Nature Communications - 27 November 2013

Advertisement Frontiers are launching a new collaborative peer review forum We are excited to announce that we will be launching a new collaborative peer-review forum where referees and authors work together to improve the paper until consensus is met. Our new peer-review forum will provide online-tools and increased efficiency to ensure a transparent and fast review process. Follow us for more information! We'll be posting updates about the launch on Twitter and Facebook     Weekly Content Alert 27 November 2013  Featured image: Ivanova et al. show that surface nanostructure and antibacterial properties of black silicon are similar to those of dragonfly wings. Latest content: Articles Corrigenda Erratum Advertisement The Salk Institute present: The 8th annual Salk Institute, Fondation IPSEN, and Nature Symposium on Biological Complexity: Genes and Physiology January 29-31, 2014 Salk Institute for Biological Studies La Jolla, CA, USA  Click here for more information or to register for this conference today! Journal homepage Recommend to library Web feed     Latest Articles View all Articles     Bactericidal activity of black silicon OPEN Elena P. Ivanova, Jafar Hasan, Hayden K. Webb, Gediminas Gervinskas, Saulius Juodkazis, Vi Khanh Truong, Alex H.F. Wu, Robert N. Lamb, Vladimir A. Baulin, Gregory S. Watson, Jolanta A. Watson, David E. Mainwaring and Russell J. Crawford The topographical features of insect wings result in some interesting surface properties, including hydrophobicity and antibacterial activity. Here, the authors identify the surface of black silicon as a mimic of dragonfly wings and show that it too possesses antibacterial activity. 26 November 2013 | doi: 10.1038/ncomms3838 Chemical Sciences  Materials science  Nanotechnology  Morphology of seahorse head hydrodynamically aids in capture of evasive prey Brad J. Gemmell, Jian Sheng and Edward J. Buskey Seahorses are very slow swimmers, yet they are specialized hunters of fast and evasive prey. Here, the authors show that seahorse head morphology functions to create a zone of minimum hydrodynamic disturbance, which allows the seahorse to slowly approach the prey, and to position itself within capture range. 26 November 2013 | doi: 10.1038/ncomms3840 Biological Sciences  Zoology  A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice OPEN Katrin Rössger, Ghislaine Charpin-El-Hamri and Martin Fussenegger Designer gene circuits allow the controlled expression of proteins in response to specific stimuli. Here, Rössger et al. use synthetic biology approaches to create a fatty-acid biosensor that controls the production of a satiety hormone and use it to control diet-induced obesity in mice. 26 November 2013 | doi: 10.1038/ncomms3825 Biological Sciences  Biotechnology  Medical research  Mutations in the Gabrb1 gene promote alcohol consumption through increased tonic inhibition Quentin M. Anstee, Susanne Knapp, Edward P. Maguire, Alastair M. Hosie, Philip Thomas, Martin Mortensen, Rohan Bhome, Alonso Martinez, Sophie E. Walker, Claire I. Dixon, Kush Ruparelia, Sara Montagnese, Yu-Ting Kuo, Amy Herlihy, Jimmy D. Bell, Iain Robinson, Irene Guerrini, Andrew McQuillin, Elizabeth M.C. Fisher, Mark A. Ungless et al. Mutations in the GABA A receptor have been implicated in alcohol dependence in humans. In this study, the authors show that mice with mutations in the beta 1 subunit of the GABA A receptor exhibit spontaneous GABA A channel opening and preferentially consume alcohol, working harder to access it. 26 November 2013 | doi: 10.1038/ncomms3816 Biological Sciences  Neuroscience  Arid5b facilitates chondrogenesis by recruiting the histone demethylase Phf2 to Sox9-regulated genes Kenji Hata, Rikako Takashima, Katsuhiko Amano, Koichiro Ono, Masako Nakanishi, Michiko Yoshida, Makoto Wakabayashi, Akio Matsuda, Yoshinobu Maeda, Yutaka Suzuki, Sumio Sugano, Robert H. Whitson, Riko Nishimura and Toshiyuki Yoneda The transcription factor Sox9 together with its co-regulators