Nature Communications - 26 November 2014

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Weekly Content Alert 26 November 2014  Featured image: Li et al. show how the reduction of oxygen content considerably improves the quality of cast steel ingots Latest content: Review Articles Erratum Journal homepage Recommend to library Web feed   Advertisement Poster & Webcast on CRISPR-Cas technology from Nature Publishing Group Nature Reviews Microbiology  FREE POSTER CRISPR-Cas: extraordinary editing  Presented by Nature Biotechnology  Webcast and live Q&A: A practical guide to CRISPR technology Date: November 25, 2014 Poster and Webcast produced with support from  OriGene, Your Gene Company        Latest Review View all Reviews     Global potential of biospheric carbon management for climate mitigation Josep G. Canadell and E. Detlef Schulze Carbon mitigation is considered an important and viable pathway towards climate stabilization, but competition for land is high. Here, Canadell and Schulze consider the sustainable implementation of a number of land-based biological carbon mitigation activities and assess the carbon savings achievable by 2050. 19 November 2014 | doi: 10.1038/ncomms6282 Earth Sciences  Climate science        Latest Articles View all Articles     Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum OPEN Akhil B. Vaidya, Joanne M. Morrisey, Zhongsheng Zhang, Sudipta Das, Thomas M. Daly, Thomas D. Otto, Natalie J. Spillman, Matthew Wyvratt, Peter Siegl, Jutta Marfurt, Grennady Wirjanata, Boni F. Sebayang, Ric N. Price, Arnab Chatterjee, Advait Nagle, Marcin Stasiak, Susan A. Charman, Iñigo Angulo-Barturen, Santiago Ferrer, María Belén Jiménez-Díaz et al. Novel antimalarial drugs are urgently needed to combat parasite drug resistance. Here, Vaidya et al. describe a new chemical class of potent antimalarial compounds that act by disrupting the parasite's sodium homeostasis. 25 November 2014 | doi: 10.1038/ncomms6521 Biological Sciences  Chemical biology  Medicinal chemistry  Microbiology  Inclusion flotation-driven channel segregation in solidifying steels OPEN Dianzhong Li, Xing-Qiu Chen, Paixian Fu, Xiaoping Ma, Hongwei Liu, Yun Chen, Yanfei Cao, Yikun Luan and Yiyi Li A long-term problem in the casting of alloys such as steels is macrosegregation, which are variations in composition of the cast material. Here, the authors observe that the formation and flotation of oxide-based inclusions from light metals represent a mechanism through which macrosegregation occurs in steels. 25 November 2014 | doi: 10.1038/ncomms6572 Physical Sciences  Materials science  Berberine activates thermogenesis in white and brown adipose tissue Zhiguo Zhang, Huizhi Zhang, Bo Li, Xiangjian Meng, Jiqiu Wang, Yifei Zhang, Shuangshuang Yao, Qinyun Ma, Lina Jin, Jian Yang, Weiqing Wang and Guang Ning Berberine is contained in some plant-derived medicines and is known to have anti-diabetic effects. Here the authors show that berberine activates thermogenesis in white and brown adipose tissues, thereby increasing organismal energy expenditure and limiting weight gain in genetically obese mice. 25 November 2014 | doi: 10.1038/ncomms6493 Biological Sciences  Medical research  Repurposing Blu-ray movie discs as quasi-random nanoimprinting templates for photon management Alexander J. Smith, Chen Wang, Dongning Guo, Cheng Sun and Jiaxing Huang Quasi-random nanostructures are being considered for many photon management applications but their use has been limited by their costly fabrication. Here, Smith et al. show that the quasi-random patterns on Blu-ray movie discs are already near-optimized for light-trapping applications in solar cells. 25 November 2014 | doi: 10.1038/ncomms6517 Physical Sciences  Materials science  Nanotechnology  Optical physics  The microbiome of New World vultures Michael Roggenbuck, Ida Bærholm Schnell, Nikolaj Blom, Jacob Bælum, Mads Frost Bertelsen, Thomas Sicheritz Pontén, Søren Johannes Sørensen, M. Thomas P. Gilbert, Gary R. Graves and Lars H Hansen Vultures are scavengers with a high tolerance to bacterial toxins in decaying meat. Here, Roggenbuck et al. show that the vulture’s gut microbiome displays unique features and is dominated by Clostridia and Fusobacteria, two bacterial groups commonly associated with infectious disease in other animals. 25 November 2014 | doi: 10.1038/ncomms6498 Biological Sciences  Ecology  Microbiology  Zoology  Hidden two-qubit dynamics of a four-level Josephson circuit Elisha Svetitsky, Haim Suchowski, Roy Resh, Yoni Shalibo, John M. Martinis and Nadav Katz Qudits, multiple-level quantum systems, enable more efficient scaling of physical resources in quantum computing than qubits, but they are more difficult to control. Svetitsky et al. now experimentally demonstrate a simplifying technique that converts a four-level qudit into a pair of qubits. 25 November 2014 | doi: 10.1038/ncomms6617 Physical Sciences  Applied physics  Electron transfer and coupling in graphene–tungsten disulfide van der Waals heterostructures Jiaqi He, Nardeep Kumar, Matthew Z. Bellus, Hsin-Ying Chiu, Dawei He, Yongsheng Wang and Hui Zhao Two-dimensional materials get their unusual properties because the motion of their electrons is confined to a single plane, but combining two such materials adds an extra degree of freedom: interlayer coupling. Here, the authors use ultrafast spectroscopy to show that this electron motion is highly efficient. 25 November 2014 | doi: 10.1038/ncomms6622 Physical Sciences  Condensed matter  Materials science  Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity OPEN Amy H. Buck, Gillian Coakley, Fabio Simbari, Henry J. McSorley, Juan F. Quintana, Thierry Le Bihan, Sujai Kumar, Cei Abreu-Goodger, Marissa Lear, Yvonne Harcus, Alessandro Ceroni, Simon A. Babayan, Mark Blaxter, Alasdair Ivens and Rick M. Maizels Mammalian cell-derived exosomes can carry RNA and proteins from cell to cell, but this mode of transport has not been shown in nematodes. Here the authors show that a gastrointestinal parasite secretes exosomes that transfer microRNAs to mammalian cells and regulate innate immunity. 25 November 2014 | doi: 10.1038/ncomms6488 Biological Sciences  Cell biology  Immunology  Power-controlled transition from standard to negative refraction in reorientational soft matter Armando Piccardi, Alessandro Alberucci, Nina Kravets, Oleksandr Buchnev and Gaetano Assanto Anisotropic media have interesting effects, particularly at interfaces. Piccardi et al. show that optical refraction in nonlinear nematic liquid crystals can be tuned from positive to negative by acting on beam power, altering the distribution of the optic axis and the energy flux. 25 November 2014 | doi: 10.1038/ncomms6533 Physical Sciences  Condensed matter  Optical physics  Regulatory network decoded from epigenomes of surface ectoderm-derived cell types Rebecca F. Lowdon, Bo Zhang, Misha Bilenky, Thea Mauro, Daofeng Li, Philippe Gascard, Mahvash Sigaroudinia, Peggy J. Farnham, Boris C. Bastian, Thea D. Tlsty, Marco A. Marra, Martin Hirst, Joseph F. Costello, Ting Wang and Jeffrey B. Cheng Epigenomes are thought to retain molecular memories of their developmental history. Here, by comparing differentially methylated regions of genomes from different cells, the authors reveal an epigenetic signature that underlies a shared gene regulatory network with a common developmental origin. 25 November 2014 | doi: 10.1038/ncomms6442 Biological Sciences  Genetics  Diacylglycerol mediates regulation of TASK potassium channels by Gq-coupled receptors Bettina U. Wilke, Moritz Lindner, Lea Greifenberg, Alexandra Albus, Yannick Kronimus, Moritz Bünemann, Michael G. Leitner and Dominik Oliver TASK-1 and -3 are members of the two-pore domain K+ channel family that play important roles in the regulation of cellular excitability. Here, Wilke et al. demonstrate that the second messenger lipid diacylglycerol (DAG) gates TASK1/3, defining a new role for DAG in controlling the dynamics of cellular excitability. 