Nature Communications - 12 November 2014

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Weekly Content Alert 12 November 2014  Featured image: Lyson et al. elucidate the evolution of the unique breathing system of turtles and the origin of their shell Latest content: Articles Erratum Journal homepage Recommend to library Web feed   Advertisement Nature Outlook: Medical Research Masterclass From the basic functions of the cell to cures for HIV and cancer, Nature Outlook: Medical Research Masterclass uses the 2014 Lindau Nobel Laureate Meeting as a basis to explore the latest research in medicine and physiology. Access the Outlook free online for six months.   Supported by Mars, Incorporated       Latest Articles View all Articles     SiO and CH3OH mega-masers in NGC 1068 OPEN Junzhi Wang, Jiangshui Zhang, Yu Gao, Zhi-Yu Zhang, Di Li, Min Fang and Yong Shi Astrophysical masers are interstellar sources of stimulated spectral line emission, with most SiO masers in the Milky Way existing around evolved stars. Here, Wang et al. report detections of millimetre SiO and Class I CH3OH mega-masers in NGC 1068. 11 November 2014 | doi: 10.1038/ncomms6449 Physical Sciences  Astronomy  Mind-controlled transgene expression by a wireless-powered optogenetic designer cell implant OPEN Marc Folcher, Sabine Oesterle, Katharina Zwicky, Thushara Thekkottil, Julie Heymoz, Muriel Hohmann, Matthias Christen, Marie Daoud El-Baba, Peter Buchmann and Martin Fussenegger Brain–machine interfaces offer the possibility of controlling prosthetic devices using changes in brain activity. Folcher et al. couple such a system wirelessly to an optogenetic implant in mice to control expression of a transgene, demonstrating its potential for mind-controlled drug delivery. 11 November 2014 | doi: 10.1038/ncomms6392 Biological Sciences  Bioengineering  Medical research  Neuroscience  Extending medium-range predictability of extreme hydrological events in Europe OPEN David A. Lavers, Florian Pappenberger and Ervin Zsoter Extreme winter flooding has caused devastation across Europe in recent years, highlighting the need for improved forecasts. Here, the authors show that the use of water vapour transport, rather than precipitation in weather prediction models, can extend the forecast horizon by as much as 3 days. 11 November 2014 | doi: 10.1038/ncomms6382 Earth Sciences  Atmospheric science  Climate science  Structural basis for extracellular cis and transRPTPσ signal competition in synaptogenesis OPEN Charlotte H. Coles, Nikolaos Mitakidis, Peng Zhang, Jonathan Elegheert, Weixian Lu, Andrew W. Stoker, Terunaga Nakagawa, Ann Marie Craig, E. Yvonne Jones and A. Radu Aricescu Receptor protein tyrosine phosphatase sigma (RPTPσ) promotes both neurite outgrowth and synaptic organization. Here, Coles et al. present the structural basis for this switch in function, whereby TrkC on the postsynaptic membrane and heparan sulphate proteoglycans compete for the same binding surface on RPTPσ. 11 November 2014 | doi: 10.1038/ncomms6209 Biological Sciences  Biochemistry  Protrusion force microscopy reveals oscillatory force generation and mechanosensing activity of human macrophage podosomes Anna Labernadie, Anaïs Bouissou, Patrick Delobelle, Stéphanie Balor, Raphael Voituriez, Amsha Proag, Isabelle Fourquaux, Christophe Thibault, Christophe Vieu, Renaud Poincloux, Guillaume M. Charrière and Isabelle Maridonneau-Parini Podosomes are actin-rich adhesion structures that show periodic oscillations in stiffness. Here, Labernadie et al. develop a method to measure the protrusion force and mechanosensing activity of individual podosomes, using an atomic force microscope and a flexible substrate membrane. 11 November 2014 | doi: 10.1038/ncomms6343 Biological Sciences  Biophysics  Cell biology  Rad54B serves as a scaffold in the DNA damage response that limits checkpoint strength Takaaki Yasuhara, Takahiko Suzuki, Mari Katsura and Kiyoshi Miyagawa Rad54B is a poorly characterized DNA damage repair protein homologous to Rad54, a protein implicated in DNA damage repair through homologous recombination. Here the authors implicate Rad54B as a modulator of the DNA damage response through its interaction with the MDM2–MDMX complex to regulate p53 degradation. 11 November 2014 | doi: 10.1038/ncomms6426 Biological Sciences  Biochemistry  Cancer  Molecular biology  Interplay between the Kondo effect and the Ruderman–Kittel–Kasuya–Yosida interaction Henning Prüser, Piet E. Dargel, Mohammed Bouhassoune, Rainer G. Ulbrich, Thomas Pruschke, Samir Lounis and Martin Wenderoth Building an understanding of how many bodies interact with one another starts by understanding the interaction between just two. Here, Prüser et al. show how the separation between two magnetic impurities in copper influences a many-body interaction known as the Kondo effect. 11 November 2014 | doi: 10.1038/ncomms6417 Physical Sciences  Condensed matter  Materials science  Eruption of a deep-sea mud volcano triggers rapid sediment movement OPEN Tomas Feseker, Antje Boetius, Frank Wenzhöfer, Jerome Blandin, Karine Olu, Dana R. Yoerger, Richard Camilli, Christopher R. German and Dirk de Beer Submarine mud volcanoes are difficult to observe from the sea surface and previous recordings at depth have been short term. Here, the authors provide the first long-term monitoring from Håkon Mosby and suggest that mud volcanoes may be more important to the global methane budget than previously thought. 