Nature Communications - 4 December 2013

Weekly Content Alert 04 December 2013  Featured image: Viet and Nieder characterise the activity of single neurons in carrion crows that predicts their next decision. Latest content: Articles Errata Journal homepage Recommend to library Web feed   Advertisement Scientific Reports  Fast and simple publishing! Visit our Guide to Authors page to find out more.    nature.com/scientificreports     Latest Articles View all Articles     Real-time influenza forecasts during the 2012–2013 season Jeffrey Shaman, Alicia Karspeck, Wan Yang, James Tamerius and Marc Lipsitch Our ability to accurately predict the spread of infectious diseases is still in its infancy. Here, Shaman et al. develop a model framework that produces accurate real-time forecasts of influenza peak timing for over a hundred cities in the USA. 03 December 2013 | doi: 10.1038/ncomms3837 Biological Sciences  Virology  Quantum teleportation of laser-generated photons with an entangled-light-emitting diode R. M. Stevenson, J. Nilsson, A. J. Bennett, J. Skiba-Szymanska, I. Farrer, D. A. Ritchie and A. J. Shields Quantum teleportation enables the transfer of information between different systems, and will be important for building quantum computing networks. Here, the authors show teleportation of photons between two different sources with greatly differing bandwidths, with an average fidelity of 0.77. 03 December 2013 | doi: 10.1038/ncomms3859 Physical Sciences  Applied physics  Optical physics  The femur of Orrorin tugenensis exhibits morphometric affinities with both Miocene apes and later hominins Sergio Almécija, Melissa Tallman, David M. Alba, Marta Pina, Salvador Moyà-Solà and William L. Jungers The proximal femur of the early hominin Orrorin tugenensis presents a mosaic of earlier Miocene ape and later hominin features. Here, Almécija et al. show that hominin and modern great ape femura diverged from an ancestral morphology and that Orrorin is intermediate between Miocene apes and australopiths. 03 December 2013 | doi: 10.1038/ncomms3888 Biological Sciences  Evolution  Palaeontology  Ribosome profiling reveals features of normal and disease-associated mitochondrial translation OPEN Koos Rooijers, Fabricio Loayza-Puch, Leo G. Nijtmans and Reuven Agami Mitochondrial ribosomes are uniquely affected by mutations in the mitochondrial genome. By mapping the position of ribosomes on transcripts, the authors here reveal functional differences between mitochondrial and cytosolic ribosomes, and show that mutations in mitochondrial tRNAs induce ribosome stalling. 03 December 2013 | doi: 10.1038/ncomms3886 Biological Sciences  Molecular biology  FLOWERING LOCUS T genes control onion bulb formation and flowering Robyn Lee, Samantha Baldwin, Fernand Kenel, John McCallum and Richard Macknight FLOWERING LOCUS T is an important mobile signal that regulates plant development and flowering. In this study, Lee et al. demonstrate that multiple FLOWERING LOCUS T genes are involved in onion flowering and bulb formation. 03 December 2013 | doi: 10.1038/ncomms3884 Biological Sciences  Plant sciences  MicroRNA-33 regulates sterol regulatory element-binding protein 1 expression in mice OPEN Takahiro Horie, Tomohiro Nishino, Osamu Baba, Yasuhide Kuwabara, Tetsushi Nakao, Masataka Nishiga, Shunsuke Usami, Masayasu Izuhara, Naoya Sowa, Naoya Yahagi, Hitoshi Shimano, Shigenobu Matsumura, Kazuo Inoue, Hiroyuki Marusawa, Tomoyuki Nakamura, Koji Hasegawa, Noriaki Kume, Masayuki Yokode, Toru Kita, Takeshi Kimura et al. The micro-RNA miR-33 is encoded by an intron of the gene encoding sterol regulatory-binding protein 2 (SREBP-2) and controls cholesterol homoeostasis. Here, Horie et al. identify SREBP-1 as a target of miR-33 and show that deletion of miR-33 promotes diet-induced obesity and liver steatosis in mice. 03 December 2013 | doi: 10.1038/ncomms3883 Biological Sciences  Medical research  Highly efficient methane biocatalysis revealed in a methanotrophic bacterium M. G. Kalyuzhnaya, S. Yang, O. N. Rozova, N. E. Smalley, J. Clubb, A. Lamb, G. A. Nagana Gowda, D. Raftery, Y. Fu, F. Bringel, S. Vuilleumier, D. A. C. Beck, Y. A. Trotsenko, V. N. Khmelenina and M. E. Lidstrom Methane is a promising renewable carbon source for chemical synthesis, yet methane bio-gas is currently underutilised as a feedstock. Here, the authors examine the metabolic processes of methanotrophic bacteria to assess their use for conversion of methane to value-added chemical products. 