Nature Communications - 9 October 2013

Weekly Content Alert 09 October 2013  Featured image: Kim et al. map the global distribution of condensin I binding sites in the chicken genome. Latest content: Articles Journal homepage Recommend to library Web feed   Advertisement nature.com webcasts   Macmillan Science Communication presents a custom webcast on: Multi-omics in metabolic disease: investigating the potential to predict diabetes   Friday October 11th 7am PDT / 10am EDT / 3pm BST / 4pm CEST   Register for the free webcast followed by our live Q & A session    Sponsored by:         Latest Articles View all Articles     A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages OPEN Marta D. Costa, Joana B. Pereira, Maria Pala, Verónica Fernandes, Anna Olivieri, Alessandro Achilli, Ugo A. Perego, Sergei Rychkov, Oksana Naumova, Jiři Hatina, Scott R. Woodward, Ken Khong Eng, Vincent Macaulay, Martin Carr, Pedro Soares, Luísa Pereira and Martin B. Richards Ashkenazi mitochondrial DNA variation has four major founders whose sources are difficult to trace due to the rarity of Ashkenazi Jews in the general population. Here, the authors provide evidence that all four major founders originated from Europe and provide a genealogical record of the Ashkenazi. 08 October 2013 | doi: 10.1038/ncomms3543 Biological Sciences  Evolution  Genetics  First evidence of a 200-day non-stop flight in a bird Felix Liechti, Willem Witvliet, Roger Weber and Erich Bächler Being airborne is energetically costly for vertebrates, and migrating birds are expected to spend some resting time on the ground. Here, Liechti et al. show that the Alpine swift (Tachymarptis melba) can stay airborne for more than 6 months, implying that this bird can sleep in flight. 08 October 2013 | doi: 10.1038/ncomms3554 Biological Sciences  Zoology  Fusion reactions initiated by laser-accelerated particle beams in a laser-produced plasma C. Labaune, C. Baccou, S. Depierreux, C. Goyon, G. Loisel, V. Yahia and J. Rafelski The nuclear fusion of hydrogen and boron nuclei has potential advantages over the fusion of deuterium and tritium for energy production as it produces no neutrons. Labaune et al. report progress towards achieving this by colliding a laser-driven particle beam into a laser-generated plasma. 08 October 2013 | doi: 10.1038/ncomms3506 Physical Sciences  Fluids and plasma physics  Enhanced biofuel production through coupled acetic acid and xylose consumption by engineered yeast Na Wei, Josh Quarterman, Soo Rin Kim, Jamie H.D. Cate and Yong-Su Jin Biofuel produced from renewable biomass is attractive, but inefficient conversion of cellulosic sugars and the toxicity of plant biomass hydrolysates hamper commercial production. Wei et al. use engineered yeast to address these problems simultaneously, converting both xylose and acetic acid into ethanol. 08 October 2013 | doi: 10.1038/ncomms3580 Biological Sciences  Bioengineering  Microbiology  Targeted delivery of colloids by swimming bacteria N. Koumakis, A. Lepore, C. Maggi and R. Di Leonardo Transport of colloidal cargoes to target sites can be done by controlling active carriers, like self-propelled bacteria, under external stimuli. Koumakis et al. show that bacteria can autonomously achieve the same goal when moving over pre-designed asymmetric microstructures. 08 October 2013 | doi: 10.1038/ncomms3588 Physical Sciences  Biophysics  Biotechnology  Macromolecular semi-rigid nanocavities for cooperative recognition of specific large molecular shapes Takane Imaoka, Yuki Kawana, Takuto Kurokawa and Kimihisa Yamamoto Large molecular shape-consistent host molecules are required for molecular recognition applications and the development of artificial enzymes. Here, the authors synthesize semi-rigid dendritic molecules with cavities capable of tunable discrimination between a range of large guest molecules. 08 October 2013 | doi: 10.1038/ncomms3581 Chemical Sciences  Catalysis  Organic chemistry  Physical chemistry  Distinct charge dynamics in battery electrodes revealed by in situ and operando soft X-ray spectroscopy OPEN Xiaosong Liu, Dongdong Wang, Gao Liu, Venkat Srinivasan, Zhi Liu, Zahid Hussain and Wanli Yang Soft X-ray spectroscopy is a sensitive probe for electronic states in battery materials but has so far been mainly limited to ex situ work. Liu et al. develop in situ and operando soft X-ray absorption spectroscopy, which leads to new findings of charge dynamics of lithium-ion battery cathodes. 