25 November 2014 | doi: 10.1038/ncomms6540 Biological Sciences  Cell biology  Neuroscience  ERG induces taxane resistance in castration-resistant prostate cancer OPEN Giuseppe Galletti, Alexandre Matov, Himisha Beltran, Jacqueline Fontugne, Juan Miguel Mosquera, Cynthia Cheung, Theresa Y. MacDonald, Matthew Sung, Sandra O’Toole, James G. Kench, Sung Suk Chae, Dragi Kimovski, Scott T. Tagawa, David M. Nanus, Mark A. Rubin, Lisa G. Horvath, Paraskevi Giannakakou and David S. Rickman Metastatic castration-resistant prostate cancer is treated with the microtubule-stabilizing drugs taxanes, but resistance ultimately develops. Here Galletti et al. show that ERG, a transcription factor commonly overexpressed in prostate cancers, confers taxane resistance by binding to soluble tubulin. 25 November 2014 | doi: 10.1038/ncomms6548 Biological Sciences  Cancer  Medical research  Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea Neil J. Rzechorzek, John K. Blackwood, Sian M. Bray, Joseph D. Maman, Luca Pellegrini and Nicholas P. Robinson Thermophilic archaea have a minimal double-strand DNA break repair apparatus consisting of the HerA ATPase, NurA nuclease and Mre11–Rad50 complex. Here the authors solve the structure of a hexameric HerA ring from Sulfolobus solfataricus, and provide insight into a novel mechanism of DNA repair. 25 November 2014 | doi: 10.1038/ncomms6506 Biological Sciences  Biochemistry  Cell cycle-linked MeCP2 phosphorylation modulates adult neurogenesis involving the Notch signalling pathway Hongda Li, Xiaofen Zhong, Kevin F. Chau, Nicholas J. Santistevan, Weixiang Guo, Guangyao Kong, Xuekun Li, Mitul Kadakia, Jamie Masliah, Jingyi Chi, Peng Jin, Jing Zhang, Xinyu Zhao and Qiang Chang Methyl-CpG-binding protein 2 (MeCP2) is phosphorylated in neurons in response to neuronal activity. Here, Li et al. show that it is also phosphorylated by aurora kinase B in neural progenitor cells, and cell cycle-dependent phosphorylation of MeCP2 regulates the balance between proliferation and differentiation via Notch signalling. 25 November 2014 | doi: 10.1038/ncomms6601 Biological Sciences  Cell biology  Neuroscience  Identification of novel DNA-damage tolerance genes reveals regulation of translesion DNA synthesis by nucleophosmin OPEN Omer Ziv, Amit Zeisel, Nataly Mirlas-Neisberg, Umakanta Swain, Reinat Nevo, Nir Ben-Chetrit, Maria Paola Martelli, Roberta Rossi, Stefan Schiesser, Christine E. Canman, Thomas Carell, Nicholas E. Geacintov, Brunangelo Falini, Eytan Domany and Zvi Livneh Cells cope with replication-blocking DNA lesions by translesion DNA synthesis (TLS) polymerases, including polη. Here, the authors show that NPM1, a gene frequently mutated in acute myeloid leukaemia, protects polη from proteasomal degradation, and that NPM1 deficiency causes a TLS defect. 25 November 2014 | doi: 10.1038/ncomms6437 Biological Sciences  Cell biology  Molecular biology  Loss of PHD3 allows tumours to overcome hypoxic growth inhibition and sustain proliferation through EGFR OPEN Anne-Theres Henze, Boyan K. Garvalov, Sascha Seidel, Angel M. Cuesta, Mathias Ritter, Alina Filatova, Franziska Foss, Higinio Dopeso, Clara L. Essmann, Patrick H. Maxwell, Guido Reifenberger, Peter Carmeliet, Amparo Acker-Palmer and Till Acker Little is known on how solid tumours overcome growth inhibitory signals within its hypoxic microenvironment. Here Henze et al. show that oxygen sensor PHD3 is frequently lost in gliomas, and that this loss hyperactivates EGFR signaling to sustain tumour cell proliferation and survival in hypoxia. 25 November 2014 | doi: 10.1038/ncomms6582 Biological Sciences  Cancer  Ultralow mode-volume photonic crystal nanobeam cavities for high-efficiency coupling to individual carbon nanotube emitters OPEN R. Miura, S. Imamura, R. Ohta, A. Ishii, X. Liu, T. Shimada, S. Iwamoto, Y. Arakawa and Y. K. Kato Efficient coupling to photonic structures is essential to exploit the emission properties of carbon nanotubes (CNTs). Here, Miura et al. demonstrate spontaneous emission coupling efficiency exceeding 85% from a single CNT to a silicon photonic crystal nanobeam cavity with an ultralow mode-volume. 25 November 2014 | doi: 10.1038/ncomms6580 Physical Sciences  Applied physics  Nanotechnology  Optical physics  PHD3 regulates EGFR internalization and signalling in tumours OPEN Boyan K. Garvalov, Franziska Foss, Anne-Theres Henze, Ioanna Bethani, Sabine Gräf-Höchst, Devendra Singh, Alina Filatova, Higinio Dopeso, Sascha Seidel, Miriam Damm, Amparo Acker-Palmer and Till Acker PHD3 is a hypoxia-inducible prolyl hydroxylase that regulates stability of HIF-1. Here Garvalov et al. report a hydroxylase-independent role of PHD3 in gliomas as a scaffolding protein that promotes internalization and limits signalling of EGFR upon ligand binding, thus inhibiting growth in hypoxia. 25 November 2014 | doi: 10.1038/ncomms6577 Biological Sciences  Cancer  Reciprocal functions of Cryptococcus neoformans copper homeostasis machinery during pulmonary infection and meningoencephalitis Tian-Shu Sun, Xiao Ju, Hui-Ling Gao, Tao Wang, Dennis J. Thiele, Jia-Yi Li, Zhan-You Wang and Chen Ding The fungus Cryptococcus neoformans can cause lethal meningoencephalitis in humans after initiating infection in the lung. Here, the authors describe the roles played by two C. neoformans copper transporters in pathogen’s survival during lung and brain infection. 24 November 2014 | doi: 10.1038/ncomms6550 Biological Sciences  Microbiology  Large-scale mutational analysis of Kv11.1 reveals molecular insights into type 2 long QT syndrome Corey L. Anderson, Catherine E. Kuzmicki, Ryan R. Childs, Caleb J. Hintz, Brian P. Delisle and Craig T. January Type 2 Long QT syndrome is a cardiac disease associated with hundreds of individual mutations within the Kv11.1 potassium channel. Here, the authors systematically investigate the trafficking defects associated with different types of Kv11.1 mutations and to what extent they can be corrected pharmacologically. 24 November 2014 | doi: 10.1038/ncomms6535 Biological Sciences  Biochemistry  Biophysics  Medical research  Pathological roles of the VEGF/SphK pathway in Niemann–Pick type C neurons OPEN Hyun Lee, Jong Kil Lee, Min Hee Park, Yu Ri Hong, Hugo H. Marti, Hyongbum Kim, Yohei Okada, Makoto Otsu, Eul-Ju Seo, Jae-Hyung Park, Jae-Hoon Bae, Nozomu Okino, Xingxuan He, Edward H. Schuchman, Jae-sung Bae and Hee Kyung Jin Sphingosine is abnormally accumulated in Niemann–Pick type C disease (NP–C), but the causes of this accumulation have not been fully characterized. Here the authors show that sphingosine kinase activity is reduced in NP–C patient fibroblasts and NP–C mouse neurons due to defective vascular endothelial growth factor levels, suggesting therapeutic avenues. 24 November 2014 | doi: 10.1038/ncomms6514 Biological Sciences  Medical research  Neuroscience  Wavefront modulation and subwavelength diffractive acoustics with an acoustic metasurface Yangbo Xie, Wenqi Wang, Huanyang Chen, Adam Konneker, Bogdan-Ioan Popa and Steven A. Cummer Metasurfaces are subwavelength structures that manipulate impinging waves into desired output waveforms, but building them for acoustic applications remains challenging. Exploiting tapered labyrinthine structures, Xie et al. present an acoustic metasurface that manipulates sound waves in a variety of ways. 24 November 2014 | doi: 10.1038/ncomms6553 Physical Sciences  Applied physics  Materials science  Recurrent de novo mutations implicate novel genes underlying simplex autism risk B. J. O'Roak, H. A. Stessman, E. A. Boyle, K. T. Witherspoon, B. Martin, C. Lee, L. Vives, C. Baker, J. B. Hiatt, D. A. Nickerson, R. Bernier, J. Shendure and E. E. Eichler Autism spectrum disorder (ASD) is a common disorder with a strong and complex genetic component. Here, the authors resequence 64 candidate neurodevelopmental disorder risk genes in almost 6,000 samples and identify novel genes associated with ASD. 24 November 2014 | doi: 10.1038/ncomms6595 Biological Sciences  Genetics  Neuroscience  Mechanistic insight into the interaction of BLM helicase with intra-strand G-quadruplex structures Sujoy Chatterjee, Jennifer Zagelbaum, Pavel Savitsky, Andreas Sturzenegger, Diana Huttner, Pavel Janscak, Ian D. Hickson, Opher Gileadi and Eli Rothenberg G-quadruplexes (G4) are DNA structures found throughout the genome previously shown to be bound with high specificity by the RecQ family helicase BLM. Here the authors describe how BLM interacts with G4 DNA and propose an integrated model of the cooperative binding between BLM and G4 structures. 