03 December 2013 | doi: 10.1038/ncomms3785 Biological Sciences  Biochemistry  Catalysis  Microbiology  Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups OPEN India Project Team of the International Cancer Genome Consortium, Arindam Maitra, Nidhan K. Biswas, Kishore Amin, Pradnya Kowtal, Shantanu Kumar, Subrata Das, Rajiv Sarin, Partha P. Majumder, I Bagchi, B. B. Bairagya, A. Basu, M. K. Bhan, P. Chaturvedi, D. Das, A. D'Cruz, R. Dhar, D. Dutta, D. Ganguli, P. Gera et al. Gingivo-buccal oral squamous cell carcinoma (OSCC-GB) is the leading cancer among males in India. Here, the authors carry out exome sequencing and recurrence testing in patients with OSCC-GB and highlight genes and biological pathways associated with the disease. 02 December 2013 | doi: 10.1038/ncomms3873 Biological Sciences  Cancer  Genetics  Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without FtsZ Martin Pilhofer, Karin Aistleitner, Jacob Biboy, Joe Gray, Erkin Kuru, Edward Hall, Yves V. Brun, Michael S. VanNieuwenhze, Waldemar Vollmer, Matthias Horn and Grant J. Jensen Chlamydiae are sensitive to beta-lactam antibiotics, which target cell-wall peptidoglycan (PG), but it is unclear whether these bacteria possess PG. Pilhofer et al. now demonstrate that cell walls of a chlamydial species, Protochlamydia amoebophila, contain a PG layer. 02 December 2013 | doi: 10.1038/ncomms3856 Biological Sciences  Biophysics  Cell biology  Microbiology  Renewable and metal-free carbon nanofibre catalysts for carbon dioxide reduction Bijandra Kumar, Mohammad Asadi, Davide Pisasale, Suman Sinha-Ray, Brian A. Rosen, Richard Haasch, Jeremiah Abiade, Alexander L. Yarin and Amin Salehi-Khojin The efficient catalysis of the electrochemical reduction of carbon dioxide is an important industrial process, usually performed by noble metal catalysts. Here, the authors report a metal-free carbon nanofibre-based catalyst operating with a negligible overpotential, high current density and long-term stability. 02 December 2013 | doi: 10.1038/ncomms3819 Chemical Sciences  Catalysis  Materials science  Proteasomal degradation of Nck1 but not Nck2 regulates RhoA activation and actin dynamics Lisa Buvall, Priyanka Rashmi, Esther Lopez-Rivera, Svetlana Andreeva, Astrid Weins, Hanna Wallentin, Anna Greka and Peter Mundel Nck1/2 adaptor proteins control the assembly and activity of protein complexes that promote actin polymerization. Buvall et al. show that Nck1 abundance is regulated by the E3 ubiquitin ligase c-Cbl, which competes for Nck binding with the actin-binding protein synaptopodin in podocytes. 29 November 2013 | doi: 10.1038/ncomms3863 Biological Sciences  Cell biology  Hysteresis of ligand binding in CNGA2 ion channels OPEN Vasilica Nache, Thomas Eick, Eckhard Schulz, Ralf Schmauder and Klaus Benndorf Cyclic nucleotide-gated channels mediate olfactory and visual responses. Using a fluorescent cGMP derivative, Nache et al. show that the rate of cyclic nucleotide release from CNGA2 depends on the extent to which this tetrameric receptor is liganded, revealing hysteresis in the gating mechanism. 29 November 2013 | doi: 10.1038/ncomms3866 Biological Sciences  Biochemistry  Biophysics  Strong coupling in the sub-wavelength limit using metamaterial nanocavities OPEN A. Benz, S. Campione, S. Liu, I. Montaño, J.F. Klem, A Allerman, J.R. Wendt, M.B. Sinclair, F. Capolino and I. Brener Interactions between material structures and the modes of cavities they are placed in can give rise to strongly coupled light-matter states. Benz et al. show that this regime can be reached using sub-wavelength metamaterial resonators coupled to semiconductor heterostructures in the mid- and near-infrared. 29 November 2013 | doi: 10.1038/ncomms3882 Physical Sciences  Nanotechnology  Optical physics  Mitochondrial inner membrane protease promotes assembly of presequence translocase by removing a carboxy-terminal targeting sequence Raffaele Ieva, Anna K. Heißwolf, Michael Gebert, F.