitzer, Jochen B. Geigl, Christian Windpassinger, Gerald Hoefler et al. It is known that hereditary factors contribute to familial colorectal cancer type X. Here, the authors uncover the SEMA4A p.Val78Met germline mutation and show that the protein product is associated with changes in cell cycle progression in colorectal cancer cells. 13 October 2014 | doi: 10.1038/ncomms6191 Biological Sciences  Cancer  Genetics  Dual-comb spectroscopy based on quantum-cascade-laser frequency combs Gustavo Villares, Andreas Hugi, Stéphane Blaser and Jérôme Faist The fundamental vibrational bands of many molecules lie on the mid-infrared, so generating all solid-state, compact frequency combs in that region is important for molecular spectroscopy. Here, Villares et al. use quantum-cascade-laser frequency combs to demonstrate a high resolution, broadband dual-comb spectrometer. 13 October 2014 | doi: 10.1038/ncomms6192 Physical Sciences  Applied physics  Nanotechnology  Optical physics  Improving battery safety by early detection of internal shorting with a bifunctional separator Hui Wu, Denys Zhuo, Desheng Kong and Yi Cui Dendrite growth in lithium-based batteries is hazardous as it could cause internal shorts and raise safety concerns. Here, the authors design a bifunctional separator in lithium-ion batteries, which serves as a sensing terminal and is able to detect early dendrite growth inside the batteries. 13 October 2014 | doi: 10.1038/ncomms6193 Chemical Sciences  Materials science  Nanotechnology  A polarity-induced defect mechanism for conductivity and magnetism at polar–nonpolar oxide interfaces Liping Yu and Alex Zunger The interface between LaAlO3 and SrTiO3 shows unusual phenomena such as a two-dimensional electron gas as well as magnetism. Here, Yu and Zunger show how the formation of defects contributes to the properties of this system. 13 October 2014 | doi: 10.1038/ncomms6118 Physical Sciences  Condensed matter  Materials science  Trinucleotide duplex formation inside a confined nanospace under supercooled conditions Hiroyuki Arafune, Akira Yamaguchi, Manato Namekawa, Yusuke Sato, Tetsuji Itoh, Ryoko Yoshida and Norio Teramae The hybridization of DNA in solution is more difficult the shorter the strands become, making trimer duplexes difficult to isolate and study. Here, the authors use a silica pore in supercooled conditions to isolate and study complementary and mismatched trimer DNA duplexes. 13 October 2014 | doi: 10.1038/ncomms6151 Physical Sciences  Nanotechnology  Direct measurement of dysprosium(III)˙˙˙dysprosium(III) interactions in a single-molecule magnet Eufemio Moreno Pineda, Nicholas F. Chilton, Raphael Marx, María Dörfel, Daniel O. Sells, Petr Neugebauer, Shang-Da Jiang, David Collison, Joris van Slageren, Eric J.L. McInnes and Richard E.P. Winpenny Modelling magnetic data for lanthanide clusters is challenging due to spin–orbit coupling and crystal field effects. Here, the authors use multi-frequency electron paramagnetic resonance spectroscopy to measure directly the interaction between two dysprosium(III) ions in a dimeric system. 13 October 2014 | doi: 10.1038/ncomms6243 Chemical Sciences  Inorganic chemistry  Nanotechnology  Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids OPEN A. San Millan, R. Peña-Miller, M. Toll-Riera, Z. V. Halbert, A. R. McLean, B. S. Cooper and R. C. MacLean Plasmids are important for bacterial evolution but the evolutionary mechanisms behind their maintenance are unclear. Here the authors show that the interplay between compensatory adaptation and positive selection for plasmid-encoded antibiotic resistance determines plasmid persistence in P. aeruginosa. 