24 November 2014 | doi: 10.1038/ncomms6556 Biological Sciences  Biochemistry  Biophysics  Retinoid X receptor α attenuates host antiviral response by suppressing type I interferon Feng Ma, Su-Yang Liu, Bahram Razani, Neda Arora, Bing Li, Hiroyuki Kagechika, Peter Tontonoz, Vanessa Núñez, Mercedes Ricote and Genhong Cheng The role of retinoic X receptor α (RXRα) in the antiviral immune response is not well understood. Here the authors show that ligand activation of RXRα inhibits production of type 1 interferon and interferon-stimulated genes by preventing nuclear translocation of ß-Catenin. 24 November 2014 | doi: 10.1038/ncomms6494 Biological Sciences  Immunology  Ferroelectric tunnel junctions with graphene electrodes H. Lu, A. Lipatov, S. Ryu, D. J. Kim, H. Lee, M. Y. Zhuravlev, C. B. Eom, E. Y. Tsymbal, A. Sinitskii and A. Gruverman Ferroelectric tunnel junctions, where electrical transport occurs across two electrodes separated by a ferroelectric layer, could be used for future non-volatile computer memories. Here, the authors employ graphene as an electrode in tunnel junctions for interface-facilitated enhancement of device performance. 24 November 2014 | doi: 10.1038/ncomms6518 Physical Sciences  Condensed matter  Materials science  Nanotechnology  Reward-timing-dependent bidirectional modulation of cortical microcircuits during optical single-neuron operant conditioning Riichiro Hira, Fuki Ohkubo, Yoshito Masamizu, Masamichi Ohkura, Junichi Nakai, Takashi Okada and Masanori Matsuzaki The mammalian brain is able to rapidly adapt to environmental changes, but it is unclear how this occurs at the level of the single neuron. Hira et al. use two-photon calcium imaging of neurons in the mouse motor cortex after a lever-pull task to demonstrate rapid operant conditioning of single neurons. 24 November 2014 | doi: 10.1038/ncomms6551 Biological Sciences  Neuroscience  TALEN and CRISPR/Cas9-mediated genome editing in the early-branching metazoan Nematostella vectensis Aissam Ikmi, Sean A. McKinney, Kym M. Delventhal and Matthew C. Gibson Genome editing has yet to be performed in non-bilaterian phyla. Here, Ikmi et al. develop techniques to use both TALEN and CRISPR/Cas9 in the sea anemone, Nematostella vectensis, and further leverage a locus expressing an endogenous fluorescent protein as a landing site for homologous recombination-mediated transgenesis. 24 November 2014 | doi: 10.1038/ncomms6486 Biological Sciences  Biotechnology  A far-off-resonance optical trap for a Ba+ ion Thomas Huber, Alexander Lambrecht, Julian Schmidt, Leon Karpa and Tobias Schaetz Trapped ions are promising for studies of atomic and quantum physics, but their need for radiofrequency fields poses numerous technical limitations. Huber et al. present an approach using far-off-resonance optical traps, circumventing radiofrequency fields to improve on photon scattering and recoil heating. 24 November 2014 | doi: 10.1038/ncomms6587 Physical Sciences  Atomic and molecular physics  Experimental demonstration of spinor slow light OPEN Meng-Jung Lee, Julius Ruseckas, Chin-Yuan Lee, Viačeslav Kudriašov, Kao-Fang Chang, Hung-Wen Cho, Gediminas Juzeliānas and Ite A. Yu Slow and stored light induced by electromagnetically induced transparency can enhance the strength of light–matter interaction and enable nonlinear optical processes even at single-photon levels. Here Lee, et al. demonstrate spinor slow light using a double-tripod atom–light coupling scheme. 24 November 2014 | doi: 10.1038/ncomms6542 Physical Sciences  Atomic and molecular physics  Optical physics  Ubiquitous long-range antiferromagnetic coupling across the interface between superconducting and ferromagnetic oxides G. M. De Luca, G. Ghiringhelli, C. A. Perroni, V. Cataudella, F. Chiarella, C. Cantoni, A. R. Lupini, N. B. Brookes, M. Huijben, G. Koster, G. Rijnders and M. Salluzzo When tightly coupled, a metallic magnet and a conventional superconductor are known to disturb each-other's order also at some distance from the interface. Here, the authors observe how this proximity effect between a ferromagnetic oxide and a high-T c superconductor develops at microscopic scale. 24 November 2014 | doi: 10.1038/ncomms6626 Physical Sciences  Condensed matter  Materials science  Cerebellar plasticity and motor learning deficits in a copy-number variation mouse model of autism Claire Piochon, Alexander D. Kloth, Giorgio Grasselli, Heather K. Titley, Hisako Nakayama, Kouichi Hashimoto, Vivian Wan, Dana H. Simmons, Tahra Eissa, Jin Nakatani, Adriana Cherskov, Taisuke Miyazaki, Masahiko Watanabe, Toru Takumi, Masanobu Kano, Samuel S.-H. Wang and Christian Hansel Impairments of cerebellar-dependent motor control and learning are implicated in some forms of autism spectrum disorder (ASD). In this study, the authors provide a characterization of the motor deficits and cerebellar function abnormalities in a transgenic mouse model of ASD. 24 November 2014 | doi: 10.1038/ncomms6586 Biological Sciences  Neuroscience  Negative refraction of elastic waves at the deep-subwavelength scale in a single-phase metamaterial R. Zhu, X. N. Liu, G. K. Hu, C. T. Sun and G. L. Huang Acoustic metamaterials passively manipulate sound waves propagating through them, which is attractive for applications. Zhu et al. present a single-phase metamaterial based on a microstructure with simultaneous translational and rotational resonances, enabling negative refraction at deep-subwavelength scales. 24 November 2014 | doi: 10.1038/ncomms6510 Physical Sciences  Applied physics  Materials science  Regulation of Drosophila circadian rhythms by miRNA let-7 is mediated by a regulatory cycle Wenfeng Chen, Zhenxing Liu, Tianjiao Li, Ruifeng Zhang, Yongbo Xue, Yang Zhong, Weiwei Bai, Dasen Zhou and Zhangwu Zhao The CWO protein is part of a feedback loop that contributes to the high-amplitude circadian oscillation in Drosophila. Here, the authors identify microRNA let-7 as a regulator of circadian rhythm via repression of cwo, and show the circadian expression of let-7 is regulated by ecdysteroid and its receptor. 24 November 2014 | doi: 10.1038/ncomms6549 Biological Sciences  Cell biology  Molecular biology  Optical freezing of charge motion in an organic conductor Takahiro Ishikawa, Yuto Sagae, Yota Naitoh, Yohei Kawakami, Hirotake Itoh, Kaoru Yamamoto, Kyuya Yakushi, Hideo Kishida, Takahiko Sasaki, Sumio Ishihara, Yasuhiro Tanaka, Kenji Yonemitsu and Shinichiro Iwai In strongly correlated systems, the material properties can be drastically altered through subtle external perturbations. Here, the authors show that photoexcitation of the organic conductor α-(ET)2I3 with ultrashort pulses leads to a counter-intuitive freezing of the electron motion. 24 November 2014 | doi: 10.1038/ncomms6528 Physical Sciences  Condensed matter  Optical physics  An intuitive and efficient method for cell voltage prediction of lithium and sodium-ion batteries M. Saubanère, M. Ben Yahia, S. Lebègue and M. -L. Doublet Cell voltage is a key indicator of battery performance, but its prediction often involves first-principles calculations. Here, the authors propose a simple approach that allows rapid assessment of the cell potential as well as provides insights into factors influencing potential amplitude. 24 November 2014 | doi: 10.1038/ncomms6559 Chemical Sciences  Materials science  Physical chemistry  Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells Andreas R. Gruber, Georges Martin, Philipp Müller, Alexander Schmidt, Andreas J. Gruber, Rafal Gumienny, Nitish Mittal, Rajesh Jayachandran, Jean Pieters, Walter Keller, Erik van Nimwegen and Mihaela Zavolan The use of alternative polyadenylation sites can potentially result in mRNA being more or less susceptible to interaction with modulators of translation or stability. Here Gruber et al. find that the shortening of 3′UTRs observed in proliferating T cells does not significantly impact protein abundance. 