-Nora Vögtle, Florian Wollweber, Carola S. Mehnert, Silke Oeljeklaus, Bettina Warscheid, Chris Meisinger, Martin van der Laan and Nikolaus Pfanner Many proteins destined for the inner mitochondrial membrane are imported via amino-terminal targeting sequences that are subsequently cleaved. Ieva et al. identify an alternative mechanism for mitochondrial protein import that depends on a carboxyl-terminal targeting sequence. 29 November 2013 | doi: 10.1038/ncomms3853 Biological Sciences  Cell biology  Experimental recovery of quantum correlations in absence of system-environment back-action OPEN Jin-Shi Xu, Kai Sun, Chuan-Feng Li, Xiao-Ye Xu, Guang-Can Guo, Erika Andersson, Rosario Lo Franco and Giuseppe Compagno In quantum systems, information can flow back and forth between the system and its environment, leading to revivals of quantum correlations. Using a simple model, Xu et al. experimentally show how revivals can occur with a classical environment despite the absence of back-action from the environment. 29 November 2013 | doi: 10.1038/ncomms3851 Physical Sciences  Optical physics  A truncated Wnt7a retains full biological activity in skeletal muscle OPEN Julia von Maltzahn, Radoslav Zinoviev, Natasha C. Chang, C. Florian Bentzinger and Michael A. Rudnicki Wnt7a regulates various aspects of skeletal muscle function. Here, the authors show that a truncated Wnt7a protein lacking the palmitoylation domain retains its biological activity in skeletal muscle, suggesting that simplified Wnt7a proteins may be viable as Wnt-based therapeutics. 29 November 2013 | doi: 10.1038/ncomms3869 Biological Sciences  Medical research  Cyclin D1 induction of Dicer governs microRNA processing and expression in breast cancer Zuoren Yu, Liping Wang, Chenguang Wang, Xiaoming Ju, Min Wang, Ke Chen, Emanuele Loro, Zhiping Li, Yuzhen Zhang, Kongming Wu, Mathew C. Casimiro, Michael Gormley, Adam Ertel, Paolo Fortina, Yihan Chen, Aydin Tozeren, Zhongmin Liu and Richard G. Pestell Whether microRNA processing mediated by Dicer is regulated in a cell-cycle-dependent manner is unknown. Here, Chen et al. show that Cyclin D1, which is important in the control of the cell cycle, regulates the expression of Dicer, and that Cyclin D1 and Dicer expression levels correlate in breast cancer. 29 November 2013 | doi: 10.1038/ncomms3812 Biological Sciences  Cancer  Molecular biology  Long-distance distribution of genuine energy-time entanglement OPEN A. Cuevas, G. Carvacho, G. Saavedra, J. Cariñe, W.A.T. Nogueira, M. Figueroa, A. Cabello, P. Mataloni, G. Lima and G.B. Xavier Practical implementations of quantum communication need to securely deliver information over long distances without line-of-sight. Towards this goal, Cuevas et al. use an actively stabilized interferometer to close the geometry loophole for a Bell inequality violation over 1 km of optical fibre. 29 November 2013 | doi: 10.1038/ncomms3871 Physical Sciences  Applied physics  Optical physics  Protective CD8+ T-cell immunity to human malaria induced by chimpanzee adenovirus-MVA immunisation OPEN Katie J. Ewer, Geraldine A. O'Hara, Christopher J. A. Duncan, Katharine A. Collins, Susanne H. Sheehy, Arturo Reyes-Sandoval, Anna L. Goodman, Nick J. Edwards, Sean C. Elias, Fenella D. Halstead, Rhea J. Longley, Rosalind Rowland, Ian D. Poulton, Simon J. Draper, Andrew M. Blagborough, Eleanor Berrie, Sarah Moyle, Nicola Williams, Loredana Siani, Antonella Folgori et al. Induction of protective immunity mediated by CD8+ T cells has been a long sought goal in vaccinology. Here, Ewer et al. report induction of protective efficacy against Plasmodium falciparum malaria in a phase IIa prime-boost vaccine trial where efficacy correlates strongly with induced CD8 T-cell responses. 28 November 2013 | doi: 10.1038/ncomms3836 Biological Sciences  Immunology  Medical research  Microbiology  Skin thymic stromal lymphopoietin initiates Th2 responses through an orchestrated immune cascade Juan Manuel Leyva-Castillo, Pierre Hener, Paula Michea, Hajime Karasuyama, Susan Chan, Vassili Soumelis and Mei Li Thymic stromal lymphopoietin is an important initiator of Th2 responses, but, to date, little is known about how it drives the immune cascade in the tissue microenvironment in vivo. Here, the authors show that skin thymic stromal lymphopoietin orchestrate interactions between immune cells, leading to Th2 priming. 