Nature Communications - 5 November 2014

If you are unable to see the message below, click here to view.

Weekly Content Alert 05 November 2014  Featured image: Lacis et al. propose a new mechanism to explain locomotion of organisms with passive appendages in flowing fluids. Latest content: Articles Journal homepage Recommend to library Web feed   Advertisement A picture of health Reporter Lorna Stewart travels to the German island of Lindau to meet 600 of science’s brightest young minds and 37 rock stars – Nobel laureates. In a series of four films, Stewart asks some of the most profound questions in medicine.  Watch the videos online.  Published weekly from 24th Sep- 15th Oct 2014 Supported by Mars, Incorporated       Latest Articles View all Articles     Swimming by reciprocal motion at low Reynolds number OPEN Tian Qiu, Tung-Chun Lee, Andrew G. Mark, Konstantin I. Morozov, Raphael Münster, Otto Mierka, Stefan Turek, Alexander M. Leshansky and Peer Fischer Operating devices that can navigate biomedical fluids and tissues is one of the ultimate goals of microrobotics. Whilst the current designs are restricted to non-reciprocal actuations, Qiu et al. report swimming via simple reciprocal motion by exploiting the non-Newtonian rheology of viscous fluids. 04 November 2014 | doi: 10.1038/ncomms6119 Physical Sciences  Applied physics  Fluids and plasma physics  Three-dimensional plasmonic stereoscopic prints in full colour Xiao Ming Goh, Yihan Zheng, Shawn J. Tan, Lei Zhang, Karthik Kumar, Cheng-Wei Qiu and Joel K. W. Yang Plasmonic nanostructures enable control over the spatial and spectral dependence of scattered light. Here, the authors use pixels formed of nanoellipse or nanosquare dimers to show polarization-dependent full-colour scattering in reflection, and build 3D stereoscopic colour microprints from them. 04 November 2014 | doi: 10.1038/ncomms6361 Physical Sciences  Applied physics  Nanotechnology  Optical physics  PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity Je-Hyun Yoon, Supriyo De, Subramanya Srikantan, Kotb Abdelmohsen, Ioannis Grammatikakis, Jiyoung Kim, Kyoung Mi Kim, Ji Heon Noh, Elizabeth J. F. White, Jennifer L. Martindale, Xiaoling Yang, Min-Ju Kang, William H. Wood, Nicole Noren Hooten, Michele K. Evans, Kevin G. Becker, Vidisha Tripathi, Kannanganattu V. Prasanth, Gerald M. Wilson, Thomas Tuschl et al. AUF1 is an RNA-binding protein believed to function mostly by regulating the decay of its target transcripts. Here, Yoon et al. systematically identify the targets of AUF1 and provide insights into how AUF1 functions to regulate various cellular processes by enhancing the decay, stability or translation of specific RNAs. 04 November 2014 | doi: 10.1038/ncomms6248 Biological Sciences  Molecular biology  Systems biology  A heavy analogue of the smallest bridgehead alkene stabilized by a base Takeaki Iwamoto, Naohiko Akasaka and Shintaro Ishida The highly strained nature of small bridgehead alkenes means that they often cannot be isolated, despite being postulated as transient intermediates. Here, the authors report base-stabilized heavy analogues of the smallest bridgehead alkene, with silicon occupying the vertices. 04 November 2014 | doi: 10.1038/ncomms6353 Chemical Sciences  Inorganic chemistry  Organic chemistry  Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg2+ channel MgtE OPEN Hironori Takeda, Motoyuki Hattori, Tomohiro Nishizawa, Keitaro Yamashita, Syed T. A. Shah, Martin Caffrey, Andrés D. Maturana, Ryuichiro Ishitani and Osamu Nureki MgtE is a magnesium ion-selective channel conserved in all domains of life that contributes to the maintenance of cellular Mg2+ homeostasis. Here, the authors provide high-resolution crystal structures of MgtE combined with biochemical analyses that reveal the molecular basis for selectivity. 04 November 2014 | doi: 10.1038/ncomms6374 Biological Sciences  Biochemistry  Biophysics  CD95 and CD95L promote and protect cancer stem cells Paolo Ceppi, Abbas Hadji, Frederick J. Kohlhapp, Abhinandan Pattanayak, Annika Hau, Xia Liu, Huiping Liu, Andrea E. Murmann and Marcus E. Peter The death receptor CD95/Fas induces apoptosis of many normal cells but prevents necrotic death of cancer cells. Here the authors demonstrate that CD95 activation promotes a cancer stem cell (CSC) phenotype, and that CSCs but not differentiated cancer cells are resistant to CD95-mediated apoptosis and depend on CD95 signalling to prevent necrosis. 