21 November 2014 | doi: 10.1038/ncomms6465 Biological Sciences  Molecular biology  Systems biology  Experimental protocol for high-fidelity heralded photon-to-atom quantum state transfer Christoph Kurz, Michael Schug, Pascal Eich, Jan Huwer, Philipp Müller and Jürgen Eschner The conversion of quantum states between single photons and single atoms is an essential ingredient for the implementation of quantum memories. Here, Kurz et al. demonstrate a photon-to-atom quantum state conversion protocol characterized by mapping fidelities as high as 95%. 21 November 2014 | doi: 10.1038/ncomms6527 Physical Sciences  Optical physics  Theoretical physics  Experimental demonstration of graph-state quantum secret sharing B. A. Bell, D. Markham, D. A. Herrera-Martí, A. Marin, W. J. Wadsworth, J. G. Rarity and M. S. Tame Quantum communication schemes rely on cryptographically secure quantum resources to distribute private information. Here, the authors show that graph states—nonlocal states based on networks of qubits—can be exploited to implement quantum secret sharing of quantum and classical information. 21 November 2014 | doi: 10.1038/ncomms6480 Physical Sciences  Applied physics  Optical physics  RHOA inactivation enhances Wnt signalling and promotes colorectal cancer Paulo Rodrigues, Irati Macaya, Sarah Bazzocco, Rocco Mazzolini, Elena Andretta, Higinio Dopeso, Silvia Mateo-Lozano, Josipa Bilić, Fernando Cartón-García, Rocio Nieto, Lucia Suárez-López, Elsa Afonso, Stefania Landolfi, Javier Hernandez-Losa, Kazuto Kobayashi, Santiago Ramón y Cajal, Josep Tabernero, Niall C. Tebbutt, John M. Mariadason, Simo Schwartz et al. The small GTPase RhoA has oncogenic effects in several cancer types. Here the authors show that loss of RhoA accelerates colon cancer progression by promoting accumulation of nuclear ß-catenin, resulting in enhanced proliferation and invasion mediated by the Wnt signalling pathway in human and murine colon cancer cells. 21 November 2014 | doi: 10.1038/ncomms6458 Biological Sciences  Cancer  Molecular biology  Larval dispersal drives trophic structure across Pacific coral reefs Adrian C. Stier, Andrew M. Hein, Valeriano Parravicini and Michel Kulbicki Species richness of predators in Pacific coral reef communities is less sensitive to habitat isolation than the species richness of their prey. Here, Stier et al. develop a colonization–extinction model to show that this pattern can be explained by limitations in prey dispersal at the larval stage. 21 November 2014 | doi: 10.1038/ncomms6575 Biological Sciences  Ecology  Oceanography  Deciphering the scaling of single-molecule interactions using Jarzynski’s equality Sangeetha Raman, Thomas Utzig, Theodoros Baimpos, Buddha Ratna Shrestha and Markus Valtiner Adhesion forces depend on the strength and density of the individual molecular interactions of which they are composed. Here, the authors use surface force apparatus and atomic force microscopy to experimentally probe the scaling of single-molecule interactions into macroscopic properties. 21 November 2014 | doi: 10.1038/ncomms6539 Chemical Sciences  Condensed matter  Materials science  Physical chemistry  VAV-1 acts in a single interneuron to inhibit motor circuit activity in Caenorhabditis elegans OPEN Amanda L. Fry, Jocelyn T. Laboy and Kenneth R. Norman VAV proteins are guanine nucleotide exchange factors that have various neuromodulatory roles in the nervous system. Here, Fry et al. show that in Caenorhabditis elegans, VAV-1 negatively regulates locomotor speed and only needs to be expressed in a specific interneuron to do so. 21 November 2014 | doi: 10.1038/ncomms6579 Biological Sciences  Neuroscience  The immunoglobulin tail tyrosine motif upgrades memory-type BCRs by incorporating a Grb2-Btk signalling module OPEN Niklas Engels, Lars M. König, Wiebke Schulze, Daniel Radtke, Kanika Vanshylla, Johannes Lutz, Thomas H. Winkler, Lars Nitschke and Jürgen Wienands How class-switched memory B cells signal to respond robustly to recurring pathogens is incompletely understood. Here the authors show that immunoglobulin tail tyrosine motifs in membrane-bound immunoglobulin isotypes of class-switched cells amplify signalling in memory B cells, in a mechanism that includes distinct kinases and adaptor proteins. 21 November 2014 | doi: 10.1038/ncomms6456 Biological Sciences  Immunology  A walk along DNA using bipedal migration of a dynamic and covalent crosslinker Fazel Fakhari and Steven E. Rokita The predictable assembly of DNA makes it a useful scaffold for creating pathways to guide nanotransport systems. Here, the authors use reversible covalent capture of DNA by quinone methide generation, as well as diffusion along the nucleophilic surface of DNA to guide migration. 21 November 2014 | doi: 10.1038/ncomms6591 Chemical Sciences  Biochemistry  Nanotechnology  Divergent paths for the selection of immunodominant epitopes from distinct antigenic sources AeRyon Kim, Isamu Z. Hartman, Brad Poore, Tatiana Boronina, Robert N. Cole, Nianbin Song, M. Teresa Ciudad, Rachel R. Caspi, Dolores Jaraquemada and Scheherazade Sadegh-Nasseri Whether antigen processing and presentation differs between pathogen-derived antigens and self-antigens is not clear. Here the authors use a reductionist cell-free approach to study antigen processing, uncovering differences in antigen sensitivity to digestion by cathepsins and resistance to DM. 21 November 2014 | doi: 10.1038/ncomms6369 Biological Sciences  Immunology  PKM2 phosphorylates MLC2 and regulates cytokinesis of tumour cells Yuhui Jiang, Yugang Wang, Ting Wang, David H. Hawke, Yanhua Zheng, Xinjian Li, Qin Zhou, Sadhan Majumder, Erfei Bi, David X. Liu, Suyun Huang and Zhimin Lu The pyruvate kinase type M2 (PKM2) has a well-established role in cancer due to its functions in regulating glucose metabolism, G1-S transition and mitotic checkpoint. Here the authors identified a novel role for PKM2 in regulating cytokinesis in cancer cells through the phosphorylation of the myosin light chain 2 at the contractile ring. 21 November 2014 | doi: 10.1038/ncomms6566 Biological Sciences  Cancer  Molecular biology  Asymmetric trapping of zwitterionic intermediates by sulphur ylides in a palladium-catalysed decarboxylation-cycloaddition sequence Tian-Ren Li, Fen Tan, Liang-Qiu Lu, Yi Wei, Ya-Ni Wang, Yi-Yin Liu, Qing-Qing Yang, Jia-Rong Chen, De-Qing Shi and Wen-Jing Xiao Sulphur ylides are useful reagents in organic synthesis, typically reacting with highly polar reagents. Here, the authors show a catalytic asymmetric process for the addition of sulphur ylides to cyclic allylic esters with loss of CO2, giving access to chiral, highly functionalised indolines. 21 November 2014 | doi: 10.1038/ncomms6500 Chemical Sciences  Catalysis  Organic chemistry  The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer OPEN Dimple Chakravarty, Andrea Sboner, Sujit S. Nair, Eugenia Giannopoulou, Ruohan Li, Sven Hennig, Juan Miguel Mosquera, Jonathan Pauwels, Kyung Park, Myriam Kossai, Theresa Y. MacDonald, Jacqueline Fontugne, Nicholas Erho, Ismael A. Vergara, Mercedeh Ghadessi, Elai Davicioni, Robert B. Jenkins, Nallasivam Palanisamy, Zhengming Chen, Shinichi Nakagawa et al. While prostate cancer predominantly exhibits androgen dependence, oestrogen receptor (ER) signalling is also involved. Here, Chakravarty et al. show that ERα regulates the expression of the NEAT1 long non-coding RNA, which in turn promotes tumorigenesis by maintaining an oncogenic programme/cascade. 21 November 2014 | doi: 10.1038/ncomms6383 Biological Sciences  Cancer  Cell biology  Erosion influences the seismicity of active thrust faults Philippe Steer, Martine Simoes, Rodolphe Cattin and J. Bruce H. Shyu Deep tectonic processes are considered to be responsible for stress loading of faults over a seismic cycle. Here, the authors use a mechanical model to demonstrate that erosion also significantly influences the stress loading of faults on this short time scale, potentially leading to fault failure and earthquakes. 