28 November 2013 | doi: 10.1038/ncomms3847 Biological Sciences  Immunology  Local models of fractional quantum Hall states in lattices and physical implementation Anne E. B. Nielsen, Germán Sierra and J. Ignacio Cirac The realization of the fractional quantum Hall effect with ultracold atoms in optical lattices is much sought after. Here, the authors propose a new way of obtaining fractional quantum Hall states in lattice systems by transforming a nonlocal abstract model into an implementable scheme. 28 November 2013 | doi: 10.1038/ncomms3864 Physical Sciences  Atomic and molecular physics  Condensed matter  Theoretical physics  TRAF1 is a critical regulator of cerebral ischaemia–reperfusion injury and neuronal death OPEN Yan-Yun Lu, Zuo-Zhi Li, Ding-Sheng Jiang, Lang Wang, Yan Zhang, Ke Chen, Xiao-Fei Zhang, Yi Liu, Guo-Chang Fan, Yingjie Chen, Qinglin Yang, Yan Zhou, Xiao-Dong Zhang, De-Pei Liu and Hongliang Li TRAF1 is an intracellular signalling molecule that has diverse biological functions. In this study, the authors show that TRAF1 is expressed in mice soon after they have suffered a stroke and that increased TRAF1 expression increases susceptibility to ischaemia-induced apoptosis and brain injury. 28 November 2013 | doi: 10.1038/ncomms3852 Biological Sciences  Medical research  Neuroscience  Abstract rule neurons in the endbrain support intelligent behaviour in corvid songbirds Lena Veit and Andreas Nieder The corvid songbird family comprises crows, jays, magpies and other close relatives. Veit and Nieder investigate neuronal processing underlying executive control in crows and identify single neurons that encode behavioural rules in an abstract fashion and that predict the crows' decisions. 28 November 2013 | doi: 10.1038/ncomms3878 Biological Sciences  Neuroscience  Epigenetic diversity increases the productivity and stability of plant populations Vít Latzel, Eric Allan, Amanda Bortolini Silveira, Vincent Colot, Markus Fischer and Oliver Bossdorf It is generally assumed that ecologically relevant intraspecific diversity is restricted to DNA sequence variation. Here, Latzel et al. show that epigenetic diversity can increase the productivity of plant populations as well as their ability to suppress competitors. 28 November 2013 | doi: 10.1038/ncomms3875 Biological Sciences  Ecology  Evolution  Pits confined in ultrathin cerium(IV) oxide for studying catalytic centers in carbon monoxide oxidation Yongfu Sun, Qinghua Liu, Shan Gao, Hao Cheng, Fengcai Lei, Zhihu Sun, Yong Jiang, Haibin Su, Shiqiang Wei and Yi Xie Catalytic carbon monoxide oxidation is an industrially important process. Here, the authors show that ultrathin cerium(IV) oxide with surface confined pits provides an ideal platform for investigating and optimizing the role of local atomic structure on carbon monoxide adsorption and oxygen activation. 27 November 2013 | doi: 10.1038/ncomms3899 Chemical Sciences  Catalysis  Triggers of key calcium signals during erythrocyte invasion by Plasmodium falciparum OPEN Xiaohong Gao, Karthigayan Gunalan, Sally Shu Lin Yap and Peter R. Preiser Plasmodium falciparum reticulocyte-binding protein homologue 1 (PfRH1) and erythrocyte-binding-like protein EBA175 are important for parasite invasion of host cells. Here, Gao et al. show that PfRH1 activates calcium signalling, which induces release of EBA175 and allows junction formation between host cell and parasite. 27 November 2013 | doi: 10.1038/ncomms3862 Biological Sciences  Cell biology  Microbiology  Thymic epithelial cell expansion through matricellular protein CYR61 boosts progenitor homing and T-cell output Yalin Emre, Magali Irla, Isabelle Dunand-Sauthier, Romain Ballet, Mehdi Meguenani, Stephane Jemelin, Christian Vesin, Walter Reith and Beat A. Imhof Thymic epithelial cells provide the microenvironment required for the expansion of T cells in the thymus, but their exact function is not well understood. Here, the authors report that thymic epithelial cells are the source of matricellular protein CYR61, which is involved in thymic function and T cell development. 27 November 2013 | doi: 10.1038/ncomms3842 Biological Sciences  Immunology  Role of domain walls in the abnormal photovoltaic effect in BiFeO3 OPEN Akash Bhatnagar, Ayan Roy Chaudhuri, Young Heon Kim, Dietrich Hesse and Marin Alexe The origin of the abnormal photovoltaic effect in bismuth ferrite thin films, which causes voltages larger than the band gap, is poorly understood. Bhatnagar et al. show that this effect can be attributed to a bulk photovoltaic effect and that it can be enhanced by controlling domain wall conductivity. 