08 October 2013 | doi: 10.1038/ncomms3568 Chemical Sciences  Materials science  Cell–cell adhesion genes CTNNA2 and CTNNA3 are tumour suppressors frequently mutated in laryngeal carcinomas Miriam Fanjul-Fernández, Víctor Quesada, Rubén Cabanillas, Juan Cadiñanos, Tania Fontanil, Álvaro Obaya, Andrew J. Ramsay, José L. Llorente, Aurora Astudillo, Santiago Cal and Carlos López-Otín Laryngeal carcinoma is a heterogeneous disease and multiple genes have been implicated in its pathogenesis. Here, Fanjul-Fernández et al. identify mutations in the cell–cell adhesion genes catenin α2 and catenin α3 in 15% of a cohort of homogeneous laryngeal carcinomas. 08 October 2013 | doi: 10.1038/ncomms3531 Biological Sciences  Cancer  Cell biology  Tip-enhanced nano-Raman analytical imaging of locally induced strain distribution in carbon nanotubes Taka-aki Yano, Taro Ichimura, Shota Kuwahara, Fekhra H'Dhili, Kazumasa Uetsuki, Yoshito Okuno, Prabhat Verma and Satoshi Kawata Tip-enhanced Raman scattering microscopy gives high-resolution information on nanostructures, yet measurements on more intrinsic properties have been elusive. Yano et al. develop a tip-enhanced method to induce strain in carbon nanotubes and image its distribution along the tube length. 07 October 2013 | doi: 10.1038/ncomms3592 Physical Sciences  Nanotechnology  Optical physics  Network modularity reveals critical scales for connectivity in ecology and evolution Robert J. Fletcher, Andre Revell, Brian E. Reichert, Wiley M. Kitchens, Jeremy D. Dixon and James D. Austin Spatial scale is important for ecological and evolutionary processes, yet objectively identifying critical scales has been challenging. Here, the authors illustrate how network modularity can identify critical scales in animal movement and significantly alter our understanding of ecological processes. 07 October 2013 | doi: 10.1038/ncomms3572 Biological Sciences  Ecology  Evolution  Control of the conformations of ion Coulomb crystals in a Penning trap OPEN Sandeep Mavadia, Joseph F. Goodwin, Graham Stutter, Shailen Bharadia, Daniel R. Crick, Daniel M. Segal and Richard C. Thompson Ion traps form the core of many studies of fundamental physics and are a possible route to quantum computation. Using a Penning trap, Mavadia et al. demonstrate the formation and control of different configurations of ion Coulomb crystals, which may be useful for future ion-based applications. 07 October 2013 | doi: 10.1038/ncomms3571 Physical Sciences  Atomic and molecular physics  Optical physics  Exceptional fossil preservation demonstrates a new mode of axial skeleton elongation in early ray-finned fishes Erin E. Maxwell, Heinz Furrer and Marcelo R. Sánchez-Villagra An elongate body plan has evolved multiple times through the addition of more vertebras or an increase in their length. In this study, Maxwell et al. describe a new mechanism of body elongation in a saurichthyid: doubling the number of dorsal arches without an increase in the number of myomeres. 07 October 2013 | doi: 10.1038/ncomms3570 Biological Sciences  Evolution  Palaeontology  Connexin40 regulates platelet function OPEN Sakthivel Vaiyapuri, Leonardo A. Moraes, Tanya Sage, Marfoua S. Ali, Kirsty R. Lewis, Martyn P. Mahaut-Smith, Ernesto Oviedo-Orta, Alexander M. Simon and Jonathan M. Gibbins Hemichannels and gap junctions containing the connexin Cx37 are required for platelet functions such as aggregation and granule secretion through poorly defined mechanisms. Vaiyapuri et al. show that Cx40 is also required and can act independently of Cx37 in mouse platelets. 07 October 2013 | doi: 10.1038/ncomms3564 Biological Sciences  Cell biology  Smad6 inhibits non-canonical TGF-β1 signalling by recruiting the deubiquitinase A20 to TRAF6 Su Myung Jung, Ji-Hyung Lee, Jinyoung Park, Young Sun Oh, Sung Kyun Lee, Jin Seok Park, Youn Sook Lee, Jun Hwan Kim, Jae Young Lee, Yoe-Sik Bae, Seung-Hoi Koo, Seong-Jin Kim and Seok Hee Park The cytokine TGF-β signals through canonical, Smad-dependent, and non-canonical, Smad-independent pathways. Jung et al. show that Smad6, an inhibitor of canonical TGF-β signalling, also inhibits a non-canonical pathway by recruiting a deubiquitinase to TRAF6. 