21 November 2014 | doi: 10.1038/ncomms6564 Earth Sciences  Geology and geophysics  An antioxidant nanozyme that uncovers the cytoprotective potential of vanadia nanowires Amit A. Vernekar, Devanjan Sinha, Shubhi Srivastava, Prasath U. Paramasivam, Patrick D’Silva and Govindasamy Mugesh It is known that some nanomaterials can exhibit enzyme-like activities, prompting interest in the novel applications this property may allow. Here, the authors show how vanadia nanowires possess glutathione peroxidase-like activity, and can effectively protect cells from oxidative damage. 21 November 2014 | doi: 10.1038/ncomms6301 Biological Sciences  Biochemistry  Materials science  Medicinal chemistry  Epithelial rotation promotes the global alignment of contractile actin bundles during Drosophila egg chamber elongation Maureen Cetera, Guillermina R. Ramirez-San Juan, Patrick W. Oakes, Lindsay Lewellyn, Michael J. Fairchild, Guy Tanentzapf, Margaret L. Gardel and Sally Horne-Badovinac During Drosophila oogenesis, migration of follicle cells causes the egg chamber to rotate, changing the shape of the egg chamber from spherical to oval. Here the authors show, using live imaging, that lamellopodia on the follicle cells are required for this rotation and alignment of contractile actin bundles. 21 November 2014 | doi: 10.1038/ncomms6511 Biological Sciences  Cell biology  Developmental biology  Emergence of single-molecular chirality from achiral reactants OPEN René R. E. Steendam, Jorge M. M. Verkade, Tim J. B. van Benthem, Hugo Meekes, Willem J. P. van Enckevort, Jan Raap, Floris P. J. T. Rutjes and Elias Vlieg Conversion of achiral starting materials into enantiopure products without additional chiral additives is a challenging task. Here, the authors show a reaction where the precipitation of chiral product induces autocatalysis, ultimately leading to an enantiopure compound. 21 November 2014 | doi: 10.1038/ncomms6543 Chemical Sciences  Catalysis  Organic chemistry  Singular localization of sodium channel β4 subunit in unmyelinated fibres and its role in the striatum Haruko Miyazaki, Fumitaka Oyama, Ritsuko Inoue, Toshihiko Aosaki, Takaya Abe, Hiroshi Kiyonari, Yoshihiro Kino, Masaru Kurosawa, Jun Shimizu, Ikuo Ogiwara, Kazuhiro Yamakawa, Yoshinori Koshimizu, Fumino Fujiyama, Takeshi Kaneko, Hideaki Shimizu, Katsuhiro Nagatomo, Katsuya Yamada, Tomomi Shimogori, Nobutaka Hattori, Masami Miura et al. Voltage-gated Na+ channel β-subunits are concentrated in the nodes of Ranvier and axon initial segments of myelinated axons and have a variety of functions. Here the authors show, using genetically modified mice, that this subunit is present in unmyelinated fibres in the striatum and is required for generation of resurgent Na+ current in striatal neurons. 21 November 2014 | doi: 10.1038/ncomms6525 Biological Sciences  Neuroscience  Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12 Rama K. Koppisetti, Yan G. Fulcher, Alexander Jurkevich, Stephen H. Prior, Jia Xu, Marc Lenoir, Michael Overduin and Steven R. Van Doren Matrix metalloprotease-12 is secreted by macrophages during the inflammatory response, but was reported to be active near cell surfaces. Koppisetti et al. reveal the enzyme’s unprecedented use of two distinct surfaces to interact with lipid bilayers, thereby targeting it to cellular membranes. 21 November 2014 | doi: 10.1038/ncomms6552 Biological Sciences  Biochemistry  Cell biology  Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3 OPEN Chun-Min Shan, Xiao-Xia Shangguan, Bo Zhao, Xiu-Fang Zhang, Lu-men Chao, Chang-Qing Yang, Ling-Jian Wang, Hua-Yu Zhu, Yan-Da Zeng, Wang-Zhen Guo, Bao-Liang Zhou, Guan-Jing Hu, Xue-Ying Guan, Z. Jeffrey Chen, Jonathan F. Wendel, Tian-Zhen Zhang and Xiao-Ya Chen Cotton fibre is the most important renewable material for textiles, with a huge economic output. Here the authors show that a homeodomain-leucine zipper transcription factor, GhHOX3, transduces a gibberellin signal that in turn promotes fibre cell elongation. 21 November 2014 | doi: 10.1038/ncomms6519 Biological Sciences  Genetics  Plant sciences  Bacteria slingshot more on soft surfaces OPEN Rongrong Zhang, Lei Ni, Zhenyu Jin, Jiahong Li and Fan Jin Pseudomonas aeruginosa migrate by deploying their type-IV pili. Here, Zhang et al. show that P. aeruginosa can adapt to the physical microenvironment by using their type-IV pili to ‘slingshot’ more across soft surfaces to exploit inherent shear thinning properties of the surface. 21 November 2014 | doi: 10.1038/ncomms6541 Biological Sciences  Biophysics  Microbiology  Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells Alf Honigmann, Veronika Mueller, Haisen Ta, Andreas Schoenle, Erdinc Sezgin, Stefan W. Hell and Christian Eggeling The extent to which lipids in biological membranes self-organise into nanodomains is a subject of debate. Honigmann et al. combine scanning FCS and STED microscopies to monitor lipid diffusion over wide areas, and find that local trapping of sphingolipids may not depend on phase separation. 20 November 2014 | doi: 10.1038/ncomms6412 Biological Sciences  Biophysics  Cell biology  Mercury nano-trap for effective and efficient removal of mercury(II) from aqueous solution Baiyan Li, Yiming Zhang, Dingxuan Ma, Zhan Shi and Shengqian Ma Decontamination of mercury pollution from fresh water is a serious environmental issue. Here, the authors report a porous organic polymer-based nano-trap, functionalized with mercury chelating groups, capable of efficient and rapid mercury removal from aqueous media. 20 November 2014 | doi: 10.1038/ncomms6537 Chemical Sciences  Inorganic chemistry  Materials science  Early Eocene fossils suggest that the mammalian order Perissodactyla originated in India Kenneth D. Rose, Luke T. Holbrook, Rajendra S. Rana, Kishor Kumar, Katrina E. Jones, Heather E. Ahrens, Pieter Missiaen, Ashok Sahni and Thierry Smith The phylogenetic and biogeographic origin of Perissodactyla (horses, rhinoceroses and tapirs) is unclear. Here the authors report 54.5 Myr fossils from a sister taxa of Perissodactyla found in India, which suggests that the group may have originated in India before its collision with Asia. 20 November 2014 | doi: 10.1038/ncomms6570 Biological Sciences  Evolution  Palaeontology  In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme Aiming Ren, Marija Košutić, Kanagalaghatta R. Rajashankar, Marina Frener, Tobias Santner, Eric Westhof, Ronald Micura and Dinshaw J. Patel Twisters ribozymes are a recently discovered class of non-coding, site-specific self-cleaving RNAs. Here Ren et al. describe a crystal structure of the env22 twister ribozyme, propose an ion coordination and catalytic mechanism, and contrast their findings with those of two recently reported twister structures. 20 November 2014 | doi: 10.1038/ncomms6534 Biological Sciences  Biochemistry  Biophysics  Field-induced assembly of colloidal ellipsoids into well-defined microtubules OPEN Jérôme J. Crassous, Adriana M. Mihut, Erik Wernersson, Patrick Pfleiderer, Jan Vermant, Per Linse and Peter Schurtenberger Building artificial nanostructures via self-assembly normally starts with shape-specific building blocks of colloidal particles or monomers. Here, Crassous et al. challenge this convention by showing that simple ellipsoids can form sheet-like or tubular structures in an alternating electric field. 20 November 2014 | doi: 10.1038/ncomms6516 Physical Sciences  Condensed matter  Materials science  Dynamic operation of optical fibres beyond the single-mode regime facilitates the orientation of biological cells OPEN Moritz Kreysing, Dino Ott, Michael J. Schmidberger, Oliver Otto, Mirjam Schürmann, Estela Martín-Badosa, Graeme Whyte and Jochen Guck Transmitting spatial information through optical fibres is difficult because scalar high-order modes deteriorate. Here, the authors counter deterioration using adaptive optics to excite vectorial modes, achieving high-quality beams robust against fibre bending and use those to rotate cells in a laser trap. 20 November 2014 | doi: 10.1038/ncomms6481 Physical Sciences  Biophysics  Optical physics  Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types Zheng Xia, Lawrence A. Donehower, Thomas A. Cooper, Joel R. Neilson, David A. Wheeler, Eric J. Wagner and Wei Li Alternative polyadenylation (APA) has been implicated in diverse physiological and pathological conditions including cancer. The authors present a new algorithm, DaPars, for APA analysis using available RNA-seq data and suggest CstF64 as a master regulator of 3′-UTR shortening across multiple tumour types. 