10 October 2014 | doi: 10.1038/ncomms6208 Biological Sciences  Evolution  Genetics  Temperature-dependent elastic anisotropy and mesoscale deformation in a nanostructured ferritic alloy G.M. Stoica, A.D. Stoica, M.K. Miller and D. Ma Nanostructured ferritic alloys offer many attractive properties that make them suitable for use in extreme environments. Here, the authors use neutron diffraction to determine single-crystal elastic constants of nanoscale ferrite grains, observing a large temperature-induced elastic anisotropy. 10 October 2014 | doi: 10.1038/ncomms6178 Physical Sciences  Materials science  Lin28/let-7 axis regulates aerobic glycolysis and cancer progression via PDK1 Xiaoyu Ma, Chenchen Li, Linchong Sun, De Huang, Tingting Li, Xiaoping He, Gongwei Wu, Zheng Yang, Xiuying Zhong, Libing Song, Ping Gao and Huafeng Zhang The RNA-binding proteins Lin28A and Lin28B are known to have key roles in a variety of pathological states including cancer, obesity and diabetes. Here the authors show that Lin28A and -B alter cancer metabolism through let-7-mediated upregulation of pyruvate dehydrogenase kinase 1. 10 October 2014 | doi: 10.1038/ncomms6212 Biological Sciences  Cancer  Molecular biology  SLO-2 potassium channel is an important regulator of neurotransmitter release in Caenorhabditis elegans Ping Liu, Bojun Chen and Zhao-Wen Wang Slo2 potassium channels are a major conductor of delayed outward current in neurons but their physiological roles are unclear. Here, the authors show that Slo-2 channels in Caenorhabditis elegans motor neurons regulate neurotransmitter release, which is dependent on L-type voltage-gated calcium channels. 10 October 2014 | doi: 10.1038/ncomms6155 Biological Sciences  Neuroscience  The mediator subunit Med23 contributes to controlling T-cell activation and prevents autoimmunity Yang Sun, Xiaoyan Zhu, Xufeng Chen, Haifeng Liu, Yu Xu, Yajing Chu, Gang Wang and Xiaolong Liu T-cell activation is controlled by signalling through the T-cell receptor and other molecules. Here the authors show that Med23 is a negative regulator of T-cell activation at a transcriptional level and that Med23 deficiency in T cells results in development of autoimmunity in aged mice. 10 October 2014 | doi: 10.1038/ncomms6225 Biological Sciences  Immunology  Cassava genome from a wild ancestor to cultivated varieties OPEN Wenquan Wang, Binxiao Feng, Jingfa Xiao, Zhiqiang Xia, Xincheng Zhou, Pinghua Li, Weixiong Zhang, Ying Wang, Birger Lindberg Møller, Peng Zhang, Ming-Cheng Luo, Gong Xiao, Jingxing Liu, Jun Yang, Songbi Chen, Pablo D. Rabinowicz, Xin Chen, Hong-Bin Zhang, Henan Ceballos, Qunfeng Lou et al. Cassava is a major source of food in tropical and subtropical regions. Here the authors sequence the genomes of wild and domesticated cassava varieties and identify genes that have been selected for and against during the evolution and domestication of this economically important crop. 10 October 2014 | doi: 10.1038/ncomms6110 Biological Sciences  Genetics  Plant sciences  Sexual dimorphism in epigenomic responses of stem cells to extreme fetal growth Fabien Delahaye, N. Ari Wijetunga, Hye J. Heo, Jessica N. Tozour, Yong Mei Zhao, John M. Greally and Francine H. Einstein Extreme fetal growth is associated with increased risk of various adult diseases, although the mechanism underlying these associations is poorly understood. Here the authors show that abnormal fetal growth correlates with increased DNA methylation levels and report sex-specific epigenetic patterns associated with fetal growth. 10 October 2014 | doi: 10.1038/ncomms6187 Biological Sciences  Developmental biology  Chiral magnetism and spontaneous spin Hall effect of interacting Bose superfluids Xiaopeng Li, Stefan S. Natu, Arun Paramekanti and S. Das Sarma Ultracold atoms in optical lattices exhibit many exotic phenomena. Using interacting spinor Bose gases as a model, Li et al. show how spin-valley degeneracy arising in a multivalley band is broken by quantum fluctuations, resulting in a counterintuitive chiral spin order and a spontaneous spin Hall effect. 