Nature Communications - 11 June 2014

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Weekly Content Alert 11 June 2014  Featured image: Schwarz et al. fabricate an integrated laser and detector on a chip, exploiting the mid-infrared spectral region for molecular sensing. Latest content: Articles Journal homepage Recommend to library Web feed   Advertisement Join the most influential in European science at EuroScience Open Forum (ESOF) 2014 Copenhagen - June 21-26, 2014. More than 2500 registered already, 450 speakers, including 6 Nobels - see who here. Sign up on www.esof2014.org   Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast on: Biomarker discovery: Translating proteomics into clinical diagnostics  Now available on demand!  Sponsored by:       Latest Articles View all Articles     Generation of three-dimensional retinal tissue with functional photoreceptors from human iPSCs Xiufeng Zhong, Christian Gutierrez, Tian Xue, Christopher Hampton, M. Natalia Vergara, Li-Hui Cao, Ann Peters, Tea Soon Park, Elias T. Zambidis, Jason S. Meyer, David M. Gamm, King-Wai Yau and M. Valeria Canto-Soler Induced pluripotent stem cells (iPSCs) hold great potential for modelling human developmental processes and diseases. Here the authors induce human iPSCs to spontaneously form fully laminated three-dimensional retinal tissue containing functional photoreceptor cells. 10 June 2014 | doi: 10.1038/ncomms5047 Biological Sciences  Developmental biology  Dysregulation of hydrogen sulphide metabolism impairs oviductal transport of embryos Nannan Ning, Jianchun Zhu, Yahui Du, Xiaolin Gao, Chuanyong Liu and Jingxin Li Enzymes required for the production of hydrogen sulphide (H2S) are expressed in mammalian reproductive tracts. Here, the authors show that production of H2S regulates contraction in excised human fallopian tube samples and is required for transport of the embryo through the fallopian tube in mice. 10 June 2014 | doi: 10.1038/ncomms5107 Biological Sciences  Developmental biology  Oxytocin is an age-specific circulating hormone that is necessary for muscle maintenance and regeneration Christian Elabd, Wendy Cousin, Pavan Upadhyayula, Robert Y. Chen, Marc S. Chooljian, Ju Li, Sunny Kung, Kevin P. Jiang and Irina M. Conboy The age-related decline in the regenerative capacity of muscle can be reversed in mice by exposure to young circulation. Elabd et al. identify the hormone, oxytocin, as a potential mediator of this effect, showing that its plasma levels decline with age and that administration of oxytocin to aged mice improves muscle regeneration. 10 June 2014 | doi: 10.1038/ncomms5082 Biological Sciences  Medical research  A synthetic sex ratio distortion system for the control of the human malaria mosquito OPEN Roberto Galizi, Lindsey A. Doyle, Miriam Menichelli, Federica Bernardini, Anne Deredec, Austin Burt, Barry L. Stoddard, Nikolai Windbichler and Andrea Crisanti Extreme reproductive sex ratios could result in the suppression or elimination of pest populations. Here, the authors design a synthetic sex distortion system in Anopheles gambiae that gives rise to fertile mosquito strains that produce over 95% male offsprings and could therefore be used to suppress mosquito populations. 10 June 2014 | doi: 10.1038/ncomms4977 Biological Sciences  Biotechnology  Genetics  LSD1 promotes oxidative metabolism of white adipose tissue Delphine Duteil, Eric Metzger, Dominica Willmann, Panagiota Karagianni, Nicolaus Friedrichs, Holger Greschik, Thomas Günther, Reinhard Buettner, Iannis Talianidis, Daniel Metzger and Roland Schüle Brown adipocytes are rich in mitochondria and influence whole-body energy balance. Here, Duteil et al. show that the lysine-specific demethylase 1 (LSD1) controls mitochondrial biogenesis and the formation of brown-like adipocytes, and that LSD1 overexpression in white fat reduces weight gain of mice on a high-fat diet. 10 June 2014 | doi: 10.1038/ncomms5093 Biological Sciences  Cell biology  Medical research  A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms OPEN Gijsbert D. A. Werner, William K. Cornwell, Janet I. Sprent, Jens Kattge and E. Toby Kiers Symbiotic associations are widespread, yet their evolutionary histories remain poorly understood. Here, Werner et. al. show a single evolutionary innovation driving symbiotic nitrogen fixation, followed by multiple gains and losses of the symbiosis and the emergence of groups with stable nitrogen fixers. 