11 November 2014 | doi: 10.1038/ncomms6385 Earth Sciences  Geology and geophysics  The staphylococcal toxins γ-haemolysin AB and CB differentially target phagocytes by employing specific chemokine receptors András N. Spaan, Manouk Vrieling, Pierre Wallet, Cédric Badiou, Tamara Reyes-Robles, Elizabeth A. Ohneck, Yvonne Benito, Carla J. C. de Haas, Christopher J. Day, Michael P. Jennings, Gérard Lina, François Vandenesch, Kok P. M. van Kessel, Victor J. Torres, Jos A. G. van Strijp and Thomas Henry Genes encoding two pore-forming toxins (γ-haemolysins HlgAB and HlgCB) are present in almost all human Staphylococcus aureus isolates. Here Spaan et al. show that HlgAB and HlgCB target different phagocyte types by interacting with specific chemokine receptors and complement receptors, respectively. 11 November 2014 | doi: 10.1038/ncomms6438 Biological Sciences  Immunology  Microbiology  S-nitrosothiols regulate nitric oxide production and storage in plants through the nitrogen assimilation pathway Lucas Frungillo, Michael J. Skelly, Gary J. Loake, Steven H. Spoel and Ione Salgado Assimilation of nitrate by plant roots leads to the generation of the signalling molecule, nitric oxide. Here Frungillo et al. show that nitric oxide fine-tunes nitrate homeostasis by feedback regulating nitrate transporters and reductases, while also promoting its own storage. 11 November 2014 | doi: 10.1038/ncomms6401 Biological Sciences  Plant sciences  Genome sequence of mungbean and insights into evolution within Vigna species OPEN Yang Jae Kang, Sue K. Kim, Moon Young Kim, Puji Lestari, Kil Hyun Kim, Bo-Keun Ha, Tae Hwan Jun, Won Joo Hwang, Taeyoung Lee, Jayern Lee, Sangrea Shim, Min Young Yoon, Young Eun Jang, Kwang Soo Han, Puntaree Taeprayoon, Na Yoon, Prakit Somta, Patcharin Tanya, Kwang Soo Kim, Jae-Gyun Gwag et al. Mungbean is a fast-growing and warm-season legume crop, cultivated mainly in Asia. Here, the authors sequence the genomes of both wild and domesticated mungbean varieties and, together with detailed transcriptome data, provide insight into mungbean domestication, polyploidization and speciation. 11 November 2014 | doi: 10.1038/ncomms6443 Biological Sciences  Evolution  Genetics  High-pressure radiative conductivity of dense silicate glasses with potential implications for dark magmas Motohiko Murakami, Alexander F. Goncharov, Naohisa Hirao, Ryo Masuda, Takaya Mitsui, Sylvia-Monique Thomas and Craig R. Bina Understanding of the Earth’s interior requires insight into the thermal properties of silicate melts under high pressure. Here, the authors present high-pressure spectroscopic measurements of iron-enriched dense silicate glasses and infer the radiative conductivity of dense melts at the core–mantle boundary. 11 November 2014 | doi: 10.1038/ncomms6428 Earth Sciences  Geology and geophysics  Materials science  Site-selective hexa-hetero-functionalization of α-cyclodextrin an archetypical C6-symmetric concave cycle Bo Wang, Elena Zaborova, Samuel Guieu, Marta Petrillo, Maxime Guitet, Yves Blériot, Mickaël Ménand, Yongmin Zhang and Matthieu Sollogoub Site-selective modification of symmetrical concave molecules is a highly challenging task because of the rapid increase in potential combinations as the number of sites increases. Here, the authors show routes to selectively functionalize six symmetrical positions, leading to a hexa-differentiated α-cyclodextrin. 10 November 2014 | doi: 10.1038/ncomms6354 Chemical Sciences  Organic chemistry  PARP13 regulates cellular mRNA post-transcriptionally and functions as a pro-apoptotic factor by destabilizing TRAILR4 transcript Tanya Todorova, Florian J. Bock and Paul Chang The poly(ADP-ribose) polymerase PARP13 targets RNA viruses by binding to viral RNA and promoting its degradation by cellular decay factors such as the exosome. Todorova et al. find that PARP13 also plays a much broader role as a regulator of host mRNA stability, and promotes apoptosis by degrading TRAILR4 transcripts. 10 November 2014 | doi: 10.1038/ncomms6362 Biological Sciences  Molecular biology  The mTORC1 effectors S6K1 and 4E-BP play different roles in CNS axon regeneration Liu Yang, Linqing Miao, Feisi Liang, Haoliang Huang, Xiuyin Teng, Shaohua Li, Jaloliddin Nuriddinov, Michael E. Selzer and Yang Hu Activation of the mammalian target of rapamycin complex 1 in mature retinal ganglion cells promotes axonal regeneration in a mouse optic nerve crush model but the role of its downstream effectors is not clear. Here the authors show that S6K1 plays a dual role in axon regeneration, whereas 4E-BP inhibition is not sufficient but necessary for axon regeneration. 