10 October 2014 | doi: 10.1038/ncomms6174 Physical Sciences  Condensed matter  Theoretical physics  Engineering polar discontinuities in honeycomb lattices Marco Gibertini, Giovanni Pizzi and Nicola Marzari It has been predicted that when a polar discontinuity occurs in honeycomb lattices, wires of electrons or holes would appear. Here, the authors suggest different and realistic routes to engineer such wires in current two-dimensional materials, and validate these with first-principles calculations. 10 October 2014 | doi: 10.1038/ncomms6157 Physical Sciences  Materials science  Nanotechnology  Exponential rise of dynamical complexity in quantum computing through projections OPEN Daniel Klaus Burgarth, Paolo Facchi, Vittorio Giovannetti, Hiromichi Nakazato, Saverio Pascazio and Kazuya Yuasa It is an old adage in quantum physics that the observation of a system changes its properties, as exemplified by the quantum Zeno effect. Now, Burgarth et al. show that such repeated measurement of a quantum system actually enriches its dynamics, letting it explore a much larger algebra than it did before. 10 October 2014 | doi: 10.1038/ncomms6173 Physical Sciences  Atomic and molecular physics  Theoretical physics  Inflammation-driven carcinogenesis is mediated through STING Jeonghyun Ahn, Tianli Xia, Hiroyasu Konno, Keiko Konno, Phillip Ruiz and Glen N. Barber Chronic inflammation is known to promote tumorigenesis, but the mechanisms underlying this are incompletely understood. Here, the authors show that several carcinogens induce DNA leakage into the cytoplasm, which activates STING-dependent cytokine production and inflammation-driven tumorigenesis. 10 October 2014 | doi: 10.1038/ncomms6166 Biological Sciences  Cancer  Immunology  Visualized effect of oxidation on magnetic recording fidelity in pseudo-single-domain magnetite particles OPEN Trevor P. Almeida, Takeshi Kasama, Adrian R. Muxworthy, Wyn Williams, Lesleis Nagy, Thomas W. Hansen, Paul D. Brown and Rafal E. Dunin-Borkowski Magnetite provides a valuable record of the Earth's geomagnetic history. Here, Almeida et al. combine electron microscopy and energy-loss spectroscopy to study the effects of in situ oxidation on the magnetization fidelity and crystalline phase of pseudo-single domain magnetite grains. 10 October 2014 | doi: 10.1038/ncomms6154 Earth Sciences  Geology and geophysics  Chiral spin liquid and emergent anyons in a Kagome lattice Mott insulator B. Bauer, L. Cincio, B.P. Keller, M. Dolfi, G. Vidal, S. Trebst and A.W.W. Ludwig Chiral spin liquids, a topological phase in frustrated quantum spin systems, have been recently very sought-after. Here, Bauer et al. present a model for a Mott insulator on the Kagome lattice with broken time-reversal symmetry exhibiting such a topological phase. 10 October 2014 | doi: 10.1038/ncomms6137 Physical Sciences  Condensed matter  Theoretical physics  A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar Jason L. Brown, Alison Cameron, Anne D. Yoder and Miguel Vences Inferring evolutionary processes from biogeographic patterns is challenging. Here, the authors present a new method to examine spatial patterns of biodiversity and show that biogeographic patterns of Malagasy amphibians and reptiles are influenced by a combination of diversification processes. 09 October 2014 | doi: 10.1038/ncomms6046 Biological Sciences  Ecology  Evolution  STIM1 triggers a gating rearrangement at the extracellular mouth of the ORAI1 channel Aparna Gudlur, Ariel Quintana, Yubin Zhou, Nupura Hirve, Sahasransu Mahapatra and Patrick G. Hogan The plasma membrane Ca2+ channel ORAI1 is gated directly by the ER-resident protein STIM1. Here Gudlur et al. show that STIM1 elicits conformational changes near the extracellular opening of the channel, involving the Ca2+-binding residue E106 and the pore-lining residue V102, which forms a barrier to ion conduction in the closed state. 