10 June 2014 | doi: 10.1038/ncomms5087 Biological Sciences  Ecology  Evolution  Craniometric analysis of European Upper Palaeolithic and Mesolithic samples supports discontinuity at the Last Glacial Maximum Ciaraán Brewster, Christopher Meiklejohn, Noreen von Cramon-Taubadel and Ron Pinhasi The Last Glacial Maximum (LGM) represents the most severe climatic event since modern humans arrived in Europe and it is likely that it has changed their morphology. Here, Brewster et al. examine human cranial morphology from before and after the LGM and show significant differences across periods. 10 June 2014 | doi: 10.1038/ncomms5094 Biological Sciences  Evolution  Palaeontology  Visualization of a polytopic membrane protein during SecY-mediated membrane insertion Lukas Bischoff, Stephan Wickles, Otto Berninghausen, Eli O. van der Sluis and Roland Beckmann Membrane protein topogenesis is not fully understood, although the path that proteins take through the ribosome and Sec-complex has been described. Here, Bischoff et al. present the structure of a ribosome-SecY complex containing an intermediate of proteorhodopsin, which provides further insight into this topogenesis. 10 June 2014 | doi: 10.1038/ncomms5103 Biological Sciences  Biochemistry  Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population Susan F. Bailey, Aaron Hinz and Rees Kassen Synonymous mutations, nucleotide changes that do not alter the encoded amino acid, are usually seen not to have an effect on organism survival. Here, Bailey et al. show that two synonymous mutations in Pseudomonas fluorescens had a beneficial effect and acted via increased gene expression. 10 June 2014 | doi: 10.1038/ncomms5076 Biological Sciences  Evolution  Genetics  Microbiology  Differential developmental requirement and peripheral regulation for dermal Vγ4 and Vγ6T17 cells in health and inflammation Yihua Cai, Feng Xue, Chris Fleming, Jie Yang, Chuanlin Ding, Yunfeng Ma, Min Liu, Huang-ge Zhang, Jie Zheng, Na Xiong and Jun Yan Skin-resident IL-17-producing γδT cells play an important role in skin inflammation but their development and trafficking is not well established. Here, Cai et al. unveil differences in the developmental requirements and functional regulation of two subsets of dermal γδT cells. 09 June 2014 | doi: 10.1038/ncomms4986 Biological Sciences  Immunology  Complete determination of molecular orbitals by measurement of phase symmetry and electron density M. Wießner, D. Hauschild, C. Sauer, V. Feyer, A. Schöll and F. Reinert The position of an electron in a molecule is defined at the quantum-mechanical level by its wavefunction. Wießner et al. demonstrate a technique for imaging both the wavefunction amplitude and phase by measuring the distribution of photoelectrons generated by circularly polarized light. 09 June 2014 | doi: 10.1038/ncomms5156 Physical Sciences  Atomic and molecular physics  MRTF-A controls vessel growth and maturation by increasing the expression of CCN1 and CCN2 Rabea Hinkel, Teresa Trenkwalder, Björn Petersen, Wira Husada, Florian Gesenhues, Seungmin Lee, Ewald Hannappel, Ildiko Bock-Marquette, Daniel Theisen, Laura Leitner, Peter Boekstegers, Czeslaw Cierniewski, Oliver J. Müller, Ferdinand le Noble, Ralf H. Adams, Christine Weinl, Alfred Nordheim, Bruno Reichart, Christian Weber, Eric Olson et al. Myocardin-related transcription factors (MRTFs) increase muscle growth and regeneration. Here, Hinkel et al. show that MRTFs also promote microvessel growth and maturation in chronic ischaemic disease of the heart or peripheral muscle by increasing the expression of the pro-angiongenic factors, CCN1 and CCN2. 09 June 2014 | doi: 10.1038/ncomms4970 Biological Sciences  Medical research  Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour OPEN Giovana T. Torrezan, Elisa N. Ferreira, Adriana M. Nakahata, Bruna D. F. Barros, Mayra T. M. Castro, Bruna R. Correa, Ana C. V. Krepischi, Eloisa H. R. Olivieri, Isabela W. Cunha, Uri Tabori, Paul E. Grundy, Cecilia M. L. Costa, Beatriz de Camargo, Pedro A. F. Galante and Dirce M. Carraro Wilms tumour (WT) is the most common paediatric kidney cancer and few driver genes related to its development have been identified. Here, the authors identify DROSHA mutations that may contribute to WT tumorigenesis through their effect on primary microRNA processing. 09 June 2014 | doi: 10.1038/ncomms5039 Biological Sciences  Cancer  Genetics  Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes OPEN Nicholas E. IIott, James A. Heward, Benoit Roux, Eleni Tsitsiou, Peter S. Fenwick, Luca Lenzi, Ian Goodhead, Christiane Hertz-Fowler, Andreas Heger, Neil Hall, Louise E. Donnelly, David Sims and Mark A. Lindsay Long non-coding RNAs (lncRNAs) are important regulators of gene expression. Ilott et al. characterize changes in the expression of lncRNAs and enhancer RNAs during the inflammatory response in human monocytes and show that these RNAs can be involved in the regulation of the innate immunity. 