04 November 2014 | doi: 10.1038/ncomms6238 Biological Sciences  Cancer  The MST1/2-SAV1 complex of the Hippo pathway promotes ciliogenesis Miju Kim, Minchul Kim, Mi-Sun Lee, Cheol-Hee Kim and Dae-Sik Lim Although much is known about the structural and trafficking molecules involved in generation of primary cilia, the signalling proteins that regulate ciliogenesis are poorly defined. Here, Kim et al. identify the MST1/2-SAV1 complex, a core component of the Hippo pathway, as a key regulator of ciliogenesis in cells and zebrafish. 04 November 2014 | doi: 10.1038/ncomms6370 Biological Sciences  Cell biology  Observation of Dicke superradiance for two artificial atoms in a cavity with high decay rate J. A. Mlynek, A. A. Abdumalikov, C. Eichler and A. Wallraff Individual emitters of light in close proximity, such as atoms, can couple together via the light they create leading to a concentrated burst of radiation. Here Mlynek et al. experminetally explore the fundamental origin of this superradiance by studying two superconducting qubits coupled to a microwave cavity. 04 November 2014 | doi: 10.1038/ncomms6186 Physical Sciences  Applied physics  Optical physics  The quantum nature of skyrmions and half-skyrmions in Cu2OSeO3 Oleg Janson, Ioannis Rousochatzakis, Alexander A. Tsirlin, Marilena Belesi, Andrei A. Leonov, Ulrich K. Rößler, Jeroen van den Brink and Helge Rosner In chiral helimagnets, the Dzyaloshinskii–Moriya interaction is known to stabilize skyrmions, but the microscopic roots remain enigmatic. Here, Janson et al. apply a multi-scale approach to Cu2OSeO3 and show that its skyrmions can be traced back to magnetic tetrahedra of a quantum nature. 04 November 2014 | doi: 10.1038/ncomms6376 Physical Sciences  Materials science  Theoretical physics  NF-κB-induced KIAA1199 promotes survival through EGFR signalling OPEN Kateryna Shostak, Xin Zhang, Pascale Hubert, Serkan Ismail Göktuna, Zheshen Jiang, Iva Klevernic, Julien Hildebrand, Patrick Roncarati, Benoit Hennuy, Aurélie Ladang, Joan Somja, André Gothot, Pierre Close, Philippe Delvenne and Alain Chariot The cross-talk between constitutively active EGFR- and NF-κB-dependent pathways in cancer is poorly understood. Here, the authors identify KIAA1199 as a BCL3 and NF-κB-regulated protein that is expressed in cervical lesions and promotes tumorigenesis through Plexin A2 binding and regulation of EGFR stability. 04 November 2014 | doi: 10.1038/ncomms6232 Biological Sciences  Cancer  Molecular biology  Conflict acts as an implicit cost in reinforcement learning James F. Cavanagh, Sean E. Masters, Kevin Bath and Michael J. Frank Conflict monitoring and value learning are often researched as separate processes within psychology, but they share many common neural mechanisms. Here Cavanagh et al. reveal that conflict acts as a cost during value learning, therefore suggesting a general link between conflict monitoring and value learning. 04 November 2014 | doi: 10.1038/ncomms6394 Biological Sciences  Neuroscience  Strongly interacting confined quantum systems in one dimension A. G. Volosniev, D. V. Fedorov, A. S. Jensen, M. Valiente and N. T. Zinner A problem in the treatment of 1D quantum magnetic systems is the shortage of theoretical models applicable for general confinement. Here, Volosniev et al. introduce an energy-functional technique to solve 1D fermionic and bosonic systems with strong short-range interaction in arbitrary geometry. 04 November 2014 | doi: 10.1038/ncomms6300 Physical Sciences  Theoretical physics  Autophagy supports genomic stability by degrading retrotransposon RNA Huishan Guo, Maneka Chitiprolu, David Gagnon, Lingrui Meng, Carol Perez-Iratxeta, Diane Lagace and Derrick Gibbings Retrotransposons replicate via a copy-paste mechanism involving a cytoplasmic intermediate. Guo et al. report that autophagy can suppress genetic variation by degrading cytoplasmic retrotransposon RNA, suggesting additional means by which autophagy may influence tumorigenesis. 04 November 2014 | doi: 10.1038/ncomms6276 Biological Sciences  Cell biology  Molecular biology  Tracing carbonate–silicate interaction during subduction using magnesium and oxygen isotopes Shui-Jiong Wang, Fang-Zhen Teng and Shu-Guang Li Carbon fluxes between the Earth’s surface and its interior are ultimately controlled by subduction of carbonated eclogites and carbonates, although the processes are not well understood. Here, the authors demonstrate that coupled Mg and O isotopic studies may help us to trace deep carbon recycling. 