09 October 2014 | doi: 10.1038/ncomms6164 Biological Sciences  Biochemistry  Biophysics  Laser-targeted photofabrication of gold nanoparticles inside cells Nicholas I. Smith, Kentaro Mochizuki, Hirohiko Niioka, Satoshi Ichikawa, Nicolas Pavillon, Alison J. Hobro, Jun Ando, Katsumasa Fujita and Yutaro Kumagai Photonic methods can be greatly improved by metal nanoparticles, but biological targets such as cells prevent spatial control of particles, excluding key regions of interest. Here, the authors show laser light can control nanoparticle growth locations in the cell, and probe intracellular molecules. 09 October 2014 | doi: 10.1038/ncomms6144 Physical Sciences  Nanotechnology  Optical physics  Direct visualization of flow-induced conformational transitions of single actin filaments in entangled solutions Inka Kirchenbuechler, Donald Guu, Nicholas A. Kurniawan, Gijsje H. Koenderink and M. Paul Lettinga Semi-flexible polymers are an important structural building block in living cells, which possess unique mechanical properties. Here, the authors visualize the shear-induced conformational transition of actin filaments as a model system to study cell formation in cytoplasmic flows. 09 October 2014 | doi: 10.1038/ncomms6060 Physical Sciences  Biophysics  Materials science  Physical chemistry  Pin1-dependent signalling negatively affects GABAergic transmission by modulating neuroligin2/gephyrin interaction OPEN Roberta Antonelli, Rocco Pizzarelli, Andrea Pedroni, Jean-Marc Fritschy, Giannino Del Sal, Enrico Cherubini and Paola Zacchi The cell adhesion molecule Neuroligin2 (NL2) interacts with the scaffolding protein gephyrin to ensure the functional organization of GABAA receptors at inhibitory synapses. Here the authors show that NL2 binding of Pin1 negatively regulates its ability to complex with gephyrin at these synapses. 09 October 2014 | doi: 10.1038/ncomms6066 Biological Sciences  Cell biology  Neuroscience  Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene Manish Shankla and Aleksei Aksimentiev Advancing our understanding of the interactions between DNA and synthetic nanopores will help in the design of rapid new DNA sequencing techniques. Here, the authors analyse the effect of graphene charge on DNA adhesion and pore translocation, showing controllable stop-and-go transport. 09 October 2014 | doi: 10.1038/ncomms6171 Physical Sciences  Biophysics  Nanotechnology  Magneto-fluorescent core-shell supernanoparticles Ou Chen, Lars Riedemann, Fred Etoc, Hendrik Herrmann, Mathieu Coppey, Mariya Barch, Christian T. Farrar, Jing Zhao, Oliver T. Bruns, He Wei, Peng Guo, Jian Cui, Russ Jensen, Yue Chen, Daniel K. Harris, Jose M. Cordero, Zhongwu Wang, Alan Jasanoff, Dai Fukumura, Rudolph Reimer et al. Magneto-fluorescent nanoparticles hold promise for bioimaging applications, but synthesizing uniform particles with tunable sizes remains challenging. Chen et al. propose an approach for co-assembling magnetic particles with fluorescent quantum dots, leading to well-defined core-shell structures. 09 October 2014 | doi: 10.1038/ncomms6093 Biological Sciences  Cell biology  Neuroscience  A hybrid absorption–adsorption method to efficiently capture carbon OPEN Huang Liu, Bei Liu, Li-Chiang Lin, Guangjin Chen, Yuqing Wu, Jin Wang, Xueteng Gao, Yining Lv, Yong Pan, Xiaoxin Zhang, Xianren Zhang, Lanying Yang, Changyu Sun, Berend Smit and Wenchuan Wang Common approaches for carbon dioxide capture include absorption in amine solutions or adsorption in porous materials. Here, the authors combine these two strategies and report carbon dioxide capture in a slurry of metal-organic frameworks in glycol-2-methylimidazole, which has advantages of both techniques. 