07 October 2013 | doi: 10.1038/ncomms3562 Biological Sciences  Cell biology  Broadband asymmetric waveguiding of light without polarization limitations Yadong Xu, Chendong Gu, Bo Hou, Yun Lai, Jensen Li and Huanyang Chen Symmetry breaking at metamaterial interfaces is increasingly being used to obtain new optical device functionalities. Xu et al. discuss its use for building polarization-independent waveguides with asymmetric propagation properties and build such a device that operates at microwave frequencies. 07 October 2013 | doi: 10.1038/ncomms3561 Physical Sciences  Applied physics  Optical physics  Anisotropic breakdown of Fermi liquid quasiparticle excitations in overdoped La2-xSrxCuO4 J. Chang, M. Månsson, S. Pailhès, T. Claesson, O. J. Lipscombe, S. M. Hayden, L. Patthey, O. Tjernberg and J. Mesot An outstanding question regarding cuprate superconductors is how the Fermi liquid behaviour of their normal state breaks down. Chang et al. conduct a systematic ARPES study of how the Fermi liquid quasiparticle excitations break down in momentum space, and find it to be highly anisotropic in La2-xSrxCuO4. 07 October 2013 | doi: 10.1038/ncomms3559 Physical Sciences  Condensed matter  An electrostatic model for the determination of magnetic anisotropy in dysprosium complexes Nicholas F. Chilton, David Collison, Eric J. L. McInnes, Richard E. P. Winpenny and Alessandro Soncini Understanding the anisotropic electronic structure of lanthanide complexes is useful for a range of advanced applications. Here, the authors present a simple electrostatic method, capable of predicting the magnetic anisotropy of low-symmetry mononuclear and polynuclear dysprosium(III) complexes. 07 October 2013 | doi: 10.1038/ncomms3551 Chemical Sciences  Inorganic chemistry  Physical chemistry  Imaging energy status in live cells with a fluorescent biosensor of the intracellular ATP-to-ADP ratio Mathew Tantama, Juan Ramón Martínez-François, Rebecca Mongeon and Gary Yellen The ratio between ATP and ADP within the cell is a key indicator of metabolic status. Tantama et al. describe a ratiometric, genetically encoded fluorescent sensor for ATP:ADP that is now optimized for mammalian cells, and demonstrate that it can detect physiological changes in energy consumption and production. 07 October 2013 | doi: 10.1038/ncomms3550 Biological Sciences  Cell biology  Bio-inspired voltage-dependent calcium channel blockers Tingting Yang, Lin-Ling He, Ming Chen, Kun Fang and Henry M. Colecraft Calcium channel blockers are used as treatments for hypertension, angina and pain. Yang et al. show that diverse cytosolic calcium channel-binding proteins act as blockers when targeted to the plasma membrane, and suggest how this property might be used to screen for small-molecule inhibitors. 07 October 2013 | doi: 10.1038/ncomms3540 Biological Sciences  Biochemistry  Dispersant-free conducting pastes for flexible and printed nanocarbon electrodes Joong Tark Han, Bo Hwa Jeong, Seon Hee Seo, Kwang Chul Roh, Sumi Kim, Sua Choi, Jong Seok Woo, Ho Young Kim, Jeong In Jang, Du-Chul Shin, Sooyeon Jeong, Hee Jin Jeong, Seung Yol Jeong and Geon-Woong Lee The realization of highly conductive, dispersant-free pastes based on nanocarbon materials has been hindered by agglomeration of particles. Han et al. demonstrate conducting pastes that do not agglomerate due to quadruple hydrogen-bonding motifs among the nanocarbon particles. 07 October 2013 | doi: 10.1038/ncomms3491 Chemical Sciences  Materials science  Revealing the ultrafast process behind the photoreduction of graphene oxide Régis Y. N. Gengler, Daniel S. Badali, Dongfang Zhang, Konstantinos Dimos, Konstantinos Spyrou, Dimitrios Gournis and R. J. Dwayne Miller Photoreduction is a promising method for the synthesis of reduced graphene oxide, but the dynamics of the process are unclear. Here, the authors explore the process via a pump–probe technique, revealing its ultrafast nature and the involvement of solvated electrons produced by irradiation of the solvent. 04 October 2013 | doi: 10.1038/ncomms3560 Chemical Sciences  Materials science  Physical chemistry  Growth of carbon nanotubes via twisted graphene nanoribbons OPEN Hong En Lim, Yasumitsu Miyata, Ryo Kitaura, Yoshifumi Nishimura, Yoshio Nishimoto, Stephan Irle, Jamie H. Warner, Hiromichi Kataura and Hisanori Shinohara Carbon nanotubes can be considered as rolled-up small sheets of graphene. Here, Lim and colleagues demonstrate this process, by fabricating carbon nanotubes through a thermally induced process of self-intertwining of graphene nanoribbons. 