04 November 2014 | doi: 10.1038/ncomms6328 Earth Sciences  Geology and geophysics  MTCL1 crosslinks and stabilizes non-centrosomal microtubules on the Golgi membrane Yoshinori Sato, Kenji Hayashi, Yoshiko Amano, Mikiko Takahashi, Shigenobu Yonemura, Ikuko Hayashi, Hiroko Hirose, Shigeo Ohno and Atsushi Suzuki Microtubules that nucleate from the surface of the Golgi network are important for polarized trafficking and cell migration. Sato et al. find that these microtubules are crosslinked and stabilized by the microtubule-binding protein MTCL1, and show that this activity is required for Golgi structure and function. 04 November 2014 | doi: 10.1038/ncomms6266 Biological Sciences  Cell biology  Cell type-specific plasticity of striatal projection neurons in parkinsonism and L-DOPA-induced dyskinesia Tim Fieblinger, Steven M. Graves, Luke E. Sebel, Cristina Alcacer, Joshua L. Plotkin, Tracy S. Gertler, C. Savio Chan, Myriam Heiman, Paul Greengard, M. Angela Cenci and D. James Surmeier Parkinson’s disease and L-DOPA-induced dyskinesia are both associated with imbalances in activity between populations of spiny projection neurons. Fieblinger et al. show that homeostatic adaptations in excitability are engaged by these disease states, but synaptic strengths are not scaled accordingly. 31 October 2014 | doi: 10.1038/ncomms6316 Biological Sciences  miR-24 limits aortic vascular inflammation and murine abdominal aneurysm development OPEN Lars Maegdefessel, Joshua M. Spin, Uwe Raaz, Suzanne M. Eken, Ryuji Toh, Junya Azuma, Matti Adam, Futoshi Nagakami, Helen M. Heymann, Ekaterina Chernugobova, Hong Jin, Joy Roy, Rebecka Hultgren, Kenneth Caidahl, Sonja Schrepfer, Anders Hamsten, Per Eriksson, Michael V. McConnell, Ronald L. Dalman and Philip S. Tsao Abdominal aortic aneurysm (AAA) is a potentially fatal and often asymptomatic disease whose causes remain unclear. Here the authors show that a microRNA, miR-24, and its target, the glycoprotein chitinase 3-like 1, represent key regulators of AAA development. 31 October 2014 | doi: 10.1038/ncomms6214 Biological Sciences  Medical research  Functional reconstitution of mitochondrial Fe/S cluster synthesis on Isu1 reveals the involvement of ferredoxin Holger Webert, Sven-Andreas Freibert, Angelo Gallo, Torsten Heidenreich, Uwe Linne, Stefan Amlacher, Ed Hurt, Ulrich Mühlenhoff, Lucia Banci and Roland Lill The action of iron–sulphur proteins has been found in many important biological processes. Here, the authors present a reconstituted in vitro system for the characterization of a ferredoxin–ferredoxin reductase pair as an electron transfer chain in the initial step of iron–sulphur protein biogenesis. 31 October 2014 | doi: 10.1038/ncomms6013 Biological Sciences  Biochemistry  Chemical biology  Functional characterization of the TERRA transcriptome at damaged telomeres Antonio Porro, Sascha Feuerhahn, Julien Delafontaine, Harold Riethman, Jacques Rougemont and Joachim Lingner Telomere uncapping in senescent cells is accompanied by loss of the TRF2 telomere capping factor and upregulation of the long noncoding RNA TERRA. Here the authors characterize the TERRA transcriptome and show that TERRA upregulation may promote SUV39H1 recruitment, H3K9 trimethylation and telomere end-to-end fusions. 31 October 2014 | doi: 10.1038/ncomms6379 Biological Sciences  Molecular biology  MS-GF+ makes progress towards a universal database search tool for proteomics Sangtae Kim and Pavel A. Pevzner The development of software tools to analyse large mass spectrometry data sets lags behind the increase in diversity of the data. Here the authors develop MS-GF+, a database search tool that outperforms other popular tools in identifying peptides from a variety of data sets. 31 October 2014 | doi: 10.1038/ncomms6277 Biological Sciences  Bioinformatics  Multiple enzymatic activities of ParB/Srx superfamily mediate sexual conflict among conjugative plasmids Priyank Maindola, Rahul Raina, Parveen Goyal, Krishnamohan Atmakuri, Abhishek Ojha, Sourabh Gupta, Peter J. Christie, Lakshminarayan M. Iyer, L. Aravind and Arulandu Arockiasamy Conjugative plasmids block translocation of rival plasmids using fertility inhibition factors (FINs). Here Maindola et al. present the structure of the FIN Osa and show that it contains a