20 November 2014 | doi: 10.1038/ncomms6274 Biological Sciences  Bioinformatics  Cancer  A general strategy for developing cell-permeable photo-modulatable organic fluorescent probes for live-cell super-resolution imaging OPEN Deng Pan, Zhe Hu, Fengwu Qiu, Zhen-Li Huang, Yilong Ma, Yina Wang, Lingsong Qin, Zhihong Zhang, Shaoqun Zeng and Yu-Hui Zhang Single-molecule localization microscopy depends on the use of photo-modulatable fluorescent probes; however, many cannot be used in live-cell studies due to poor cell permeability. Pan et al. present a strategy for constructing cell-permeable probes and use it to image actin filament dynamics and lysosomes. 20 November 2014 | doi: 10.1038/ncomms6573 Biological Sciences  Cell biology  Neuroligin-associated microRNA-932 targets actin and regulates memory in the honeybee Alexandre S. Cristino, Angel R. Barchuk, Flavia C. P. Freitas, Ramesh K. Narayanan, Stephanie D. Biergans, Zhengyang Zhao, Zila L. P. Simoes, Judith Reinhard and Charles Claudianos MicroRNAs are increasingly recognized as important regulators of experience-dependent plasticity in the brain. Cristino et al. show that miR-932 targets actin mRNA in trained honeybees, and that loss of miR-932 impairs long-term memory formation. 20 November 2014 | doi: 10.1038/ncomms6529 Biological Sciences  Cell biology  Neuroscience  High-throughput imaging of self-luminous objects through a single optical fibre Roman Barankov and Jerome Mertz Imaging through a single optical fibre offers attractive possibilities in applications such as micro-endoscopy or remote sensing. Using spread-spectrum encoding, Barankov and Mertz demonstrate two-dimensional imaging of self-luminous objects with high throughput, in theory independent of pixel number. 20 November 2014 | doi: 10.1038/ncomms6581 Physical Sciences  Applied physics  Optical physics  Lonsdaleite is faulted and twinned cubic diamond and does not exist as a discrete material Péter Németh, Laurence A. J. Garvie, Toshihiro Aoki, Natalia Dubrovinskaia, Leonid Dubrovinsky and Peter R. Buseck Lonsdaleite has been used as a marker of asteroid impacts and is thought to have mechanical properties superior to diamond; however, pure lonsdaleite has not been described or fabricated. Here, the authors show that it does not exist as a discrete material and is in fact faulted and twinned cubic diamond. 20 November 2014 | doi: 10.1038/ncomms6447 Physical Sciences  Materials science  Planetary sciences  Vesicles derived via AP-3-dependent recycling contribute to asynchronous release and influence information transfer Alesya Evstratova, Simon Chamberland, Victor Faundez and Katalin Tóth Neurotransmitter release involves a fast synchronous component and a slower asynchronous phase, which is poorly understood. Evstratova et al. show that asynchronous release increases the precision of postsynaptic action potential firing in an activity-dependent manner, which is dependent on adaptor protein 3. 20 November 2014 | doi: 10.1038/ncomms6530 Biological Sciences  Neuroscience  Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes OPEN Bernd Stadelmayer, Gaël Micas, Adrien Gamot, Pascal Martin, Nathalie Malirat, Slavik Koval, Raoul Raffel, Bijan Sobhian, Dany Severac, Stéphanie Rialle, Hugues Parrinello, Olivier Cuvier and Monsef Benkirane RNA polymerase II (RNAPII) pausing at transcriptional start sites is an important element of gene transcription regulation. Here, the authors implicate the Integrator complex as a regulator of RNAPII pause-release and completion of mRNA synthesis at a subset of the negative elongation factor target genes. 20 November 2014 | doi: 10.1038/ncomms6531 Biological Sciences  Biochemistry  Molecular biology  The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication OPEN Wenjun Song, Pui Wang, Bobo Wing-Yee Mok, Siu-Ying Lau, Xiaofeng Huang, Wai-Lan Wu, Min Zheng, Xi Wen, Shigui Yang, Yu Chen, Lanjuan Li, Kwok-Yung Yuen and Honglin Chen Mutations in the viral polymerase, such as PB2-E627K, contribute to adaptation of avian influenza strains to mammalian hosts. Here the authors show that another mutation, PB2-K526R, is found in seasonal H3N2 and avian-origin human influenza isolates, and facilitates replication of these viruses in mammals. 20 November 2014 | doi: 10.1038/ncomms6509 Biological Sciences  Microbiology  Virology  Controlling the spectrum of photons generated on a silicon nanophotonic chip OPEN Ranjeet Kumar, Jun Rong Ong, Marc Savanier and Shayan Mookherjea The controlled creation of single and pair photon sources on a silicon chip is important for the realisation of quantum optical communications. Here, the authors control the spectrum of such photons generated on a silicon chip. 20 November 2014 | doi: 10.1038/ncomms6489 Physical Sciences  Applied physics  Nanotechnology  Optical physics  Permafrost thawing as a possible source of abrupt carbon release at the onset of the Bølling/Allerød OPEN Peter Köhler, Gregor Knorr and Edouard Bard Ice core records show evidence for an abrupt, and thus far unexplained, increase in atmospheric CO2 levels ~14,600 years ago. Here, the authors combine ice core data, a precisely dated decline in atmospheric 14C and numerical simulations, and propose thawing permafrost as a possible source of this event. 20 November 2014 | doi: 10.1038/ncomms6520 Earth Sciences  Biogeochemistry  Climate science  Prediction and quantification of bioactive microbiota metabolites in the mouse gut Gautham V. Sridharan, Kyungoh Choi, Cory Klemashevich, Charmian Wu, Darshan Prabakaran, Long Bin Pan, Shelby Steinmeyer, Carrie Mueller, Mona Yousofshahi, Robert C. Alaniz, Kyongbum Lee and Arul Jayaraman Metabolites produced by the gut microbiota can potentially affect our physiology. Here, the authors present a metabolomics strategy that models microbiota metabolism as a reaction network and uses pathway analysis to facilitate identification and characterization of microbial metabolites. 20 November 2014 | doi: 10.1038/ncomms6492 Biological Sciences  Biochemistry  Microbiology  Giant enhancement in vertical conductivity of stacked CVD graphene sheets by self-assembled molecular layers Yanpeng Liu, Li Yuan, Ming Yang, Yi Zheng, Linjun Li, Libo Gao, Nisachol Nerngchamnong, Chang Tai Nai, C. S. Suchand Sangeeth, Yuan Ping Feng, Christian A. Nijhuis and Kian Ping Loh Poor electronic coupling between planes significantly reduces stacked graphene conductivity. Here, the authors measure plane-to-plane conductivity using the eutectic GaIn technique to show that insertion of self-assembled monolayers between graphene layers improves vertical conductivity by six orders of magnitude. 20 November 2014 | doi: 10.1038/ncomms6461 Physical Sciences  Materials science  Nanotechnology  Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9 OPEN Shota Nakade, Takuya Tsubota, Yuto Sakane, Satoshi Kume, Naoaki Sakamoto, Masanobu Obara, Takaaki Daimon, Hideki Sezutsu, Takashi Yamamoto, Tetsushi Sakuma and Ken-ichi T. Suzuki One challenge facing the use of programmable nucleases in genome engineering is the requirement for homologous recombination. Here, Nakade et al. harness microhomology-mediated end-joining as a means of inserting exogenous coding sequences into the genome using both TALEN and CRISPR/Cas9 technologies. 20 November 2014 | doi: 10.1038/ncomms6560 Biological Sciences  Genetics  Molecular biology  Calcium-induced conformational changes of the regulatory domain of human mitochondrial aspartate/glutamate carriers OPEN Chancievan Thangaratnarajah, Jonathan J. Ruprecht and Edmund R. S. Kunji Human mitochondrial aspartate/glutamate carriers, citrin and aralar, are regulated by calcium. Here, the authors report the dimeric structure of calcium-free and -bound versions of the regulatory domains to elucidate calcium-dependent conformational changes that could regulate access of substrate to the carrier domain. 