10 November 2014 | doi: 10.1038/ncomms6416 Biological Sciences  Neuroscience  Aggregation and morphology control enables multiple cases of high-efficiency polymer solar cells OPEN Yuhang Liu, Jingbo Zhao, Zhengke Li, Cheng Mu, Wei Ma, Huawei Hu, Kui Jiang, Haoran Lin, Harald Ade and He Yan Polymer solar cells promise a cost-effective way to harness solar energy, but cell performance is held back by limited choices of suitable materials. Here, Liu et al. demonstrate record cell efficiencies for multiple material combinations via a new approach of aggregation and morphology control. 10 November 2014 | doi: 10.1038/ncomms6293 Physical Sciences  Materials science  Optical physics  Programmable energy landscapes for kinetic control of DNA strand displacement Robert R. F. Machinek, Thomas E. Ouldridge, Natalie E. C. Haley, Jonathan Bath and Andrew J. Turberfield The operation of DNA-based molecular devices often relies on toehold-mediated strand displacement. Here, the authors show how mismatches in base pairing can be used for the kinetic control of strand displacement, tuning the rate constant over three orders of magnitude. 10 November 2014 | doi: 10.1038/ncomms6324 Physical Sciences  Biophysics  Chemical biology  Resonant Raman spectroscopy of twisted multilayer graphene Jiang-Bin Wu, Xin Zhang, Mari Ijäs, Wen-Peng Han, Xiao-Fen Qiao, Xiao-Li Li, De-Sheng Jiang, Andrea C. Ferrari and Ping-Heng Tan Stacking of two-dimensional materials in heterostructures is known to yield interesting electronic structures. Here, the authors study shear modes via Raman spectroscopy in twisted multilayer graphene, finding that the interlayer coupling at the interface is weaker than in Bernal-stacked systems. 10 November 2014 | doi: 10.1038/ncomms6309 Physical Sciences  Materials science  High-resolution nanotransfer printing applicable to diverse surfaces via interface-targeted adhesion switching Jae Won Jeong, Se Ryeun Yang, Yoon Hyung Hur, Seong Wan Kim, Kwang Min Baek, Soonmin Yim, Hyun-Ik Jang, Jae Hong Park, Seung Yong Lee, Chong-Ook Park and Yeon Sik Jung There is an ongoing need for high resolution, versatile and simplistic nanoscale lithography and transfer. Here the authors report a solvent-assisted nanotransfer printing route, which allows for the easy release of 8–20 nm scale features on to a range of substrates. 10 November 2014 | doi: 10.1038/ncomms6387 Physical Sciences  Materials science  Nanotechnology  Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution OPEN Andrew D. W. Geering, Florian Maumus, Dario Copetti, Nathalie Choisne, Derrick J. Zwickl, Matthias Zytnicki, Alistair R. McTaggart, Simone Scalabrin, Silvia Vezzulli, Rod A. Wing, Hadi Quesneville and Pierre-Yves Teycheney Endogenous viral elements have been extensively described in animals but their significance in plants is less well understood. Here, Geering et al. describe a new group of endogenous pararetroviruses, called florendoviruses, which have colonized the genomes of many important crop species. 10 November 2014 | doi: 10.1038/ncomms6269 Biological Sciences  Evolution  Virology  High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na+-coupled ATP synthase Doreen Matthies, Wenchang Zhou, Adriana L. Klyszejko, Claudio Anselmi, Özkan Yildiz, Karsten Brandt, Volker Müller, José D. Faraldo-Gómez and Thomas Meier Rotary ATPases exhibit similar architecture and mechanism but distinct physiological functions, operating either as ion pumps or ATP synthases. Here the authors report the structure and mechanism of the c-ring from the A. woodii ATP synthase, and suggest an evolutionary path between synthases and pumps through adaptations in this molecular rotor. 10 November 2014 | doi: 10.1038/ncomms6286 Biological Sciences  Biochemistry  Biophysics  Molecular biology  Highly accelerated inverse electron-demand cycloaddition of electron-deficient azides with aliphatic cyclooctynes Jan Dommerholt, Olivia van Rooijen, Annika Borrmann, Célia Fonseca Guerra, F. Matthias Bickelhaupt and Floris L. van Delft Strain-promoted cycloadditions are relatively slow and most work on increasing reactivity focuses on cycloalkyne structure. Here, the authors show a marked dependence upon the nature of the azide, which not only leads to increased rates but also enables orthogonality between coupling partners. 10 November 2014 | doi: 10.1038/ncomms6378 Chemical Sciences  Chemical biology  Organic chemistry  Genome-wide association study of Arabidopsis thaliana leaf microbial community Matthew W. Horton, Natacha Bodenhausen, Kathleen Beilsmith, Dazhe Meng, Brian D. Muegge, Sathish Subramanian, M. Madlen Vetter, Bjarni J. Vilhjálmsson, Magnus Nordborg, Jeffrey I. Gordon and Joy Bergelson The effect of a host's genetic variation on the structure of its microbial community is poorly understood. Here, Horton et al. reveal associations between genetic variants in the plant model species Arabidopsis thaliana and the composition of the leaves' microbial communities. 10 November 2014 | doi: 10.1038/ncomms6320 Biological Sciences  Genetics  Microbiology  Plant sciences  Progressive contraction of the latent HIV reservoir around a core of less-differentiated CD4+ memory T Cells OPEN S. Jaafoura, M. G. de Goër de Herve, E. A. Hernandez-Vargas, H. Hendel-Chavez, M. Abdoh, M. C. Mateo, R. Krzysiek, M. Merad, R. Seng, M. Tardieu, J. F. Delfraissy, C. Goujard and Y. Taoufik HIV can persist in CD4+ T cells of patients receiving long-term antiretroviral therapy. Here the authors show the presence of intrinsic dynamics that progressively contract the latent HIV reservoir around a core of less-differentiated CD4 T-cell memory subsets. 