ParB/Sulfiredoxin fold with both ATPase and DNase activity, with general functional implications for this fold. 31 October 2014 | doi: 10.1038/ncomms6322 Biological Sciences  Biochemistry  Microbiology  Molecular biology  A haploid genetics toolbox for Arabidopsis thaliana Maruthachalam Ravi, Mohan Prem Anand Marimuthu, Ek Han Tan, Shamoni Maheshwari, Isabelle M. Henry, Brenda Marin-Rodriguez, Guillaume Urtecho, Jie Tan, Kristina Thornhill, Fan Zhu, Aneesh Panoli, Venkatesan Sundaresan, Anne B. Britt, Luca Comai and Simon W. L. Chan Haploid production technology has the potential to accelerate genetic research and breeding in plants. Here Ravi et al. describe a suite of genetic methods to demonstrate the effectiveness of haploid technology for basic research in Arabidopsis. 31 October 2014 | doi: 10.1038/ncomms6334 Biological Sciences  Genetics  Plant sciences  Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress OPEN Madana M. R. Ambavaram, Supratim Basu, Arjun Krishnan, Venkategowda Ramegowda, Utlwang Batlang, Lutfor Rahman, Niranjan Baisakh and Andy Pereira Improving photosynthetic efficiency to increase crop yield is an important goal of plant breeders. Here, Ambavaram et al. identify a transcription factor that is a key regulator of photosynthetic carbon metabolism in rice and show that its overexpression enhances grain yield. 31 October 2014 | doi: 10.1038/ncomms6302 Biological Sciences  Genetics  Plant sciences  A long Stokes shift red fluorescent Ca2+ indicator protein for two-photon and ratiometric imaging Jiahui Wu, Ahmed S. Abdelfattah, Loïs S. Miraucourt, Elena Kutsarova, Araya Ruangkittisakul, Hang Zhou, Klaus Ballanyi, Geoffrey Wicks, Mikhail Drobizhev, Aleksander Rebane, Edward S. Ruthazer and Robert E. Campbell Current calcium-sensitive probes based on red fluorescent proteins are unsuitable for two-photon excitation at the near-infrared wavelengths commonly used for green fluorescent probes. Wu et al. use a structure-guided approach to engineer a red fluorescent probe with optimal two-photon excitation at these wavelengths. 31 October 2014 | doi: 10.1038/ncomms6262 Biological Sciences  Neuroscience  Observation of strongly entangled photon pairs from a nanowire quantum dot OPEN Marijn A. M. Versteegh, Michael E. Reimer, Klaus D. Jöns, Dan Dalacu, Philip J. Poole, Angelo Gulinatti, Andrea Giudice and Val Zwiller Semiconductor quantum dots embedded in nanowires are good candidates for the realization of a nearly ideal entangled photons source. Here, Versteegh et al. demonstrate emission of single-photon pairs from a position-controlled nanowire quantum dot without the need for temporal post-selection. 31 October 2014 | doi: 10.1038/ncomms6298 Physical Sciences  Applied physics  Nanotechnology  Theoretical physics  Femtosecond electrons probing currents and atomic structure in nanomaterials Melanie Müller, Alexander Paarmann and Ralph Ernstorfer Femtosecond low-energy electron pulses allow probing ultrafast processes in nanoscale systems with high spatial and temporal resolution. Here, the authors develop a hybrid approach for studying ultrafast electric currents and structural dynamics in low-dimensional systems. 31 October 2014 | doi: 10.1038/ncomms6292 Biological Sciences  Condensed matter  Materials science  Amino- and carboxyl-terminal domains of Filamin-A interact with CRMP1 to mediate Sema3A signalling Fumio Nakamura, Kosuke Kumeta, Tomonobu Hida, Toshinari Isono, Yuichi Nakayama, Emiko Kuramata-Matsuoka, Naoya Yamashita, Yutaka Uchida, Ken-ichi Ogura, Keiko Gengyo-Ando, Shohei Mitani, Toshio Ogino and Yoshio Goshima Sema 3A is involved in the guidance of axons during nervous system development and induces the reorganization of actin filaments in the growth cones through the downstream protein CRMP1. Here the authors study the details of the molecular interaction between CRMP1 and the actin-binding protein Filamin-A in C. elegans. 31 October 2014 | doi: 10.1038/ncomms6325 Biological Sciences  Neuroscience  Biologically inspired pteridine redox centres for rechargeable batteries Jihyun Hong, Minah Lee, Byungju Lee, Dong-Hwa Seo, Chan Beum Park and Kisuk Kang Bio-inspired organic materials are a promising class of battery electrodes. Here, the authors present the use of the redox centre of pteridine derivatives, essential constituents in cellular energy metabolism, in lithium and sodium battery systems, and show some excellent electrochemical performance. 