27 November 2013 | doi: 10.1038/ncomms3835 Physical Sciences  Condensed matter  Materials science  The TSC-mTOR pathway regulates macrophage polarization Vanessa Byles, Anthony J. Covarrubias, Issam Ben-Sahra, Dudley W. Lamming, David M. Sabatini, Brendan D. Manning and Tiffany Horng Distinct macrophage phenotypes are associated with their polarization to a proinflammatory or alternative state, but it is not well understood how metabolic status affects this process. Here, Byles et al. demonstrate that the mTOR metabolic pathway regulates macrophage differentiation. 27 November 2013 | doi: 10.1038/ncomms3834 Biological Sciences  Immunology  RhoB controls coordination of adult angiogenesis and lymphangiogenesis following injury by regulating VEZF1-mediated transcription OPEN Damien Gerald, Irit Adini, Sharon Shechter, Carole Perruzzi, Joseph Varnau, Benjamin Hopkins, Shiva Kazerounian, Peter Kurschat, Stephanie Blachon, Santosh Khedkar, Mandrita Bagchi, David Sherris, George C. Prendergast, Michael Klagsbrun, Heidi Stuhlmann, Alan C. Rigby, Janice A. Nagy and Laura E. Benjamin The formation of blood and lymph vessels after injury requires precise temporal coordination. Here, the authors show that the small GTPase RhoB induces angiogenesis but inhibits lymphangiogenesis in response to dermal wounding by activating different sets of genes in blood vessels and lymphatic endothelial cells. 27 November 2013 | doi: 10.1038/ncomms3824 Biological Sciences  Cell biology  Medical research  Evolutionary conservation of early mesoderm specification by mechanotransduction in Bilateria OPEN Thibaut Brunet, Adrien Bouclet, Padra Ahmadi, Démosthène Mitrossilis, Benjamin Driquez, Anne-Christine Brunet, Laurent Henry, Fanny Serman, Gaëlle Béalle, Christine Ménager, Frédéric Dumas-Bouchiat, Dominique Givord, Constantin Yanicostas, Damien Le-Roy, Nora M. Dempsey, Anne Plessis and Emmanuel Farge Mechanical cues can induce morphogenetic processes during development. Here, the authors show that mechanical changes during embryonic development in both zebrafish and Drosophila lead to nuclear localization of β-catenin, which regulates genes required for early mesoderm development in both species. 27 November 2013 | doi: 10.1038/ncomms3821 Biological Sciences  Developmental biology  Evolution    Nature Communiactions JOBS of the week Bioinformatician Institute for Molecular Medicine Finland (FIMM) PhD Studentship MRC-University of Glasgow Centre for Virus Research Post-Doctoral Research Fellow University Frankfurt Research Fellow South Australian Health & Medical Research Institute Faculty Position Vanderbilt University Medical Center Research Fellow Harvard School of Public Health (HSPH) Research Associate Imperial College London Postdoctoral Scientist University of Oxford Junior Group Leader Justus-Liebig University - Institute of Organic Chemistry Research Associate Stanford University More Science jobs from Nature Communiactions EVENT Alzheimer's Research UK Drug Discovery Institute 14.02.14 UK More science events from       Latest Errata     Erratum: Single-cell dynamics of the chromosome replication and cell division cycles in mycobacteria Isabella Santi, Neeraj Dhar, Djenet Bousbaine, Yuichi Wakamoto and John D. McKinney 03 December 2013 | doi: 10.1038/ncomms3913 Biological Sciences  Cell biology  Microbiology      Erratum: A zero-strain layered metal oxide as the negative electrode for long-life sodium-ion batteries Yuesheng Wang, Xiqian Yu, Shuyin Xu, Jianming Bai, Ruijuan Xiao, Yong-Sheng Hu, Hong Li, Xiao-Qing Yang, Liquan Chen and Xuejie Huang 03 December 2013 | doi: 10.1038/ncomms3858 Chemical Sciences  Materials science  Physical chemistry      Erratum: Role of motor cortex NMDA receptors in learning-dependent synaptic plasticity of behaving mice Mazahir T. Hasan, Samuel Hernández-González, Godwin Dogbevia, Mario Treviño, Ilaria Bertocchi, Agnès Gruart and José M. Delgado-García 27 November 2013 | doi: 10.1038/ncomms3831 Biological Sciences  Neuroscience        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. 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