10 November 2014 | doi: 10.1038/ncomms6407 Biological Sciences  Immunology  Changing the peptide specificity of a human T-cell receptor by directed evolution Sheena N. Smith, Yuhang Wang, Javier L. Baylon, Nishant K. Singh, Brian M. Baker, Emad Tajkhorshid and David M. Kranz Whether the specificity of a TCR can be changed in vitro to recognize an entirely different peptide has not been shown. Here, the authors use directed evolution to change the specificity of a human TCR from recognition of a viral peptide to that of a melanoma antigen. 07 November 2014 | doi: 10.1038/ncomms6223 Biological Sciences  Immunology  Origin of the unique ventilatory apparatus of turtles Tyler R. Lyson, Emma R. Schachner, Jennifer Botha-Brink, Torsten M. Scheyer, Markus Lambertz, G. S. Bever, Bruce S. Rubidge and Kevin de Queiroz The origin of the unique turtle lung ventilatory apparatus is poorly understood. Here the authors show an increase in body wall rigidity early in evolution that allowed the abdominal muscles to become specialized for breathing and the ribs to eventually form the iconic turtle shell. 07 November 2014 | doi: 10.1038/ncomms6211 Biological Sciences  Evolution  NAA10 controls osteoblast differentiation and bone formation as a feedback regulator of Runx2 Haejin Yoon, Hye-Lim Kim, Yang-Sook Chun, Dong Hoon Shin, Kyoung-Hwa Lee, Chan Soo Shin, Dong Yeon Lee, Hong-Hee Kim, Zang Hee Lee, Hyun-Mo Ryoo, Mi-Ni Lee, Goo Taeg Oh and Jong-Wan Park N-alpha-acetyltransferase 10 (NAA10) regulates cell growth and proliferation. Here the authors show that NAA10 also has a role in osteogenesis, by fine-tuning the activity of the osteogenic transcription factor Runx2. 07 November 2014 | doi: 10.1038/ncomms6176 Biological Sciences  Developmental biology  Spin–orbital dynamics in a system of polar molecules Sergey V. Syzranov, Michael L. Wall, Victor Gurarie and Ana Maria Rey Spin–orbit coupling gives rise to a plethora of rich phenomena in many condensed matter and atomic systems. Syzranov et al. study the role of dipole–dipole interactions in ultracold polar molecule gases and show that they produce an effective spin–orbit coupling that generates chiral excitations. 07 November 2014 | doi: 10.1038/ncomms6391 Physical Sciences  Atomic and molecular physics  Condensed matter  Theoretical physics  n-type chalcogenides by ion implantation Mark A. Hughes, Yanina Fedorenko, Behrad Gholipour, Jin Yao, Tae-Hoon Lee, Russell M. Gwilliam, Kevin P. Homewood, Steven Hinder, Daniel W. Hewak, Stephen R. Elliott and Richard J. Curry The use of chalcogenide glasses in simple electronic devices, such as a p-n junction, is hindered by the lack of n-type material. Here, Hughes et al. demonstrate n-type doping of GeTe and GaLaSO amorphous films using bismuth-ion implantation. 07 November 2014 | doi: 10.1038/ncomms6346 Physical Sciences  Materials science  An extremely low-density human population exterminated New Zealand moa Richard N. Holdaway, Morten E. Allentoft, Christopher Jacomb, Charlotte L. Oskam, Nancy R. Beavan and Michael Bunce It is generally accepted that Polynesian settlers were directly responsible for the extinction of New Zealand moa. Here, the authors present three series of radiocarbon ages that define the brief period of interaction between Polynesians and moa, and show that high human population densities are not a prerequisite for the extinction of megafauna populations. 07 November 2014 | doi: 10.1038/ncomms6436 Biological Sciences  Ecology  Evolution  Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes OPEN Linnéa Smeds, Takeshi Kawakami, Reto Burri, Paulina Bolivar, Arild Husby, Anna Qvarnström, Severin Uebbing and Hans Ellegren The genetic basis of sex chromosome pseudoautosomal regions (PAR) in organisms with female heterogamety is largely unknown. Smeds et al. provide the first molecular characterization of the PAR in birds with differentiated sex chromosomes and show a potential recombination hotspot and no evidence for strong sexual antagonism in this region. 07 November 2014 | doi: 10.1038/ncomms6448 Biological Sciences  Evolution  Genetics  Conserved sequence-specific lincRNA–steroid receptor interactions drive transcriptional repression and direct cell fate William H. Hudson, Mark R. Pickard, Ian Mitchelle S. de Vera, Emily G. Kuiper, Mirna Mourtada-Maarabouni, Graeme L. Conn, Douglas J. Kojetin, Gwyn T. Williams and Eric A. Ortlund The abundant IincRNA growth arrest-specific 5 (Gas5) inhibits the transcriptional activity of steroid hormone receptors (SRs) through direct competition for DNA binding. Here the authors use X-ray crystallography, NMR and complementary biochemical approaches to elucidate the molecular and evolutionary mechanisms that guide Gas5 binding to SRs. 07 November 2014 | doi: 10.1038/ncomms6395 Biological Sciences  Biochemistry  Cancer  Large surface relaxation in the organic semiconductor tetracene Hazuki Morisaki, Takashi Koretsune, Chisa Hotta, Jun