31 October 2014 | doi: 10.1038/ncomms6335 Chemical Sciences  Materials science  Organic chemistry  SHP-1-mediated inhibitory signals promote responsiveness and anti-tumour functions of natural killer cells Charlotte Viant, Aurore Fenis, Gaëtan Chicanne, Bernard Payrastre, Sophie Ugolini and Eric Vivier The underlying molecular mechanisms that mediate natural killer (NK) cell tuning remain unclear. Here, the authors show that SHP-1 is essential for the function of MHC class I-specific inhibitory receptors and for setting the threshold of NK cell reactivity. 30 October 2014 | doi: 10.1038/ncomms6108 Biological Sciences  Immunology  Oxic water column methanogenesis as a major component of aquatic CH4 fluxes Matthew J Bogard, Paul A del Giorgio, Lennie Boutet, Maria Carolina Garcia Chaves, Yves T Prairie, Anthony Merante and Alison M Derry Aquatic methane originates in anoxic sediments and bottom waters, but some studies suggest it may also come from the oxic water column. Here, the authors experimentally confirm this hypothesis, and explore the rates, controls and biochemical pathways of oxic water methanogenesis. 30 October 2014 | doi: 10.1038/ncomms6350 Earth Sciences  Biogeochemistry  Presynaptic GABAergic inhibition regulated by BDNF contributes to neuropathic pain induction OPEN Jeremy Tsung-chieh Chen, Da Guo, Dario Campanelli, Flavia Frattini, Florian Mayer, Luming Zhou, Rohini Kuner, Paul A. Heppenstall, Marlies Knipper and Jing Hu Disinhibition of neural activity in the spinal cord is implicated in neuropathic pain. Chen et al. show that disinhibition of neural activity arises from a shift in reversal potential of GABA and a decrease in the conductance of presynaptic GABA, which are both regulated by brain-derived neurotrophic factor. 30 October 2014 | doi: 10.1038/ncomms6331 Biological Sciences  Neuroscience  Loss-proof self-accelerating beams and their use in non-paraxial manipulation of particles’ trajectories Ran Schley, Ido Kaminer, Elad Greenfield, Rivka Bekenstein, Yaakov Lumer and Mordechai Segev Self-accelerating beams are attractive for light-matter interaction applications but their propagation has been limited by absorption. Here, Schley et al. demonstrate self-healing in shape-maintaining, accelerating beams where the central peak intensity is preserved despite losses and apply these beams to particle manipulation. 30 October 2014 | doi: 10.1038/ncomms6189 Physical Sciences  Fluids and plasma physics  Optical physics  A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations Bryan C. Dickinson, Michael S. Packer, Ahmed H. Badran and David R. Liu Phage-assisted continuous evolution (PACE) has the potential to rapidly evolve drug-resistant mutations. Here, Dickinson et al. present a protease PACE system that identifies clinically relevant mutations conferring resistance to protease inhibitors in only a few days of continuous evolution. 30 October 2014 | doi: 10.1038/ncomms6352 Biological Sciences  Biotechnology  A developmental cell-type switch in cortical interneurons leads to a selective defect in cortical oscillations OPEN Naoki Takada, Hyun Jae Pi, Vitor H. Sousa, Jack Waters, Gord Fishell, Adam Kepecs and Pavel Osten The neocortex contains a large diversity of interneurons but the subtype-specific roles of these cells in establishing excitatory and inhibitory circuits are not well understood. Here the authors genetically delete parvalbumin- and somatostatin-positive interneurons during mouse development and study the functional effects in postnatal cortical circuits. 30 October 2014 | doi: 10.1038/ncomms6333 Biological Sciences  Neuroscience  Structural basis of IL-23 antagonism by an Alphabody protein scaffold OPEN Johan Desmet, Kenneth Verstraete, Yehudi Bloch, Eric Lorent, Yurong Wen, Bart Devreese, Karen Vandenbroucke, Stefan Loverix, Thore Hettmann, Sabrina Deroo, Klaartje Somers, Paula Henderikx, Ignace Lasters and Savvas N. Savvides Protein scaffolds can serve as alternatives to antibodies in a range of applications. Here, the authors report the design and development of Alphabodyâ„¢, a protein scaffold featuring a single-chain antiparallel triple-helix coiled-coil fold that the authors use to develop Alphabodies that can neutralize human IL-23 with high specificity and affinity. 