09 October 2014 | doi: 10.1038/ncomms6147 Chemical Sciences  Inorganic chemistry  Materials science  The evolution of cichlid fish egg-spots is linked with a cis-regulatory change OPEN M. Emília Santos, Ingo Braasch, Nicolas Boileau, Britta S. Meyer, Loïc Sauteur, Astrid Böhne, Heinz-Georg Belting, Markus Affolter and Walter Salzburger The mechanisms underlying the emergence of novel morphological traits are largely unknown. Here, the authors show that cis-regulatory changes controlling the expression of the fhl2b pigmentation gene are associated with the evolution of egg-spots colour markings in the male fins of a group of cichlids. 09 October 2014 | doi: 10.1038/ncomms6149 Biological Sciences  Evolution  Zoology  A prevalent cancer susceptibility APOBEC3A hybrid allele bearing APOBEC3B 3′UTR enhances chromosomal DNA damage Vincent Caval, Rodolphe Suspène, Milana Shapira, Jean-Pierre Vartanian and Simon Wain-Hobson Human APOBEC3A (A3A) cytidine deaminase is an enzyme that can introduce mutations into chromosomal DNA. Here the authors examine the genotoxic potential of A3A and the related enzyme A3B, and show that a highly prevalent chimaeric A3A-A3B deletion allele has increased DNA damage potential. 09 October 2014 | doi: 10.1038/ncomms6129 Biological Sciences  Cancer  Conditional deletion of Mecp2 in parvalbumin-expressing GABAergic cells results in the absence of critical period plasticity Ling-jie He, Nan Liu, Tian-lin Cheng, Xiao-jing Chen, Yi-ding Li, You-sheng Shu, Zi-long Qiu and Xiao-hui Zhang Critical period plasticity describes a developmental process whereby neural circuits are fine-tuned for specific functions. Here, the authors show that the Rett syndrome protein MeCP2 in GABAergic parvalbumin-expressing neurons is required for critical period plasticity of the visual cortex. 09 October 2014 | doi: 10.1038/ncomms6036 Biological Sciences  Neuroscience  Epistatic interactions between neuraminidase mutations facilitated the emergence of the oseltamivir-resistant H1N1 influenza viruses Susu Duan, Elena A. Govorkova, Justin Bahl, Hassan Zaraket, Tatiana Baranovich, Patrick Seiler, Kristi Prevost, Robert G. Webster and Richard J. Webby Understanding influenza evolution is challenging. Here, the authors determine the timing and order of critical amino acid changes that contributed to a world-wide predominance of oseltamivir-resistant H1N1 influenza viruses and show the role of epistasis in the emergence of novel influenza phenotypes. 09 October 2014 | doi: 10.1038/ncomms6029 Biological Sciences  Evolution  Genetics  Virology  Local determination of the amount of integration of an atom into a crystal surface K. Volgmann, H. Gawronski, Ch Zaum, G. G. Rusina, S. D. Borisova, E. V. Chulkov and K. Morgenstern Point defects in a surface can subtly alter the bulk phonon spectra. Here, the authors show phonon spectra of point defects that are capable of differentiating between different degrees of integration—alloyed or loose in a vacancy—of an atom into a surface. 09 October 2014 | doi: 10.1038/ncomms6089 Physical Sciences  Condensed matter  Nanotechnology  Physical chemistry  Suppressing qubit dephasing using real-time Hamiltonian estimation OPEN M. D. Shulman, S. P. Harvey, J. M. Nichol, S. D. Bartlett, A. C. Doherty, V. Umansky and A. Yacoby Decoherence is anathema to quantum systems, as it reduces their performance and stability. Shulman et al. show that real-time Hamiltonian parameter estimation can significantly increase the coherence time of a qubit by enabling continuous adjustment of its control parameters. 08 October 2014 | doi: 10.1038/ncomms6156 Physical Sciences  Applied physics  Theoretical physics  SNX13 reduction mediates heart failure through degradative sorting of apoptosis repressor with caspase recruitment domain Jun Li, Changming Li, Dasheng Zhang, Dan Shi, Man Qi, Jing Feng, Tianyou Yuan, Xinran Xu, Dandan Liang, Liang Xu, Hong Zhang, Yi Liu, Jinjin Chen, Jiangchuan Ye, Weifang Jiang, Yingyu Cui, Yangyang Zhang, Luying Peng, Zhaonian Zhou and Yi-Han Chen et al. Identification of pathways that drive proper cardiac function is key to prevention and treatment of heart disease. Here the authors describe a novel pathway that regulates cardiomyocyte survival, which involves a sorting protein, SNX13, and its binding partner, ARC, a multifunctional inhibitor of apoptosis. 