Takeya, Tsuyoshi Kimura and Yusuke Wakabayashi Interfacial charge transport determines the performance of organic semiconductors, yet the surface influence is poorly understood. Here, Morisaki et al. observe surface relaxation and its resulting transport properties in the first monolayer of tetracene, which are dissimilar to those of the bulk. 07 November 2014 | doi: 10.1038/ncomms6400 Physical Sciences  Condensed matter  Materials science  Cooperative dual palladium/silver catalyst for direct difluoromethylation of aryl bromides and iodides Yang Gu, Xuebing Leng and Qilong Shen Difluoromethylation of organic molecules typically requires stoichiometric metal salts or harsh conditions. Here, the authors report a dual metal catalytic system for difluoromethylation allowing mild and direct functionalization of aryl halides, including highly functionalized molecules. 07 November 2014 | doi: 10.1038/ncomms6405 Chemical Sciences  Catalysis  Organic chemistry  Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter OPEN Nina Grossmann, Ahmet S. Vakkasoglu, Sabine Hulpke, Rupert Abele, Rachelle Gaudet and Robert Tampé ABC systems are an important class of transporters involved in human pathologies for which the basis for transport remains poorly understood. Here the authors suggest a molecular basis for ATP-powered vectorial peptide export by the human transporter associated with antigen processing (TAP). 07 November 2014 | doi: 10.1038/ncomms6419 Biological Sciences  Biochemistry  Biophysics  Immunology  The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes Alexander G. Myasnikov, Zhanna A. Afonina, Jean-François Ménétret, Vladimir A. Shirokov, Alexander S. Spirin and Bruno P. Klaholz During translation, several ribosomes assemble on an mRNA strand to form polyribosomes. Here the authors describe—using cryo electron tomography—a compact state of the eukaryotic polysome where individual ribosomes contact each other and form a tight helical assembly that creates a continuous inner channel for the mRNA. 07 November 2014 | doi: 10.1038/ncomms6294 Biological Sciences  Biochemistry  Biophysics  Spatially resolved one-dimensional boundary states in graphene–hexagonal boron nitride planar heterostructures Jewook Park, Jaekwang Lee, Lei Liu, Kendal W. Clark, Corentin Durand, Changwon Park, Bobby G. Sumpter, Arthur P. Baddorf, Ali Mohsin, Mina Yoon, Gong Gu and An-Ping Li One-dimensional boundaries in lateral heterostructures of two-dimensional materials are expected to have interesting properties. Park et al. probe the electronic properties of the graphene/hexagonal-boron-nitride interface, revealing the spatial and energetic distributions of one-dimensional boundary states. 07 November 2014 | doi: 10.1038/ncomms6403 Physical Sciences  Condensed matter  Materials science  Bond competition and phase evolution on the IrTe2 surface Qing Li, Wenzhi Lin, Jiaqiang Yan, Xin Chen, Anthony G. Gianfrancesco, David J. Singh, David Mandrus, Sergei V. Kalinin and Minghu Pan Understanding the structural relationship and electronic states between incommensurate/commensurate phases remains an ongoing challenge. Here, the authors report incommensurate structures and electronic roughness on the surface of cleaved IrTe2. 07 November 2014 | doi: 10.1038/ncomms6358 Physical Sciences  Condensed matter  Materials science  Gold-promoted structurally ordered intermetallic palladium cobalt nanoparticles for the oxygen reduction reaction Kurian A. Kuttiyiel, Kotaro Sasaki, Dong Su, Lijun Wu, Yimei Zhu and Radoslav R. Adzic There is substantial research into new catalysts for oxygen reduction. Here, the authors report a structurally ordered gold–palladium–cobalt intermetallic catalyst which exhibits comparable activity to platinum/carbon in both acid and alkaline media, and probe its structure-activity behaviour. 06 November 2014 | doi: 10.1038/ncomms6185 Chemical Sciences  Catalysis  Materials science  Predicting commuter flows in spatial networks using a radiation model based on temporal ranges Yihui Ren, Mária Ercsey-Ravasz, Pu Wang, Marta C. González and Zoltán Toroczkai Mathematical tools for understanding network flows with a social component are much less developed than for, say, electric circuits. Ren et al. introduce a method by generalizing the radiation model to flows in spatial networks, which they apply to predict commuter flows in a highway network. 06 November 2014 | doi: 10.1038/ncomms6347 Physical Sciences  Theoretical physics  Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution Larissa B. Patterson, Emily J. Bain and David M. Parichy Fishes have diverse colour patterns, yet the mechanisms of pattern diversification are poorly understood. Here, the authors show that the uniform pigment pattern in Danio albolineatus is established by an early differentiation of xanthophores controlled by cis regulatory changes at the csf1a locus. 06 November 2014 | doi: 10.1038/ncomms6299 Biological Sciences  Developmental biology  Evolution  Genetics  High lithium anodic performance of highly nitrogen-doped porous carbon prepared from a metal-organic framework Fangcai Zheng, Yang Yang and Qianwang Chen Nitrogen-doped graphene can be used for lithium storage, but the nitrogen content is often quite low. Here, the authors synthesize graphene analogous with high nitrogen content using a zeolitic imidazolate framework, which show exceptional battery performances. 