04 October 2013 | doi: 10.1038/ncomms3548 Physical Sciences  Materials science  Nanotechnology  Structure of GrlR–GrlA complex that prevents GrlA activation of virulence genes Abhilash Padavannil, Chacko Jobichen, Erez Mills, Adrian Velazquez-Campoy, Mo Li, Ka Yin Leung, Yu Keung Mok, Ilan Rosenshine and J. Sivaraman The locus of enterocyte effacement is a pathogenicity island essential for virulence of some Escherichia coli pathogenic serotypes. Here, the authors solve the structure of a regulatory complex that optimizes regulation of this locus during the infection process. 04 October 2013 | doi: 10.1038/ncomms3546 Biological Sciences  Microbiology  Molecular biology  Ultrathin high-temperature oxidation-resistant coatings of hexagonal boron nitride Zheng Liu, Yongji Gong, Wu Zhou, Lulu Ma, Jingjiang Yu, Juan Carlos Idrobo, Jeil Jung, Allan H. MacDonald, Robert Vajtai, Jun Lou and Pulickel M. Ajayan There is a continuous need for high-temperature coatings that can protect a substrate from oxidation. Here, the use of hexagonal boron nitride ultrathin film as a stable coating on various substrates is reported, which significantly reduces the oxidation of nickel and other metals at temperatures up to 1,100 °C. 04 October 2013 | doi: 10.1038/ncomms3541 Physical Sciences  Materials science  Nanotechnology  Cobalt phosphate-modified barium-doped tantalum nitride nanorod photoanode with 1.5% solar energy conversion efficiency Yanbo Li, Li Zhang, Almudena Torres-Pardo, Jose M. González-Calbet, Yanhang Ma, Peter Oleynikov, Osamu Terasaki, Shunsuke Asahina, Masahide Shima, Dongkyu Cha, Lan Zhao, Kazuhiro Takanabe, Jun Kubota and Kazunari Domen The search for efficient photoanodes for water oxidation is ongoing. Here, the authors investigate the effect of barium doping on a tantalum nitride nanostructured photoanode, and report a solar energy conversion efficiency of 1.5% in the presence of a cobalt phosphate co-catalyst. 03 October 2013 | doi: 10.1038/ncomms3566 Chemical Sciences  Catalysis  Inorganic chemistry  Materials science  Metastasis-associated protein 1 is an integral component of the circadian molecular machinery Da-Qiang Li, Suresh B. Pakala, Sirigiri Divijendra Natha Reddy, Shaohua Peng, Seetharaman Balasenthil, Chu-Xia Deng, Cheng Chi Lee, Michael A. Rea and Rakesh Kumar Mammalian circadian clocks modulate the daily cycles of many cellular processes. Here, the authors find that metastasis-associated protein 1, which is upregulated in human cancers, is an intrinsic regulator of the mammalian molecular clock. 03 October 2013 | doi: 10.1038/ncomms3545 Biological Sciences  Medical research  Molecular biology  Condensin I associates with structural and gene regulatory regions in vertebrate chromosomes Ji Hun Kim, Tao Zhang, Nicholas C. Wong, Nadia Davidson, Jovana Maksimovic, Alicia Oshlack, William C. Earnshaw, Paul Kalitsis and Damien F. Hudson Condensins participate in the packaging of chromatin during mitosis. Kim et al. discover that condensin I concentrates in centromeres, telomeres and the promoters of active genes in vertebrates, revealing that condensin distribution is remarkably conserved across phylogeny. 03 October 2013 | doi: 10.1038/ncomms3537 Biological Sciences  Cell biology  Molecular biology  Miz1 is required to maintain autophagic flux Elmar Wolf, Anneli Gebhardt, Daisuke Kawauchi, Susanne Walz, Björn von Eyss, Nicole Wagner, Christoph Renninger, Georg Krohne, Esther Asan, Martine F. Roussel and Martin Eilers Miz1 is a binding partner of the transcription factor c-Myc and a regulator of cell cycle progression. Wolf et al. show that inactivation of Miz1 in the mouse central nervous system results in neurodegeneration, and find that Miz1 is essential for the transcriptional regulation of autophagic flux. 03 October 2013 | doi: 10.1038/ncomms3535 Biological Sciences  Cell biology  Neuroscience  Requirements for fault-tolerant factoring on an atom-optics quantum computer Simon J. Devitt, Ashley M. Stephens, William J. Munro and Kae Nemoto As quantum information technologies develop into practical computational engines, many technical issues must be considered. Devitt et al. estimate the resources needed to perform prime factorization with Shor's algorithm on an atom-optics quantum computer and show how to optimize the computer's performance. 