promotes chondrocyte differentiation. Here, Hata et al. find that Arid5b acts as a transcriptional co-regulator of Sox9 by regulating histone demethylation of Sox9 target genes during chondrogenesis in mice. 26 November 2013 | doi: 10.1038/ncomms3850 Biological Sciences  Developmental biology  Ferroelectric polymer networks with high energy density and improved discharged efficiency for dielectric energy storage Paisan Khanchaitit, Kuo Han, Matthew R. Gadinski, Qi Li and Qing Wang Ferroelectric polymers are attractive candidates as dielectric materials for electrical energy storage applications, but suffer from large dielectric loss. Here, the authors report a method for creating ferroelectric polymer networks with reduced dielectric loss and large charge–discharge efficiencies. 26 November 2013 | doi: 10.1038/ncomms3845 Physical Sciences  Applied physics  Materials science  Stepwise histone modifications are mediated by multiple enzymes that rapidly associate with nascent DNA during replication Svetlana Petruk, Kathryn L. Black, Sina K. Kovermann, Hugh W. Brock and Alexander Mazo Chromatin marks have to be re-established after DNA replication. Here, Petruk et al. show that many histone-modifying enzymes are found in close proximity to newly replicated DNA in cells of Drosophila embryos before the corresponding histone marks are re-established. 26 November 2013 | doi: 10.1038/ncomms3841 Biological Sciences  Cell biology  Molecular biology  Gate sequence for continuous variable one-way quantum computation OPEN Xiaolong Su, Shuhong Hao, Xiaowei Deng, Lingyu Ma, Meihong Wang, Xiaojun Jia, Changde Xie and Kunchi Peng Measurement-based one-way quantum computation with cluster states is an efficient route to processing quantum information, yet gate sequences for large states remain elusive. Su et al. present a continuous variable squeezed gate and controlled-phase gate sequence using a six-mode cluster state. 25 November 2013 | doi: 10.1038/ncomms3828 Physical Sciences  Applied physics  Optical physics  Symmetry breaking in a mechanical resonator made from a carbon nanotube A. Eichler, J. Moser, M.I. Dykman and A. Bachtold Carbon nanotube mechanical resonators are able to bend by a large amount through static strain. Here, the authors study how the bending breaks the symmetry of the restoring potential, and how the potential nonlinearity can lead to an apparent quality factor that is less than 100 at room temperature. 25 November 2013 | doi: 10.1038/ncomms3843 Physical Sciences  Nanotechnology  A quantitative telomeric chromatin isolation protocol identifies different telomeric states Larissa Grolimund, Eric Aeby, Romain Hamelin, Florence Armand, Diego Chiappe, Marc Moniatte and Joachim Lingner The protein composition of telomeres changes during development, aging, tumourigenesis and in telomere syndromes. Here, the authors develop a quantitative telomeric chromatin isolation protocol (QTIP) to analyse and quantitatively compare telomeric chromatin of different cell populations. 25 November 2013 | doi: 10.1038/ncomms3848 Biological Sciences  Molecular biology  An alternative pathway contributes to phenylalanine biosynthesis in plants via a cytosolic tyrosine:phenylpyruvate aminotransferase Heejin Yoo, Joshua R. Widhalm, Yichun Qian, Hiroshi Maeda, Bruce R. Cooper, Amber S. Jannasch, Itay Gonda, Efraim Lewinsohn, David Rhodes and Natalia Dudareva Plants primarily synthesize phenylalanine in plastids via arogenate. Here, Yoo et al. provide evidence that petunia flowers also employ an alternative microbial-like pathway to synthesize phenylalanine that is partially localized in the cytosol and interconnected with tyrosine catabolism. 25 November 2013 | doi: 10.1038/ncomms3833 Biological Sciences  Plant sciences  General nature of liquid–liquid transition in aqueous organic solutions Ken-ichiro Murata and Hajime Tanaka The existence of liquid–liquid transition is one hypothesis used to explain the anomalous properties of liquid water at low temperatures. Murata and Tanaka demonstrate that both this transition and the melting of ice can be controlled solely by water activity in 14 aqueous organic solutions. 