30 October 2014 | doi: 10.1038/ncomms6237 Biological Sciences  Immunology  Medical research  Clearance of persistent HPV infection and cervical lesion by therapeutic DNA vaccine in CIN3 patients OPEN Tae Jin Kim, Hyun-Tak Jin, Soo-Young Hur, Hyun Gul Yang, Yong Bok Seo, Sung Ran Hong, Chang-Woo Lee, Suhyeon Kim, Jung-Won Woo, Ki Seok Park, Youn-Young Hwang, Jaehan Park, In-Ho Lee, Kyung-Taek Lim, Ki-Heon Lee, Mi Seon Jeong, Charles D. Surh, You Suk Suh, Jong Sup Park and Young Chul Sung et al. While several human papilloma virus (HPV) vaccines exist, a highly effective vaccine that mediates regression of HPV-induced tumours is lacking. Here the authors show that a therapeutic DNA vaccine-induced HPV-specific polyfunctional CD8 T cell in 7 out of 9 patients who all exhibited complete regression of lesions and viral clearance. 30 October 2014 | doi: 10.1038/ncomms6317 Biological Sciences  Immunology  Medical research  Passive appendages generate drift through symmetry breaking OPEN U. Lācis, N. Brosse, F. Ingremeau, A. Mazzino, F. Lundell, H. Kellay and S. Bagheri Passive mechanisms without energy input are the only way for non-motile organisms to disperse in fluids. Here, the authors use the analogue of the inverted pendulum motion upon gravity to explain the passive drift of a body with a protrusion to the sides of an incoming fluid stream. 30 October 2014 | doi: 10.1038/ncomms6310 Physical Sciences  Applied physics  Fluids and plasma physics  Three-dimensional analysis of Nafion layers in fuel cell electrodes M. Lopez-Haro, L. Guétaz, T. Printemps, A. Morin, S. Escribano, P.-H. Jouneau, P. Bayle-Guillemaud, F. Chandezon and G. Gebel In proton exchange membrane fuel cells, little is known about distribution of ionomers inside electrodes. Here, the authors present an electron tomography technique that allows a three dimensional visualization and quantitative analysis of ionomer layers in the electrodes. 30 October 2014 | doi: 10.1038/ncomms6229 Chemical Sciences  Nanotechnology  Physical chemistry  Signatures of Dirac fermion-mediated magnetic order Paolo Sessi, Felix Reis, Thomas Bathon, Konstantin A. Kokh, Oleg E. Tereshchenko and Matthias Bode The spin texture of a topological insulator is defined by spin-momentum locked Dirac fermions in its non-trivial surface states. Here, Sessi et al. show how the spin texture of Bi2Te3 may be modified by extremely dilute magnetic adatoms, with magnetic order mediated via the RKKY interaction. 30 October 2014 | doi: 10.1038/ncomms6349 Physical Sciences  Condensed matter  Materials science  Granular acoustic switches and logic elements Feng Li, Paul Anzel, Jinkyu Yang, Panayotis G. Kevrekidis and Chiara Daraio Acoustic diodes and circulators operate on the principle that a mechanical signal is used to control the flow of mechanical energy through a solid. Here, the authors demonstrate an acoustic switch composed of a chain of spherical particles, and study the underpinning mechanism behind the process. 30 October 2014 | doi: 10.1038/ncomms6311 Physical Sciences  Materials science  Covalently linked hopanoid-lipid A improves outer-membrane resistance of a Bradyrhizobium symbiont of legumes Alba Silipo, Giuseppe Vitiello, Djamel Gully, Luisa Sturiale, Clémence Chaintreuil, Joel Fardoux, Daniel Gargani, Hae-In Lee, Gargi Kulkarni, Nicolas Busset, Roberta Marchetti, Angelo Palmigiano, Herman Moll, Regina Engel, Rosa Lanzetta, Luigi Paduano, Michelangelo Parrilli, Woo-Suk Chang, Otto Holst, Dianne K. Newman et al. Lipopolysaccharides (LPSs) in the outer membrane of Gram-negative bacteria play key roles in the microbial interactions with animals and plants. Here the authors identify a unique LPS with a covalently-attached hopanoid moiety that contributes to membrane stability in a bacterial symbiont of legumes. 30 October 2014 | doi: 10.1038/ncomms6106 Biological Sciences  Biochemistry  Microbiology  Plant sciences  Variation in genomic landscape of clear cell renal cell carcinoma across Europe Ghislaine Scelo, Yasser Riazalhosseini, Liliana Greger, Louis Letourneau, Mar Gonzàlez-Porta, Magdalena B. Wozniak, Mathieu Bourgey, Patricia Harnden, Lars Egevad, Sharon M. Jackson, Mehran Karimzadeh, Madeleine Arseneault, Pierre Lepage, Alexandre How-Kit, Antoine Daunay, Victor Renault, Hélène Blanché, Emmanuel Tubacher, Jeremy Sehmoun, Juris Viksna et al. Renal cancer accounts for 2.4% of all adult cancers and its incidence is increasing worldwide. Here, the authors carry out genome and transcriptome sequencing of clear cell renal cell carcinomas (ccRCCs) and highlight genomic aberrations and biological pathways underlying ccRCC tumorigenesis. 