09 June 2014 | doi: 10.1038/ncomms4979 Biological Sciences  Immunology  Human B cells induce dendritic cell maturation and favour Th2 polarization by inducing OX-40 ligand Mohan S. Maddur, Meenu Sharma, Pushpa Hegde, Emmanuel Stephen-Victor, Bali Pulendran, Srini V. Kaveri and Jagadeesh Bayry B lymphocytes can regulate dendritic cell (DC) functions, but the extent of this regulation and the functional outcomes have not been fully established. Here, the authors show that direct interaction with activated B cells induces maturation of DCs, driving the differentiation of T cells towards the Th2 subset. 09 June 2014 | doi: 10.1038/ncomms5092 Biological Sciences  Immunology  How dead ends undermine power grid stability Peter J. Menck, Jobst Heitzig, Jürgen Kurths and Hans Joachim Schellnhuber The cheapest way to add new power stations to a domestic power grid is by tree-like connections to the network. A numerical basin stability analysis of Menck et al. suggests that this undermines a grid's stability against blackouts but can be fixed with extra transmission lines to these otherwise 'dead ends'. 09 June 2014 | doi: 10.1038/ncomms4969 Physical Sciences  Theoretical physics  An RNA polymerase II-coupled function for histone H3K36 methylation in checkpoint activation and DSB repair Deepak Kumar Jha and Brian D. Strahl Chromatin modifications play a fundamental role in regulating the cellular response to DNA damage. Here, Jha and Strahl identify methylation of histone H3 on lysine 36 mediated by the histone-methyltransferase Set2 as a regulator of chromatin remodelling at double-strand breaks that affects DNA repair. 09 June 2014 | doi: 10.1038/ncomms4965 Biological Sciences  Molecular biology  Hybrid sensors based on colour centres in diamond and piezoactive layers Jianming Cai, Fedor Jelezko and Martin B. Plenio The sensitive measurement of physical quantities offers a wide range of applications in fundamental and applied science. Cai et al. propose a hybrid technology combining colour centres in diamond and piezoactive layers to realize force, pressure and electric field sensors with nanoscale resolution. 09 June 2014 | doi: 10.1038/ncomms5065 Physical Sciences  Applied physics  Atomic and molecular physics  Nanotechnology  Tcf3 promotes cell migration and wound repair through regulation of lipocalin 2 Qi Miao, Amy T. Ku, Yudai Nishino, Jeffrey M. Howard, Ajay S. Rao, Timothy M. Shaver, Gloria E. Garcia, Diep N. Le, Kristen L. Karlin, Thomas F. Westbrook, Valeria Poli and Hoang Nguyen The re-epithelialization phase in skin wound repair involves epidermal cell migration into the wound, proliferation and differentiation. Here the authors describe a role for the transcription factor Tcf3 and its target, the secreted factor lipocalin2, in cell migration during wound healing in mice. 09 June 2014 | doi: 10.1038/ncomms5088 Biological Sciences  Cell biology  Developmental biology  Restricted VH/VL usage and limited mutations in gluten-specific IgA of coeliac disease lesion plasma cells OPEN Øyvind Steinsbø, Carole J. Henry Dunand, Min Huang, Luka Mesin, Marlene Salgado-Ferrer, Knut E. A. Lundin, Jørgen Jahnsen, Patrick C. Wilson and Ludvig M. Sollid Coeliac disease is characterized by an inappropriate immune response to dietary gluten proteins, involving the production of antibodies reactive to gluten. Here, the authors study the intestinal antibody response against gluten and show that gluten-specific antibodies have a low degree of somatic hypermutations. 09 June 2014 | doi: 10.1038/ncomms5041 Biological Sciences  Immunology  Medical research  Quasi-specific access of the potassium channel inactivation gate OPEN Gaurav Venkataraman, Deepa Srikumar and Miguel Holmgren Inactivation of Shaker potassium channels is caused by one of the four cytoplasmic amino termini, termed the inactivation gate. Here, Venkataraman et al. show that a single gate threads through the intracellular entryway of its own subunit and interacts with all four subunits deeper in the pore, demonstrating the function of this N-terminus. 09 June 2014 | doi: 10.1038/ncomms5050 Biological Sciences  Biochemistry  Collective fluorescence switching of counterion-assembled dyes in polymer nanoparticles Andreas Reisch, Pascal Didier, Ludovic Richert, Sule Oncul, Youri Arntz, Yves Mély and Andrey S. Klymchenko Fluorescent organic nanoparticles are attractive alternatives to quantum dots for imaging applications. Here, the authors assemble dyes with bulky counterions inside polymer nanoparticles to achieve high fluorescence brightness, as well as a photoinducible and reversible on/off switching. 