25 November 2013 | doi: 10.1038/ncomms3844 Physical Sciences  Applied physics  Fluids and plasma physics  Secondary anionic phospholipid binding site and gating mechanism in Kir2.1 inward rectifier channels OPEN Sun-Joo Lee, Shizhen Wang, William Borschel, Sarah Heyman, Jacob Gyore and Colin G. Nichols Inwardly rectifying potassium channels require interactions with both PI(4,5)P2 and a second anionic phospholipid for full activation. Lee et al. locate the secondary anionic phospholipid-binding site in Kir2.1 and reveal how it synergistically promotes PI(4,5)P2 sensitivity. 25 November 2013 | doi: 10.1038/ncomms3786 Biological Sciences  Biochemistry  Biophysics  miR-1 and miR-206 target different genes to have opposing roles during angiogenesis in zebrafish embryos Cheng-Yung Lin, Hung-Chieh Lee, Chuan-Yang Fu, Yu-Yun Ding, Jie-Shin Chen, Ming-Hsuan Lee, Wei-Jhen Huang and Huai-Jen Tsai The microRNAs miR-1 and miR-206 have identical seed sequences and have been reported to regulate angiogenesis in zebrafish by repressing VegfAa expression. Here, Lin et al. describe opposing roles of the two microRNAs in regulating VegfAa expression and therefore angiogenesis in zebrafish. 22 November 2013 | doi: 10.1038/ncomms3829 Biological Sciences  Developmental biology  Molecular biology  Neovenatorid theropods are apex predators in the Late Cretaceous of North America Lindsay E. Zanno and Peter J. Makovicky Allosauroids were common Jurassic–Cretaceous megapredators that disappeared in the Late Cretaceous faunal turnover. Here, Zanno and Makovicky describe Siats meekerorum, a giant new North American allosauroid from the Late Cretaceous, demonstrating that this clade co-occurred with and competitively excluded smaller tyrannosaurs. 22 November 2013 | doi: 10.1038/ncomms3827 Biological Sciences  Ecology  Evolution  Palaeontology  Pink marine sediments reveal rapid ice melt and Arctic meltwater discharge during Dansgaard–Oeschger warmings Tine L. Rasmussen and Erik Thomsen Meltwater pulses from Northern Hemisphere ice sheets are strongly implicated in past millennial-scale shifts in ocean circulation, yet direct evidence is sparse. Here, a 30,000-year glacial meltwater history for the Svalbard–Barents Sea ice sheet is reconstructed in a marine sediment core. 22 November 2013 | doi: 10.1038/ncomms3849 Earth Sciences  Climate science  Oceanography  Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association Harish Nagarajan, Mallory Embree, Amelia-Elena Rotaru, Pravin M. Shrestha, Adam M. Feist, Bernhard Ø Palsson, Derek R. Lovley and Karsten Zengler Microbial community function depends on metabolic interdependencies between individual species, some of which include electron transfer. Nagarajan et al. use genomic, transcriptomic and modelling approaches to describe the mechanisms supporting the syntrophic relationship between Geobacter metallireducens and Geobacter sulfurreducens. 22 November 2013 | doi: 10.1038/ncomms3809 Biological Sciences  Ecology  Microbiology  Systems biology  Fate tracing reveals hepatic stellate cells as dominant contributors to liver fibrosis independent of its aetiology Ingmar Mederacke, Christine C. Hsu, Juliane S. Troeger, Peter Huebener, Xueru Mu, Dianne H. Dapito, Jean-Philippe Pradere and Robert F. Schwabe Myofibroblasts drive fibrogenesis in the liver but their cellular origins remain unclear. Here, Mederacke et al. use the Lrat gene to label hepatic stellate cells (HSCs) in transgenic mice and reveal HSCs as the major source of myofibroblasts in models of toxic, biliary and fatty liver fibrosis. 22 November 2013 | doi: 10.1038/ncomms3823 Biological Sciences  Medical research  Widespread sex differences in gene expression and splicing in the adult human brain OPEN Daniah Trabzuni, Adaikalavan Ramasamy, Sabaena Imran, Robert Walker, Colin Smith, Michael E. Weale, John Hardy, Mina Ryten and North American Brain Expression Consortium Men and women differ in terms of their neurochemistry, behaviour and susceptibility to disease. Here, the authors show that sex differences in gene expression and splicing are widespread in adult human brain, and that sex-biased expression is likely to have functional consequences. 