03 October 2013 | doi: 10.1038/ncomms3524 Physical Sciences  Applied physics  Atomic and molecular physics  Theoretical physics  Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment Norikazu Ichihashi, Kimihito Usui, Yasuaki Kazuta, Takeshi Sunami, Tomoaki Matsuura and Tetsuya Yomo Molecular evolution events are vital for the development of cellular complexity. Here, the authors construct an evolvable artificial cell model, and observe that Darwinian evolution leads to more efficient RNA replication over time. 03 October 2013 | doi: 10.1038/ncomms3494 Biological Sciences  Evolution  Molecular biology  Griffiths phases and the stretching of criticality in brain networks Paolo Moretti and Miguel A. Muñoz Neural interactions taking place in the brain seemingly occur at criticality, but little is known about how this state is achieved. Moretti and Muñoz identify the signatures of so-called Griffiths phases stemming from the hierarchical topology of brain networks, which could point to an explanation. 03 October 2013 | doi: 10.1038/ncomms3521 Physical Sciences  Biophysics  Neuroscience  Theoretical physics  Resource heterogeneity can facilitate cooperation OPEN Ádám Kun and Ulf Dieckmann Differences in resource availability or inequality of wealth are common both in nature and in human societies. Here, the authors find that such inequality facilitates cooperation when the generation of public goods is inefficient, but hinders cooperation when the efficiency of joint actions is high. 03 October 2013 | doi: 10.1038/ncomms3453 Biological Sciences  Ecology  Evolution  Virtual hyperbolic metamaterials for manipulating radar signals in air Zhaxylyk A. Kudyshev, Martin C. Richardson and Natalia M. Litchinitser Controlling the propagation of microwaves in air is hard because of their divergence and the lack of suitable optics. Kudyshev et al. show how this can be overcome using plasma channels to create virtual hyperbolic metamaterials to collimate and guide radar beams. 02 October 2013 | doi: 10.1038/ncomms3557 Physical Sciences  Applied physics  Fluids and plasma physics  Optical physics  Direct measurement of osmotic pressure via adaptive confinement of quasi hard disc colloids Ian Williams, Erdal C. Oguz, Paul Bartlett, Hartmut Löwen and C. Patrick Royall Confinement is encountered in systems varying from simple liquids to biological cells. Williams et al. introduce an adaptive confinement with an elastic wall composed of colloidal particles, whereby the osmotic pressure of the confined system can be directly obtained from the displacement of the wall. 02 October 2013 | doi: 10.1038/ncomms3555 Physical Sciences  Biophysics  Condensed matter  Single-photon-level quantum image memory based on cold atomic ensembles OPEN Dong-Sheng Ding, Zhi-Yuan Zhou, Bao-Sen Shi and Guang-Can Guo Photonic quantum memories are necessary for quantum information networks and can be built using cold atomic gases. In this work, Ding et al. show the first storage and retrieval of single photons carrying orbital angular momentum using electromagnetically induced transparency in a cold rubidium ensemble. 02 October 2013 | doi: 10.1038/ncomms3527 Physical Sciences  Atomic and molecular physics  Optical physics  Tensile testing of ultra-thin films on water surface Jae-Han Kim, Adeel Nizami, Yun Hwangbo, Bongkyun Jang, Hak-Joo Lee, Chang-Su Woo, Seungmin Hyun and Taek-Soo Kim The mechanical testing of thin films is non-trivial, due to their very fine dimensions. Kim et al. use the inherent surface tension of water as a platform for the frictionless tensile testing of gold films, with a thickness as fine as 55 nm. 02 October 2013 | doi: 10.1038/ncomms3520 Physical Sciences  Materials science    Nature Communications JOBS of the week Research Associate University of Virginia Post-doc position Department of Chemistry, University of Pavia Research Fellow University of Leeds Postdoctoral Research Associate University of Oxford Post-doctoral Fellow University of California San Francisco (UCSF) Research Technician Baylor College of Medicine Research Associate / Postdoctoral Researcher UCL Post Doctoral Researcher Ohio State University Laboratory Coordinator (Analytical Chemist) Institute for Molecular Medicine Finland (FIMM) PhD Position Goethe University Frankfurt a.M. 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