08 October 2014 | doi: 10.1038/ncomms6177 Biological Sciences  Medical research  Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice OPEN Wanneng Yang, Zilong Guo, Chenglong Huang, Lingfeng Duan, Guoxing Chen, Ni Jiang, Wei Fang, Hui Feng, Weibo Xie, Xingming Lian, Gongwei Wang, Qingming Luo, Qifa Zhang, Qian Liu and Lizhong Xiong Next-generation sequencing technology has made the generation of huge amounts of genetic data possible, but phenotype characterization remains slow and difficult. Here the authors develop a high-throughput phenotyping facility for rice that is able to accurately identify and characterize traits related to morphology, biomass and yield. 08 October 2014 | doi: 10.1038/ncomms6087 Biological Sciences  Biotechnology  Plant sciences  Chiasmatic and achiasmatic inverted meiosis of plants with holocentric chromosomes OPEN Gabriela Cabral, André Marques, Veit Schubert, Andrea Pedrosa-Harand and Peter Schlögelhofer The absence of a defined centromere in organisms with holocentric chromosomes presents particular problems for the control of chromosome segregation during meiosis. Cabral et al. present evidence that two plant species overcome this challenge by inverting the conventional sequence of meiotic divisions. 08 October 2014 | doi: 10.1038/ncomms6070 Biological Sciences  Cell biology  Plant sciences  Alternative meiotic chromatid segregation in the holocentric plant Luzula elegans OPEN Stefan Heckmann, Maja Jankowska, Veit Schubert, Katrin Kumke, Wei Ma and Andreas Houben Conventionally, meiosis depends on a two-step loss of chromosome cohesion that requires distinction between chromosome arms and sister centromeres. Heckmann et al. show that a plant that lacks a single defined centromere overcomes this problem by inverting the sequence of meiotic segregation events. 08 October 2014 | doi: 10.1038/ncomms5979 Biological Sciences  Cell biology  Plant sciences  Dynamic scaling of morphogen gradients on growing domains Patrick Fried and Dagmar Iber Differently sized tissues follow growth patterns that are defined by morphogen gradients, but how the patterns adapt to different tissue size is unclear. Here the authors describe a computational model that can explain morphogen gradient scaling in the Drosophila wing imaginal disc and that may apply to other systems. 08 October 2014 | doi: 10.1038/ncomms6077 Biological Sciences  Developmental biology  Extremely stretchable thermosensitive hydrogels by introducing slide-ring polyrotaxane cross-linkers and ionic groups into the polymer network OPEN Abu Bin Imran, Kenta Esaki, Hiroaki Gotoh, Takahiro Seki, Kohzo Ito, Yasuhiro Sakai and Yukikazu Takeoka Stimuli-responsive hydrogels have potential applications in multiple fields; however, a common problem is the brittleness of the resulting structures. Here, the authors report highly stretchable thermosensitive hydrogels by introducing sliding polyrotaxane cross-linkers and ionic groups into the system. 08 October 2014 | doi: 10.1038/ncomms6124 Chemical Sciences  Materials science  Physical chemistry  Endoplasmic reticulum stress sensitizes cells to DNA damage-induced apoptosis through p53-dependent suppression of p21CDKN1A Coraline Mlynarczyk and Robin Fåhraeus DNA damage arrests the cell cycle in G1. Mlynarczyk et al. show that endoplasmic reticulum stress impairs DNA damage-induced p21 expression in favour of 14-3-3s-mediated G2 arrest by activating the p53 isoform p53/47, resulting in increased apoptosis in cells exposed to both stressors. 