06 November 2014 | doi: 10.1038/ncomms6261 Chemical Sciences  Inorganic chemistry  Physical chemistry  Titania single crystals with a curved surface Shuang Yang, Bing Xing Yang, Long Wu, Yu Hang Li, Porun Liu, Huijun Zhao, Yan Yan Yu, Xue Qing Gong and Hua Gui Yang Thermodynamics typically favour the formation of crystals with flat facets. Here, the authors report an approach for the synthesis of curved boundaries in titania single crystals, composed of high index microfacets. 06 November 2014 | doi: 10.1038/ncomms6355 Chemical Sciences  Materials science  Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants OPEN Kalliope Panoutsopoulou, Konstantinos Hatzikotoulas, Dionysia Kiara Xifara, Vincenza Colonna, Aliki-Eleni Farmaki, Graham R. S. Ritchie, Lorraine Southam, Arthur Gilly, Ioanna Tachmazidou, Segun Fatumo, Angela Matchan, Nigel W. Rayner, Ioanna Ntalla, Massimo Mezzavilla, Yuan Chen, Chrysoula Kiagiadaki, Eleni Zengini, Vasiliki Mamakou, Antonis Athanasiadis, Margarita Giannakopoulou et al. Isolated populations can increase power to detect low frequency and rare risk variants associated with complex phenotypes. Here, the authors identify variants associated with haematological traits in two isolated Greek populations that would be difficult to detect in the general population, due to their low frequency. 06 November 2014 | doi: 10.1038/ncomms6345 Biological Sciences  Genetics  Ciliary dysfunction impairs beta-cell insulin secretion and promotes development of type 2 diabetes in rodents Jantje M. Gerdes, Sonia Christou-Savina, Yan Xiong, Tilo Moede, Noah Moruzzi, Patrick Karlsson-Edlund, Barbara Leibiger, Ingo B. Leibiger, Claes-Göran Östenson, Philip L. Beales and Per-Olof Berggren Cilia are hair-like protuberances on the cellular surface that have been implicated in sensing and signal transduction. Here Gerdes et al. show cilia are involved in insulin signalling and secretion in pancreatic β-cells of rodents, and suggest that ciliary dysfunction could contribute to type 2 diabetes. 06 November 2014 | doi: 10.1038/ncomms6308 Biological Sciences  Cell biology  Medical research  Orbital Asian summer monsoon dynamics revealed using an isotope-enabled global climate model Thibaut Caley, Didier M. Roche and Hans Renssen Asian speleothem δ18O records are widely used as a proxy for summer monsoon intensity, but their validity has been questioned. Here, the authors evaluate their validity using a 150,000-year transient simulation from an isotope-enabled global climate model. 06 November 2014 | doi: 10.1038/ncomms6371 Earth Sciences  Biogeochemistry  Climate science  Rectified directional sensing in long-range cell migration OPEN Akihiko Nakajima, Shuji Ishihara, Daisuke Imoto and Satoshi Sawai Cell migration is regulated by spatial and temporal information, but how the two are integrated is not well understood. Here, Nakajima et al. use dynamic microfluidics gradients to show that Ras activation at the leading edge of Dictyostelium is suppressed when chemoattractant concentration decreases over time. 06 November 2014 | doi: 10.1038/ncomms6367 Biological Sciences  Cell biology  Microbiology  Synthesizing AND gate genetic circuits based on CRISPR-Cas9 for identification of bladder cancer cells Yuchen Liu, Yayue Zeng, Li Liu, Chengle Zhuang, Xing Fu, Weiren Huang and Zhiming Cai Tools derived from synthetic biology offer powerful means to refine drug delivery and disease detection. Liu et al. engineer a logical AND gate using CRISPR-Cas9 to drive gene expression only cells in which two promoters are active, and use it to selectively inhibit the growth of bladder cancer cells in vitro. 06 November 2014 | doi: 10.1038/ncomms6393 Biological Sciences  Bioengineering  Cancer  Electrically controlled one-way photon flow in plasmonic nanostructures Artur Davoyan and Nader Engheta If photonics and electronics are to form hybrid information processing systems, it will be necessary to manipulate and isolate light electrically, over short distances. Davoyan and Engheta propose a route to achieve this in plasmonic waveguides by exploiting the magnetic field induced by a direct current. 06 November 2014 | doi: 10.1038/ncomms6250 Physical Sciences  Applied physics  Materials science  Optical physics  Drp1 inhibition attenuates neurotoxicity and dopamine release deficits in vivo OPEN Phillip M. Rappold, Mei Cui, Jonathan C. Grima, Rebecca Z. Fan, Karen L. de Mesy-Bentley, Linan Chen, Xiaoxi Zhuang, William J. Bowers and Kim Tieu Mitochondrial dysfunction has been associated with Parkinson’s disease but effective therapies targeting this pathway are yet to be developed. Here the authors show that inhibition of the mitochondrial fission protein Drp-1 using genetic or small-molecule approaches in mouse models of the disease, leads to improvements in the pathology. 