20 November 2014 | doi: 10.1038/ncomms6491 Biological Sciences  Biochemistry  Solution-processed hybrid perovskite photodetectors with high detectivity Letian Dou, Yang (Micheal) Yang, Jingbi You, Ziruo Hong, Wei-Hsuan Chang, Gang Li and Yang Yang Organic–inorganic hybrid perovskite materials are attracting great interest for their applications in photovoltaics where they have demonstrated excellent efficiency. Here, Dou et al. demonstrate room temperature, solution-processed hybrid perovskite photodetectors with fast response and high detectivity. 20 November 2014 | doi: 10.1038/ncomms6404 Physical Sciences  Applied physics  Materials science  Structural basis for trypanosomal haem acquisition and susceptibility to the host innate immune system Kristian Stødkilde, Morten Torvund-Jensen, Søren K. Moestrup and Christian B. F. Andersen Trypanosomes, responsible for sleeping sickness, acquire haem through binding haptoglobin(Hp)–haemoglobin(Hb) complexes in human blood. Here Stødkilde et al. determine the structure of human Hp–Hb in complex with the Hp–Hb receptor from T. brucei and show that the recognition elements are shared by a protein complex on the surface of a trypanolytic lipoprotein particle. 20 November 2014 | doi: 10.1038/ncomms6487 Biological Sciences  Biochemistry  Serotonin receptor 3A controls interneuron migration into the neocortex OPEN Sahana Murthy, Mathieu Niquille, Nicolas Hurni, Greta Limoni, Sarah Frazer, Pascal Chameau, Johannes A. van Hooft, Tania Vitalis and Alexandre Dayer During brain development, neuronal excitability controls the laminar migration of cortical interneurons from the caudal ganglionic eminences (CGEs). Here the authors identify the 5-HT3A receptor as a specific marker of CGE-derived cortical interneurons (cINs), and as a stimulator of cIN migration. 20 November 2014 | doi: 10.1038/ncomms6524 Biological Sciences  Developmental biology  Neuroscience  Widespread genetic epistasis among cancer genes Xiaoyue Wang, Audrey Q. Fu, Megan E. McNerney and Kevin P. White Cancer can result from mutations in more than one gene and these multiple mutated genes are often functionally dependent on each other; this interaction is known as epistasis. Here, the authors use a combinatorial RNAi screen to identify epistatic genes that are mutated in breast cancer and reveal large numbers of previously unreported gene interactions. 19 November 2014 | doi: 10.1038/ncomms5828 Biological Sciences  Cancer  Genetics  Semi-permeable coatings fabricated from comb-polymers efficiently protect proteins in vivo Mi Liu, Pål Johansen, Franziska Zabel, Jean-Christophe Leroux and Marc A. Gauthier The attachment of polymers to protein molecules is known to shield them from biological breakdown. Here, the authors apply this concept to an asparaginase, in order to prevent its deactiviation by host immune responses during leukaemia treatment. 19 November 2014 | doi: 10.1038/ncomms6526 Biological Sciences  Chemical biology  Materials science  Medicinal chemistry  Visible-light-enhanced gating effect at the LaAlO3/SrTiO3 interface Y. Lei, Y. Li, Y. Z. Chen, Y. W. Xie, Y. S. Chen, S. H. Wang, J. Wang, B. G. Shen, N. Pryds, H. Y. Hwang and J. R. Sun The interface between LaAlO3 and SrTiO3 is host to exotic phenomena that can be controlled by light or electric fields. Lei et al. show that combining the two controls leads to a dramatic decrease, not increase, of carrier density at the heterointerface, beyond what can be done with only one of them. 19 November 2014 | doi: 10.1038/ncomms6554 Physical Sciences  Condensed matter  Materials science  The immune synapse clears and excludes molecules above a size threshold OPEN Adam N. R. Cartwright, Jeremy Griggs and Daniel M. Davis Natural killer cells can be switched on or off by the immune synapse formed with another cell. Here, the authors show that when a natural killer cell is activated, the immune synapse also functions to clear and exclude extracellular molecules, including antibodies, in a size-dependent manner. 19 November 2014 | doi: 10.1038/ncomms6479 Biological Sciences  Immunology  Cdo suppresses canonical Wnt signalling via interaction with Lrp6 thereby promoting neuronal differentiation Myong-Ho Jeong, Seok-Man Ho, Tuan Anh Vuong, Shin-Bum Jo, Guizhong Liu, Stuart A. Aaronson, Young-Eun Leem and Jong-Sun Kang Cdo regulates early forebrain development as a co-receptor of the morphogen Shh and is required for full activation of Shh signalling. Here the authors show that Cdo interacts with the Wnt co-receptor Lrp6, thereby inhibits Wnt signalling and promotes neuronal differentiation. 19 November 2014 | doi: 10.1038/ncomms6455 Biological Sciences  Developmental biology  Neuroscience  Positron emission tomography and functional characterization of a complete PBR/TSPO knockout OPEN Richard B. Banati, Ryan J. Middleton, Ronald Chan, Claire R. Hatty, Winnie Wai-Ying Kam, Candice Quin, Manuel B. Graeber, Arvind Parmar, David Zahra, Paul Callaghan, Sandra Fok, Nicholas R. Howell, Marie Gregoire, Alexander Szabo, Tien Pham, Emma Davis and Guo-Jun Liu The 18-kDa translocator protein (TSPO) has been implicated in steroid biogenesis and neuroinflammation. Here, the authors create viable and fertile global TSPO knockout mice, challenging the assumption that TSPO is essential for mouse development but suggesting that it may have a role under certain disease conditions. 19 November 2014 | doi: 10.1038/ncomms6452 Biological Sciences  Medical research  Superconductivity in the vicinity of antiferromagnetic order in CrAs Wei Wu, Jinguang Cheng, Kazuyuki Matsubayashi, Panpan Kong, Fukun Lin, Changqing Jin, Nanlin Wang, Yoshiya Uwatoko and Jianlin Luo One trait common to most unconventional superconductors—including cuprates, heavy-fermion systems and iron-pnictides—is that the superconducting state appears near the point where antiferromagnetism is suppressed. Wu et al. report discovery of superconductivity on the verge of antiferromagnetic order in CrAs. 19 November 2014 | doi: 10.1038/ncomms6508 Physical Sciences  Condensed matter  Long noncoding RNA PANDA and scaffold-attachment-factor SAFA control senescence entry and exit OPEN Pavan Kumar Puvvula, Rohini Devi Desetty, Pascal Pineau, Agnés Marchio, Anne Moon, Anne Dejean and Oliver Bischof The gene-regulatory circuits that establish and maintain senescence remain incompletely understood. Here, the authors show that the long noncoding RNA PANDA and scaffold-attachment-factor A (SAFA) regulate entry and exit from senescence through context-specific interactions with PRC 1/2 and the transcription factor NF-YA. 19 November 2014 | doi: 10.1038/ncomms6323 Biological Sciences  Cell biology  Molecular biology  Biallelic loss-of-function mutation in NIK causes a primary immunodeficiency with multifaceted aberrant lymphoid immunity OPEN Katharina L. Willmann, Stefanie Klaver, Figen Doğu, Elisangela Santos-Valente, Wojciech Garncarz, Ivan Bilic, Emily Mace, Elisabeth Salzer, Cecilia Domínguez Conde, Heiko Sic, Peter Májek, Pinaki P. Banerjee, Gregory I. Vladimer, Şule Haskoloğlu, Musa Gökalp Bolkent, Alphan Küpesiz, Antonio Condino-Neto, Jacques Colinge, Giulio Superti-Furga, Winfried F. Pickl et al. Primary immunodeficiency disorders can be used to identify key immune functions. Here, the authors identify a biallelic mutation in the gene encoding NF-κB-inducing kinase in a family suffering a range of infections, and show that it causes defects in NK and T-cell function and has broad effects on B-cell function. 19 November 2014 | doi: 10.1038/ncomms6360 Biological Sciences  Immunology  Diversification of bacterial genome content through distinct mechanisms over different timescales OPEN Nicholas J. Croucher, Paul G. Coupland, Abbie E. Stevenson, Alanna Callendrello, Stephen D. Bentley and William P. Hanage Populations of the pathogenic bacterium Streptococcus pneumoniae consist of distinct co-circulating lineages. Here, the authors show lineages are characterized by particular combinations of stable genomic islands, whereas prophage and restriction-modification systems vary over short timescales. 