29 October 2014 | doi: 10.1038/ncomms6135 Biological Sciences  Cancer  Genetics  The key role of transient receptor potential melastatin-2 channels in amyloid-β-induced neurovascular dysfunction L. Park, G. Wang, J. Moore, H. Girouard, P. Zhou, J. Anrather and C. Iadecola Amyloid-beta has been shown to induce cerebrovascular defects that may contribute to the progression of Alzheimer's dementia. Park et al. show that amyloid-beta impairs vascular function by upregulating oxidative stress-induced DNA damage, resulting in opening of TRPM2 channels. 29 October 2014 | doi: 10.1038/ncomms6318 Biological Sciences  Neuroscience  Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis OPEN Katia Nones, Nicola Waddell, Nicci Wayte, Ann-Marie Patch, Peter Bailey, Felicity Newell, Oliver Holmes, J. Lynn Fink, Michael C. J. Quinn, Yue Hang Tang, Guy Lampe, Kelly Quek, Kelly A. Loffler, Suzanne Manning, Senel Idrisoglu, David Miller, Qinying Xu, Nick Waddell, Peter J. Wilson, Timothy J. C. Bruxner et al. Loss-of-function mutations in tumour suppressor genes are associated with oesophageal adenocarcinoma (EAC), but the mechanisms underlying EAC development remain unclear. Here, the authors show that EACs present a high frequency of genomic catastrophes resulting in amplification of potent oncogenes. 29 October 2014 | doi: 10.1038/ncomms6224 Biological Sciences  Cancer  Genetics  Hypoxia-mediated downregulation of miRNA biogenesis promotes tumour progression Rajesha Rupaimoole, Sherry Y. Wu, Sunila Pradeep, Cristina Ivan, Chad V. Pecot, Kshipra M. Gharpure, Archana S. Nagaraja, Guillermo N. Armaiz-Pena, Michael McGuire, Behrouz Zand, Heather J. Dalton, Justyna Filant, Justin Bottsford Miller, Chunhua Lu, Nouara C. Sadaoui, Lingegowda S. Mangala, Morgan Taylor, Twan van den Beucken, Elizabeth Koch, Cristian Rodriguez-Aguayo et al. MicroRNAs play important roles in the maintenance of cellular homeostasis through the post-transcriptional regulation of gene expression. Here, the authors implicate loss of the miRNA biogenesis factor Drosha and altered miRNA maturation in tumour progression under hypoxic conditions. 29 October 2014 | doi: 10.1038/ncomms6202 Biological Sciences  Cancer  Molecular biology  Diversifying evolution of competitiveness Sebastian A. Baldauf, Leif Engqvist and Franz J. Weissing Organisms exhibit considerable variation in resource competitiveness. Here, the authors explain this variation by showing that competitiveness either evolves to a state where individuals with different competitive abilities coexist, or to oscillations between periods of high and low competitiveness. 29 October 2014 | doi: 10.1038/ncomms6233 Biological Sciences  Ecology  Evolution  A critical base pair in k-turns that confers folding characteristics and correlates with biological function OPEN Scott A. McPhee, Lin Huang and David M. J. Lilley The k-turn is a widespread RNA element that adopts a kinked structure that mediates tertiary contacts and frequently binds specific proteins. Here, McPhee et al. show that the ability of a given k-turn to fold in the presence of metal ions alone—or to otherwise require protein binding—is attributable to a specific base pair. 29 October 2014 | doi: 10.1038/ncomms6127 Biological Sciences  Biophysics  Molecular biology  Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis Beben Benyamin, Tonu Esko, Janina S. Ried, Aparna Radhakrishnan, Sita H. Vermeulen, Michela Traglia, Martin Gögele, Denise Anderson, Linda Broer, Clara Podmore, Jian’an Luan, Zoltan Kutalik, Serena Sanna, Peter van der Meer, Toshiko Tanaka, Fudi Wang, Harm-Jan Westra, Lude Franke, Evelin Mihailov, Lili Milani et al. Iron deficiency is the leading cause of anaemia and is known to compromise immune function. Here, the authors identify several new genes associated with iron status in European populations and provide insight into how iron levels may be linked to the risk of metabolic disease. 