05 November 2014 | doi: 10.1038/ncomms6244 Biological Sciences  Neuroscience  Circadian rhythms of hydraulic conductance and growth are enhanced by drought and improve plant performance OPEN Cecilio F. Caldeira, Linda Jeanguenin, François Chaumont and François Tardieu Circadian rhythms allow plants to respond to diurnal fluctuations in the environment. Here Caldeira et al. find that circadian control of hydraulic conductance, aquaporin expression and leaf growth are entrained by oscillations of plant water status and promote water uptake in drought-stressed plants. 05 November 2014 | doi: 10.1038/ncomms6365 Biological Sciences  Plant sciences  A short acidic motif in ARF guards against mitochondrial dysfunction and melanoma susceptibility Claus Christensen, Jirina Bartkova, Martin Mistrík, Arnaldur Hall, Marina Krarup Lange, Ulrik Ralfkiær, Jiri Bartek and Per Guldberg Mutations within the ARF tumour suppressor—encoded by the CDKN2A locus—have been associated with familial melanoma through an unknown mechanism. Here the authors uncover a melanoma protective function of ARF through its ability to interact with dysfunctional mitochondria and maintain low levels of cellular superoxide. 05 November 2014 | doi: 10.1038/ncomms6348 Biological Sciences  Biochemistry  Cancer  Cell biology  Crystal structures of wild type and disease mutant forms of the ryanodine receptor SPRY2 domain Kelvin Lau and Filip Van Petegem Ryanodine receptors (RyRs) are endoplasmic and sarcoplasmic reticulum calcium channels. Here Lau et al. solve the structure of the SPRY2 domain from skeletal muscle RyR1, locate it within full-length RyR1 and show that a disease-causing mutation destabilizes the domain. 05 November 2014 | doi: 10.1038/ncomms6397 Biological Sciences  Biochemistry  Cotton cytochrome P450 CYP82D regulates systemic cell death by modulating the octadecanoid pathway OPEN Longqing Sun, Longfu Zhu, Li Xu, Daojun Yuan, Ling Min and Xianlong Zhang Oxylipin signalling is known to play important roles in plant growth, development and defence against pathogens. Here Sun et al. identify a novel cytochrome P450 in cotton and show that its suppression leads to activation of plant defence responses and alteration of oxylipin metabolism. 05 November 2014 | doi: 10.1038/ncomms6372 Biological Sciences  Plant sciences  Tissue-specific derepression of TCF/LEF controls the activity of the Wnt/β-catenin pathway Fu-I Lu, Yong-Hua Sun, Chang-Yong Wei, Christine Thisse and Bernard Thisse The TCF transcription factor and the co-repressor Groucho form a repressor complex in the absence of Wnt ligand. Here the authors show that during zebrafish gastrulation, the transcription factor Lbx2 enhances Wnt/β-catenin signalling by reducing the interaction between TCF and Groucho. 05 November 2014 | doi: 10.1038/ncomms6368 Biological Sciences  Developmental biology  Versatile control of Plasmodium falciparum gene expression with an inducible protein–RNA interaction Stephen J. Goldfless, Jeffrey C. Wagner and Jacquin C. Niles Rapid and stable manipulation of gene expression in the malarial parasite Plasmodium falciparum remains a significant challenge. Goldfless et al. adapt a system for the inducible control of mRNA translation for use in Plasmodium and demonstrate its use to validate targets of antimalarial drugs. 05 November 2014 | doi: 10.1038/ncomms6329 Biological Sciences  Molecular biology  Regulation of the NaV1.5 cytoplasmic domain by calmodulin Sandra B. Gabelli, Agedi Boto, Victoria Halperin Kuhns, Mario A. Bianchet, Federica Farinelli, Srinivas Aripirala, Jesse Yoder, Jean Jakoncic, Gordon F. Tomaselli and L. Mario Amzel Voltage-gated sodium channels (Nav) are transmembrane proteins that underlie action potentials in excitable tissues. Here, Gabelli et al. suggest a novel mechanism for the cytoplasmic control of switching from the inactivated to the non-inactivated form of the Nav1.5 channel that involves dimerization. 05 November 2014 | doi: 10.1038/ncomms6126 Biological Sciences  Biophysics  Cell biology  Versatile in vitro system to study translocation and functional integration of bacterial outer membrane proteins Derrick Norell, Alexander Heuck, Thuy-Anh Tran-Thi, Hansjörg Götzke, Françoise Jacob-Dubuisson, Tim Clausen, Daniel O. Daley, Volkmar Braun, Matthias Müller and Enguo Fan The mechanisms of protein translocation across and integration into bacterial outer membranes are poorly understood. Here, Norell et al. reconstitute type-V secretion and β-barrel protein biogenesis in proteoliposomes providing a versatile cell-free system to study integration and translocation. 05 November 2014 | doi: 10.1038/ncomms6396 Biological Sciences  Biochemistry  Microbiology  Effector CD4 T-cell transition to memory requires late cognate interactions that induce autocrine IL-2 K. Kai McKinstry, Tara M. Strutt, Bianca Bautista, Wenliang Zhang, Yi Kuang, Andrea M. Cooper and Susan L. Swain The role of IL-2 signalling in the transition of T cells from effector to memory cells is not well defined. Here, the authors show that T-cell receptor interactions with cognate antigen elicit IL-2 secretion from effector cells, which rescues cells from apoptosis and upregulates IL-7 receptor expression, supporting CD4 T-cell memory formation. 