19 November 2014 | doi: 10.1038/ncomms6471 Biological Sciences  Evolution  Genetics  Microbiology  Metabotropic P2Y1 receptor signalling mediates astrocytic hyperactivity in vivo in an Alzheimer’s disease mouse model Andrea Delekate, Martina Füchtemeier, Toni Schumacher, Cordula Ulbrich, Marco Foddis and Gabor C. Petzold Astrocytic network alterations are seen in Alzheimer’s disease (AD) but the underlying mechanisms have remained undefined. Here the authors use in vivo mulitphoton microscopy to monitor spontaneous network activity of astrocytes in a mouse model of AD, and find that astroglial hyperactivity was largely mediated by activation of the purinergic receptor P2Y1. 19 November 2014 | doi: 10.1038/ncomms6422 Biological Sciences  Neuroscience  Atomically resolved tomography to directly inform simulations for structure–property relationships Michael P. Moody, Anna V. Ceguerra, Andrew J. Breen, Xiang Yuan Cui, Baptiste Gault, Leigh T. Stephenson, Ross K. W. Marceau, Rebecca C. Powles and Simon P. Ringer Atom probe tomography is known to be an important tool for probing atomic-scale chemical distribution in various materials. Now, Moody and colleagues demonstrate an approach by which atom probe data can be used to directly inform first-principles calculations, for the determination of local properties. 19 November 2014 | doi: 10.1038/ncomms6501 Physical Sciences  Materials science  Structural characterization of the substrate transfer mechanism in Hsp70/Hsp90 folding machinery mediated by Hop Sara Alvira, Jorge Cuéllar, Alina Röhl, Soh Yamamoto, Hideaki Itoh, Carlos Alfonso, Germán Rivas, Johannes Buchner and José M. Valpuesta Hsp70 and Hsp90 cooperate to fold client proteins, aided by co-chaperones such as Hop. Here Alvira et al. determine EM structures of various combinations of Hsp70, Hsp90, Hop and a client protein to shed structural insight into the mechanism of client protein transfer from one chaperone to the other. 19 November 2014 | doi: 10.1038/ncomms6484 Biological Sciences  Biochemistry  ARGONAUTE PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis Xiaoming Zhang, DongDong Niu, Alberto Carbonell, Airong Wang, Angel Lee, Vinnary Tun, Zonghua Wang, James C. Carrington, Chia-en A. Chang and Hailing Jin Small RNA-binding ARGONAUTE proteins are important regulators of gene silencing and plant development. Here Zhang et al. identify conserved motifs in Arabidopsis ARGONAUTE proteins that determine binding to specific microRNA duplex structures. 19 November 2014 | doi: 10.1038/ncomms6468 Biological Sciences  Molecular biology  Plant sciences  Evolutionary triage governs fitness in driver and passenger mutations and suggests targeting never mutations R. A. Gatenby, J. J. Cunningham and J. S. Brown The accumulation of genetic and epigenetic mutations in cancer cells can drive malignant growth. Here, the authors model the evolution of intratumoral diversity and examine the classification of driver and passenger mutations, heterogeneity within tumours, and the dynamics of tumour response to targeted therapies. 19 November 2014 | doi: 10.1038/ncomms6499 Biological Sciences  Cancer  Evolution  Genetics  Genomic landscape and genetic heterogeneity in gastric adenocarcinoma revealed by whole-genome sequencing Swee Seong Wong, Kyoung-Mee Kim, Jason C. Ting, Kun Yu, Jake Fu, Shawn Liu, Razvan Cristescu, Michael Nebozhyn, Lara Gong, Yong Gang Yue, Jian Wang, Chen Ronghua, Andrey Loboda, James Hardwick, Xiaoqiao Liu, Hongyue Dai, Jason Gang Jin, Xiang S. Ye, So Young Kang, In Gu Do et al. Gastric cancer has two distinct morphologic subtypes, intestinal and diffuse, that differ in genetic composition and clinical manifestation. Here, the authors carry out whole-genome sequencing of diffuse and intestinal gastric cancer samples and characterize the mutational landscape of these different subtypes. 19 November 2014 | doi: 10.1038/ncomms6477 Biological Sciences  Cancer  Genetics  GWAS identifies four novel eosinophilic esophagitis loci Patrick M. A. Sleiman, Mei-Lun Wang, Antonella Cianferoni, Seema Aceves, Nirmala Gonsalves, Kari Nadeau, Albert J. Bredenoord, Glenn T. Furuta, Jonathan M. Spergel and Hakon Hakonarson Eosinophilic oesophagitis (EoE) is an allergic, inflammatory disorder of the oesophagus. Here the authors carry out a genome-wide association study in over 5,000 individuals and identify four genetic loci that affect the onset of EoE. 19 November 2014 | doi: 10.1038/ncomms6593 Biological Sciences  Genetics  White matter in the older brain is more plastic than in the younger brain Yuko Yotsumoto, Li-Hung Chang, Rui Ni, Russell Pierce, George J. Andersen, Takeo Watanabe and Yuka Sasaki Aspects of visual perception learning are known to change with age, but the associated structural correlates are poorly understood. Here the authors show that, surprisingly, visual perception in older individuals involves training-induced structural changes in white matter that are absent in younger individuals. 19 November 2014 | doi: 10.1038/ncomms6504 Biological Sciences  Neuroscience  Active accumulation of very diluted biomolecules by nano-dispensing for easy detection below the femtomolar range S. Grilli, L. Miccio, O. Gennari, S. Coppola, V. Vespini, L. Battista, P. Orlando and P. Ferraro Biomolecule detection is important in many fields, but obviously becomes increasingly difficult as concentrations decrease. Here, the authors demonstrate a method to dispense and concentrate biomolecules onto a target slide, greatly improving the detection limits. 19 November 2014 | doi: 10.1038/ncomms6314 Physical Sciences  Biochemistry  Fluids and plasma physics  Materials science  BRMS1L suppresses breast cancer metastasis by inducing epigenetic silence of FZD10 Chang Gong, Shaohua Qu, Xiao-Bin Lv, Bodu Liu, Weige Tan, Yan Nie, Fengxi Su, Qiang Liu, Herui Yao and Erwei Song BRMS1, a component of the Sin3A–HDAC repressor complex, blocks invasion and migration of breast cancer cells. Here the authors show that BRMS1-like (BRMS1L) inhibits breast cancer metastasis by blocking epithelial to mesenchymal transition through transcriptional suppression of the FZD10 receptor for Wnt ligands. 19 November 2014 | doi: 10.1038/ncomms6406 Biological Sciences  Cancer  Molecular biology  The draft genome of the large yellow croaker reveals well-developed innate immunity OPEN Changwen Wu, Di Zhang, Mengyuan Kan, Zhengmin Lv, Aiyi Zhu, Yongquan Su, Daizhan Zhou, Jianshe Zhang, Zhou Zhang, Meiying Xu, Lihua Jiang, Baoying Guo, Ting Wang, Changfeng Chi, Yong Mao, Jiajian Zhou, Xinxiu Yu, Hailing Wang, Xiaoling Weng, Jason Gang Jin et al. The large yellow croaker, Larimichthys crocea, is an economically important marine fish in China. Here, the authors sequence the draft genome of a wild large yellow croaker and highlight genes that may have played a role in the development of innate immunity in this species. 19 November 2014 | doi: 10.1038/ncomms6227 Biological Sciences  Evolution  Genetics    Nature Communications JOBS of the week Research Technician The Open University Research Fellowship University of Milan PhD Positions ETH Zurich PhD Studentship University of Birmingham PhD student scholarship McGill University Professor of Optics The University of Nottingham Postdoctoral Associate University of California - Davis postdoctoral fellow University of Utah Postdoctoral Research Assistants University of Dundee Post Doctoral Research Associate King's College London More Science jobs from Nature Communications EVENT 8th International Meeting on Steroids and Nervous system 14.02.15 Orbassano, Italy More science events from       Latest Erratum     Erratum: Noiseless intensity amplification of repetitive signals by coherent addition using the temporal Talbot effect Reza Maram, James Van Howe, Ming Li and José Azaña 19 November 2014 | doi: 10.1038/ncomms6609 Physical Sciences  Optical physics      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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