08 October 2014 | doi: 10.1038/ncomms6067 Biological Sciences  Cell biology  Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut OPEN Maia Chanrion, Inna Kuperstein, Cédric Barrière, Fatima El Marjou, David Cohen, Danijela Vignjevic, Lev Stimmer, Perrine Paul-Gilloteaux, Ivan Bièche, Silvina Dos Reis Tavares, Giuseppe-Fulvio Boccia, Wulfran Cacheux, Didier Meseure, Silvia Fre, Loredana Martignetti, Patricia Legoix-Né, Elodie Girard, Luc Fetler, Emmanuel Barillot, Daniel Louvard et al. Metastasizing tumour cells undergo epithelial-to-mesenchymal transition. Using both bioinformatic and in vivo approaches, Chanrion et al. identify combined Notch activation and p53 inactivation as a potent inducer of this transition, and apply this to create a highly metastatic tumour model in mice. 08 October 2014 | doi: 10.1038/ncomms6005 Biological Sciences  Cancer  Systems biology  Few-layer molybdenum disulfide transistors and circuits for high-speed flexible electronics Rui Cheng, Shan Jiang, Yu Chen, Yuan Liu, Nathan Weiss, Hung-Chieh Cheng, Hao Wu, Yu Huang and Xiangfeng Duan Molybdenum disulfide holds great potential for advanced flexible electronic devices. Here, using a transferred gate technique, the authors fabricate molybdenum disulfide-based transistors with optimized device geometry and contact, improving device speed and demonstrating gigahertz circuits with voltage gain. 08 October 2014 | doi: 10.1038/ncomms6143 Physical Sciences  Materials science  Nanotechnology  Constitutive phospholipid scramblase activity of a G protein-coupled receptor Michael A. Goren, Takefumi Morizumi, Indu Menon, Jeremiah S. Joseph, Jeremy S. Dittman, Vadim Cherezov, Raymond C. Stevens, Oliver P. Ernst and Anant K. Menon Opsin has recently been shown to equilibrate phospholipids across the photoreceptor disc membranes. Goren et al. demonstrate that the large conformational changes driven by exposure to light are not required for this activity, and provide insight into the potential mechanisms of lipid translocation. 08 October 2014 | doi: 10.1038/ncomms6115 Biological Sciences  Biochemistry  Biophysics  Ultraviolet and visible range plasmonics in the topological insulator Bi1.5Sb0.5Te1.8Se1.2 Jun-Yu Ou, Jin-Kyu So, Giorgio Adamo, Azat Sulaev, Lan Wang and Nikolay I. Zheludev Progress with metamaterials and plasmonics in more applications is stymied by a lack of low-loss media at high frequencies. In this work, Ou et al. show that the topological insulator Bi1.5Sb0.5Te1.8Se1.2 exhibits plasmonic resonances between 350 and 550 nm, and that adding gratings extends this considerably. 08 October 2014 | doi: 10.1038/ncomms6139 Physical Sciences  Condensed matter  Optical physics    Nature Communications JOBS of the week postdoctoral fellow McGill University Doctoral student University of Jyvaskyla, Finland Postdoctoral Researcher John Innes Centre (JIC) PhD Scholarships 2015 – NEW AND REDEVELOPED Arthritis Research UK Research Technician European Molecular Biology Laboratory (EMBL) Post Doctoral Research Fellow Columbia University Doctoral Researcher KU Leuven Postdoctoral Research Associate University of Oxford Four-Year Science PhD Studentships Institute of Cancer Research (ICR) Postdoctoral Fellow San Diego Biomedical Research Institute More Science jobs from Nature Communications EVENT International Symposium Bone Regeneration 11.06.15 Berlin, Germany More science events from       Latest Corrigendum     Corrigendum: Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden J. -B. Cazier, S. R. Rao, C. M. McLean, A. K. Walker, B. J. Wright, E. E. M. Jaeger, C. Kartsonaki, L. Marsden, C. Yau, C. Camps, P. Kaisaki, null null, J. Taylor, J. W. Catto, I. P. M. Tomlinson, A. E. Kiltie and F. C. Hamdy 10 October 2014 | doi: 10.1038/ncomms5809 Biological Sciences  Cancer  Genetics      Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com  More Nature Events You have been sent this Table of Contents Alert because you have opted in to receive it. 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