22 November 2013 | doi: 10.1038/ncomms3771 Biological Sciences  Genetics  Neuroscience  Integrin CD11b negatively regulates BCR signalling to maintain autoreactive B cell tolerance Chuanlin Ding, Yunfeng Ma, Xingguo Chen, Min Liu, Yihua Cai, Xiaoling Hu, Dong Xiang, Swapan Nath, Huang-ge Zhang, Hong Ye, David Powell and Jun Yan Polymorphisms in the integrin gene CD11b are associated with susceptibility to systemic lupus erythematosus, but how this relates to the function of this integrin has not been fully investigated. Here, the authors report that CD11b has a role in the intrinsic maintenance of autoreactive B cell tolerance by regulating BCR signalling. 22 November 2013 | doi: 10.1038/ncomms3813 Biological Sciences  Immunology  Genomic insights into salt adaptation in a desert poplar Tao Ma, Junyi Wang, Gongke Zhou, Zhen Yue, Quanjun Hu, Yan Chen, Bingbing Liu, Qiang Qiu, Zhuo Wang, Jian Zhang, Kun Wang, Dechun Jiang, Caiyun Gou, Lili Yu, Dongliang Zhan, Ran Zhou, Wenchun Luo, Hui Ma, Yongzhi Yang, Shengkai Pan et al. Little is known about the genes that confer salt tolerance in trees. Here, Ma et al. report the genome sequence of the desert poplar, Populus euphratica, and provide insight into the genetic architecture and adaptation of this salt tolerant desert poplar. 21 November 2013 | doi: 10.1038/ncomms3797 Biological Sciences  Evolution  Genetics  Downsizing a human inflammatory protein to a small molecule with equal potency and functionality Robert C. Reid, Mei-Kwan Yau, Ranee Singh, Johan K. Hamidon, Anthony N. Reed, Peifei Chu, Jacky Y. Suen, Martin J. Stoermer, Jade S. Blakeney, Junxian Lim, Jonathan M. Faber and David P. Fairlie Replicating the functionality of bioactive proteins using rationally designed small molecule mimics is both economically valuable and synthetically challenging. Here, the authors develop a mimic of the inflammatory protein C3a with equal biological potency but enhanced stability and bioavailability. 21 November 2013 | doi: 10.1038/ncomms3802 Chemical Sciences  Medicinal chemistry  Organic chemistry  Spatial fluctuations in barrier height at the graphene–silicon carbide Schottky junction S. Rajput, M.X. Chen, Y. Liu, Y.Y. Li, M. Weinert and L. Li The interfacing of graphene with a semiconductor creates a Schottky junction, with the formation of ripples on graphene being common. Here, the authors experimentally quantify spatial fluctuations in Schottky barrier height and the effect that ripples have. 21 November 2013 | doi: 10.1038/ncomms3752 Physical Sciences  Applied physics  Materials science  Nanotechnology  Atomic-scale mechanisms of ferroelastic domain-wall-mediated ferroelectric switching Peng Gao, Jason Britson, Jacob R. Jokisaari, Christopher T. Nelson, Seung-Hyub Baek, Yiran Wang, Chang-Beom Eom, Long-Qing Chen and Xiaoqing Pan In ferroelectric thin films, ferroelastic domains affect the features of polarization switching. Gao et al. perform real-time transmission electron microscopy measurements and show that ferroelastic domains can hinder the switching via formation of a transient interface layer with a dipole glass structure. 21 November 2013 | doi: 10.1038/ncomms3791 Physical Sciences  Condensed matter  Materials science  Hydrogen-induced nanotunnel opening within semiconductor subsurface OPEN Patrick Soukiassian, Erich Wimmer, Edvige Celasco, Claudia Giallombardo, Simon Bonanni, Luca Vattuone, Letizia Savio, Antonio Tejeda, Mathieu Silly, Marie D'angelo, Fausto Sirotti and Mario Rocca Silicon carbide surfaces offer many interesting properties induced by surface strain relief. Soukiassian et al. report hydrogen-induced self-organized nano-voids below a silicon carbide surface, and suggest the resultant nanotunnel may be used as a template to capture atoms or molecules. 