05 November 2014 | doi: 10.1038/ncomms6377 Biological Sciences  Immunology  Generation of ultra-short hydrogen atom pulses by bunch-compression photolysis Sven Kaufmann, Dirk Schwarzer, Christian Reichardt, Alec M. Wodtke and Oliver Bünermann Short pulses of atoms or molecules can act as sensitive probes for numerous physical and chemical systems, but they are typically limited to the microsecond scale. By exploiting short pulse laser photolysis, Kaufmann et al. present a method that can produce pulses of hydrogen atoms on sub-nanosecond scales. 05 November 2014 | doi: 10.1038/ncomms6373 Physical Sciences  Atomic and molecular physics  Optical physics  Physical chemistry  An epigenetic switch induced by Shh signalling regulates gene activation during development and medulloblastoma growth Xuanming Shi, Zilai Zhang, Xiaoming Zhan, Mou Cao, Takashi Satoh, Shizuo Akira, Karl Shpargel, Terry Magnuson, Qingtian Li, Rongfu Wang, Chaochen Wang, Kai Ge and Jiang Wu The Sonic hedgehog (Shh) signalling pathway plays important roles during development and its abnormal activation has been implicated in cancer. Here the authors uncover an epigenetic switch in the Shh pathway that involves the PRC2, Jmjd3/Kdm6b and Set1/MLL complexes in regulating signalling induced gene activation. 05 November 2014 | doi: 10.1038/ncomms6425 Biological Sciences  Cancer  Developmental biology  Molecular biology  Unravelling the multilayer growth of the fullerene C60 in real time OPEN S. Bommel, N. Kleppmann, C. Weber, H. Spranger, P. Schäfer, J. Novak, S.V. Roth, F. Schreiber, S.H.L. Klapp and S. Kowarik Despite the technological relevance of molecular thin films, there is limited understanding of their growth on a molecular level. Here, the authors characterize the relevant processes in real time and determine energy parameters using a combination of X-ray techniques and kinetic Monte Carlo simulations. 05 November 2014 | doi: 10.1038/ncomms6388 Chemical Sciences  Materials science  Nanotechnology  Physical chemistry  ZBTB20 regulates nociception and pain sensation by modulating TRP channel expression in nociceptive sensory neurons An-Jing Ren, Kai Wang, Huan Zhang, Anjun Liu, Xianhua Ma, Qing Liang, Dongmei Cao, John N. Wood, David Z. He, Yu-Qiang Ding, Wen-Jun Yuan, Zhifang Xie and Weiping J. Zhang The upregulation of TRP ion channels is implicated in pain processing. In this study, the authors show that the zinc-finger protein ZBTB20 is responsible for TRP channel upregulation, and eliminating ZBTB20 from pain-sensing neurons in mouse models of pain results in the reduction of pain-like sensation. 05 November 2014 | doi: 10.1038/ncomms5984 Biological Sciences  Neuroscience  Quantum yield and excitation rate of single molecules close to metallic nanostructures Phil Holzmeister, Enrico Pibiri, Jürgen J. Schmied, Tapasi Sen, Guillermo P. Acuna and Philip Tinnefeld Metal nanostructures strongly influence fluorescence of nearby molecules, ranging from significant enhancement to total quenching. To decode the precise interactions taking place, Holzmeister et al. present a method that distinguishes the contributions to excitation, radiative and non-radiative rates. 05 November 2014 | doi: 10.1038/ncomms6356 Physical Sciences  Nanotechnology  Optical physics  Physical chemistry  Fano resonance and dipolar relaxation in lead-free relaxors D. Wang, J. Hlinka, A. A. Bokov, Z. -G. Ye, P. Ondrejkovic, J. Petzelt and L. Bellaiche Relaxor ferroelectrics are important materials that are used in electronic capacitors and other devices, although the origin of their unusual properties remains poorly understood. Here, the authors predict that Fano resonances between phonon modes could explain some properties of lead-free relaxors. 05 November 2014 | doi: 10.1038/ncomms6100 Physical Sciences  Condensed matter  Materials science  Disproving the Peres conjecture by showing Bell nonlocality from bound entanglement Tamás Vértesi and Nicolas Brunner A longstanding question in quantum information is the validity of the disputed Peres conjecture stating that bound entangled state can never lead to Bell inequality violation. Here Vértesi and Brunner prove that the Peres conjecture is false by providing an explicit counter example. 05 November 2014 | doi: 10.1038/ncomms6297 Physical Sciences  Theoretical physics    Nature Communications JOBS of the week PhD Studentship The University of Sheffield Principal Research Associate - Group Leader University College London (UCL) Postdoctoral Roswell Park Cancer Institute Research Associate John Innes Centre (JIC) More Science jobs from Nature Communications EVENT 2015 IMB Conference "DNA Repair & Genome Stability in a Chromatin Environment 04.06.15 Mainz, Germany More science events from       Latest Erratum     Erratum: Yeast and mammalian autophagosomes exhibit distinct phosphatidylinositol 3-phosphate asymmetries Jinglei Cheng, Akikazu Fujita, Hayashi Yamamoto, Tsuyako Tatematsu, Soichiro Kakuta, Keisuke Obara, Yoshinori Ohsumi and Toyoshi Fujimoto 11 November 2014 | doi: 10.1038/ncomms5608 Biological Sciences  Cell biology      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. 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