29 October 2014 | doi: 10.1038/ncomms5926 Biological Sciences  Genetics  Medical research  Hypoxia promotes stem cell phenotypes and poor prognosis through epigenetic regulation of DICER Twan van den Beucken, Elizabeth Koch, Kenneth Chu, Rajesha Rupaimoole, Peggy Prickaerts, Michiel Adriaens, Jan Willem Voncken, Adrian L. Harris, Francesca M. Buffa, Syed Haider, Maud H. W. Starmans, Cindy Q. Yao, Mircea Ivan, Cristina Ivan, Chad V. Pecot, Paul C. Boutros, Anil K. Sood, Marianne Koritzinsky and Bradly G. Wouters Reduced expression of DICER—responsible for the processing of microRNA precursors—was previously linked to poor clinical outcomes in cancer patients. Here, the authors uncover an epigenetic mechanism by which hypoxia suppresses DICER expression and deregulates the miR-200-Zeb1 circuit in breast cancer to promote the tumour phenotype. 29 October 2014 | doi: 10.1038/ncomms6203 Biological Sciences  Cancer  Molecular biology  On the absence of intrahelical DNA dynamics on the μs to ms timescale OPEN Rodrigo Galindo-Murillo, Daniel R. Roe and Thomas E. Cheatham No experimental evidence exists for intra-helical motion of DNA at the μs timescale, which has been attributed to technical difficulties in observing motion in this time range. Here, the authors demonstrate, using extensive molecular dynamics simulations and experimental analysis, that such motion is effectively absent from a B-DNA duplex. 29 October 2014 | doi: 10.1038/ncomms6152 Biological Sciences  Biochemistry  Bioinformatics  Mutations in filamin C cause a new form of familial hypertrophic cardiomyopathy Rafael Valdés-Mas, Ana Gutiérrez-Fernández, Juan Gómez, Eliecer Coto, Aurora Astudillo, Diana A. Puente, Julián R. Reguero, Victoria Álvarez, César Morís, Diego León, María Martín, Xose S Puente and Carlos López-Otín Hypertrophic cardiomyopathy (HCM) is a major cause of sudden cardiac death in young adults. Here, the authors show that mutations in a sarcomeric protein filamin C contribute to the development of familial HCM and are associated with an increased incidence of sudden cardiac death. 29 October 2014 | doi: 10.1038/ncomms6326 Biological Sciences  Genetics  Vesicle-based artificial cells as chemical microreactors with spatially segregated reaction pathways OPEN Yuval Elani, Robert V. Law and Oscar Ces In biological systems, cells are divided into compartments, typically with lipid layers. Here, the authors design a multipart vesicle system for sequential enzymatic reactions, where the product from one reaction traverses into the next, allowing multiple spatially separated reaction steps. 29 October 2014 | doi: 10.1038/ncomms6305 Chemical Sciences  Bioengineering  Biophysics  Chemical biology  Implementation of the CRISPR-Cas9 system in fission yeast Jake Z. Jacobs, Keith M. Ciccaglione, Vincent Tournier and Mikel Zaratiegui The fission yeast, Schizosaccharomyces pombe, is a valuable model organism, but the lack of a portable RNA Pol III promoter has prevented the implementation of the CRISPR/Cas9 system. Here the authors develop a CRISPR/Cas9 system that achieves selection-free specific mutagenesis with very high efficiencies in S. pombe. 29 October 2014 | doi: 10.1038/ncomms6344 Biological Sciences  Genetics  Molecular biology    Nature Communications JOBS of the week Postdoctoral Research Fellow University of Leeds Research Assistant University of Cambridge Postdoctoral Scientist Medical Research Council PhD studentship University of Aberdeen Postdoctoral Felow Oregon Health & Science University (OHSU) Scientific Director Basque Centre for Climate Change Postdoctoral Fellowships The Rockefeller University Research Fellow The University of Nottingham More Science jobs from Nature Communications EVENT 7th Ocular Diseases Drug Discovery Conference 19.03.15 San Diego, USA More science events from     Advertisement Nature Communications is now fully open access All new submissions to Nature Communications, if accepted, will be published open access and an article processing charge will apply. For more information visit the website. Many research funders and institutions make funds available to pay open access APCs: please consult our open access funding page to check if your funder or institution has funding available. For advice on whether you are eligible for APC funding and help in approaching funders and institutions please contact us at openaccess@nature.com   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. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at:www.nature.com/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For other enquiries, please contact our customer feedback department Nature Publishing Group | 75 Varick Street, 9th Floor | New York | NY 10013-1917 | USA Nature Publishing Group's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.