21 November 2013 | doi: 10.1038/ncomms3800 Physical Sciences  Condensed matter  Materials science  Nanotechnology  Analogue encoding of physicochemical properties of proteins in their cognate messenger RNAs OPEN Anton A. Polyansky, Mario Hlevnjak and Bojan Zagrovic mRNA transport contributes to the proper localization of its cognate proteins. Here, the authors report a correlation between the physicochemical properties of mRNAs and their cognate proteins, suggesting that these properties of mRNAs can predict the subcellular localization of their cognate proteins. 20 November 2013 | doi: 10.1038/ncomms3784 Biological Sciences  Bioinformatics  Cell biology  Molecular biology  Iron-binding haemerythrin RING ubiquitin ligases regulate plant iron responses and accumulation OPEN Takanori Kobayashi, Seiji Nagasaka, Takeshi Senoura, Reiko Nakanishi Itai, Hiromi Nakanishi and Naoko K. Nishizawa Plants activate a gene transcription response under low iron conditions but how they sense insufficient iron levels is unclear. In this study, Kobayashi et al. identify two iron-binding proteins that possess ubiquitin ligase activity and are negative regulators of the iron deficiency response. 20 November 2013 | doi: 10.1038/ncomms3792 Biological Sciences  Plant sciences  A light-induced spin crossover actuated single-chain magnet Tao Liu, Hui Zheng, Soonchul Kang, Yoshihito Shiota, Shinya Hayami, Masaki Mito, Osamu Sato, Kazunari Yoshizawa, Shinji Kanegawa and Chunying Duan Spin-crossover complexes and single-chain magnets exhibit magnetic bistability and may be used in information storage applications. Here, the authors present a one-dimensional spin-crossover complex wherein the single-chain magnet behaviour is actuated by light-induced excited spin-state trapping. 20 November 2013 | doi: 10.1038/ncomms3826 Chemical Sciences  Inorganic chemistry  Nanotechnology    Nature Communications JOBS of the week Post Doctoral Research Assistant University of Bristol Research Associate Loma Linda University (LLU) PhD position Molecular Oncology Department, University of Goettingen Postdoctoral Researchers International Institute for Applied Systems Analysis (IIASA) Postdoctoral Research Associate University of Illinois Clinical Scientist University of Oxford Post-doctoral research position Biomedical Sciences Research Center "Alexander Fleming" (BSRC Fleming) graduate student Dalhousie University Post Doctoral Scientist University of Cambridge Senior Technician Cardiff University More Science jobs from Nature Communications EVENT Clinical Virology Symposium 27.04.14 Florida, USA More science events from       Latest Corrigenda     Corrigendum: Carbon precipitation from heavy hydrocarbon fluid in deep planetary interiors Sergey S. Lobanov, Pei-Nan Chen, Xiao-Jia Chen, Chang-Sheng Zha, Konstantin D. Litasov, Ho-Kwang Mao and Alexander F Goncharov 26 November 2013 | doi: 10.1038/ncomms3868 Earth Sciences  Materials science  Physical chemistry  Planetary sciences      Corrigendum: A C-terminal PDZ domain-binding sequence is required for striatal distribution of the dopamine transporter Mattias Rickhag, Freja Herborg Hansen, Gunnar Sørensen, Kristine Nørgaard Strandfelt, Bjørn Andresen, Kamil Gotfryd, Kenneth L. Madsen, Ib Vestergaard Klewe, Ina Ammendrup-Johnsen, Jacob Eriksen, Amy H. Newman, Ernst-Martin Füchtbauer, Jesus Gomeza, David P.D. Woldbye, Gitta Wörtwein and Ulrik Gether 22 November 2013 | doi: 10.1038/ncomms3589 Biological Sciences  Neuroscience        Latest Erratum     Erratum: Selective contacts drive charge extraction in quantum dot solids via asymmetry in carrier transfer kinetics Ivan Mora-Sero, Luca Bertoluzzi, Victoria Gonzalez-Pedro, Sixto Gimenez, Francisco Fabregat-Santiago, Kyle W. Kemp, Edward H. Sargent and Juan Bisquert 22 November 2013 | doi: 10.1038/ncomms3839 Physical Sciences  Applied physics  Condensed matter      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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