09 June 2014 | doi: 10.1038/ncomms5089 Chemical Sciences  Nanotechnology  Physical chemistry  A histone H3K36 chromatin switch coordinates DNA double-strand break repair pathway choice Chen-Chun Pai, Rachel S. Deegan, Lakxmi Subramanian, Csenge Gal, Sovan Sarkar, Elizabeth J. Blaikley, Carol Walker, Lydia Hulme, Eric Bernhard, Sandra Codlin, Jürg Bähler, Robin Allshire, Simon Whitehall and Timothy C. Humphrey DNA double strand breaks are repaired by nonhomologous end-joining (NHEJ) or homologous recombination (HR) pathways. Here, Pai et al. discover that post-translational modification of lysine 36 of histone H3 plays a key role in determining double strand repair pathway choice. 09 June 2014 | doi: 10.1038/ncomms5091 Biological Sciences  Genetics  Molecular biology  Hypoxia-inducible hydrogels Kyung Min Park and Sharon Gerecht Oxygen is vital for all multicellular organisms and oxygen deprivation, hypoxia, influences cellular functions. Here, the authors develop an oxygen-controlling hydrogel that can be used as a three-dimensional hypoxic microenvironment, and may aid the study of hypoxia-related biological conditions. 09 June 2014 | doi: 10.1038/ncomms5075 Biological Sciences  Bioengineering  Phosphatidylinositol 5-phosphate regulates invasion through binding and activation of Tiam1 Julien Viaud, Frédéric Lagarrigue, Damien Ramel, Sophie Allart, Gaëtan Chicanne, Laurie Ceccato, Delphine Courilleau, Jean-Marie Xuereb, Olivier Pertz, Bernard Payrastre and Frédérique Gaits-Iacovoni Phosphatidylinositol 5-phosphate (PtdIns5P) is known to induce actin depolymerisation and cell migration; however, the mechanisms by which this occurs remain unclear. Viaud et al. show that PtdIns5P regulates actin dynamics and invasiveness by recruiting and activating the Rac-GTPase exchange factor Tiam1. 06 June 2014 | doi: 10.1038/ncomms5080 Biological Sciences  Cell biology  Redox chemistry and metal–insulator transitions intertwined in a nano-porous material Sergey N. Maximoff and Berend Smit Interactions between nano-porous materials and gases possess rich redox chemistry. Here, the authors report a metal organic framework, a nano-porous material, that undergoes an atypical metal–insulator–metal transition intertwined with oxygen adsorption-desorption, which defies the classical picture. 06 June 2014 | doi: 10.1038/ncomms5032 Chemical Sciences  Atomic and molecular physics  Materials science  Rift migration explains continental margin asymmetry and crustal hyper-extension OPEN Sascha Brune, Christian Heine, Marta Pérez-Gussinyé and Stephan V. Sobolev During continental rifting, various stages and structures are observed, the least understood being hyper-extended continental crust at magma-poor margins. Here, the authors use finite-element thermomechanical models to investigate the mechanism causing observed margin asymmetry and crustal hyper-extension. 06 June 2014 | doi: 10.1038/ncomms5014 Earth Sciences  Geology and geophysics  Dynamic haematopoietic cell contribution to the developing and adult epicardium OPEN Gemma M. Balmer, Sveva Bollini, Karina N. Dubé, Juan Pedro Martinez-Barbera, Owen Williams and Paul R. Riley The murine epicardium forms an envelope around the heart and contains cells that can participate in cardiac repair. Here the authors discover a population of epicardial cells derived from blood cells, which proliferate and change their surrounding extracellular matrix in response to cardiac injury. 06 June 2014 | doi: 10.1038/ncomms5054 Biological Sciences  Medical research  Roaming dynamics in radical addition–elimination reactions Baptiste Joalland, Yuanyuan Shi, Alexander Kamasah, Arthur G. Suits and Alexander M. Mebel Roaming dynamics have been shown to be important in unimolecular decompositions, but the relevance to bimolecular reactions has been less clear. Here, the authors study radical addition/elimination reactions and implicate a roaming transition state in a bimolecular reaction. 06 June 2014 | doi: 10.1038/ncomms5064 Chemical Sciences  Atmospheric science  Atomic and molecular physics  Physical chemistry  Singlet oxygen triplet energy transfer-based imaging technology for mapping protein–protein proximity in intact cells Tsz-Leung To, Michael J. Fadul and Xiaokun Shu Fluorescence imaging can be used for the characterization of protein interactions in cells, although typical methods require the interacting groups to be quite close. Here, the authors present a fluorescent technique using singlet oxygen for the imaging of more distant protein–protein interactions. 06 June 2014 | doi: 10.1038/ncomms5072 Biological Sciences  Biochemistry  Cell biology  Monolithically integrated mid-infrared lab-on-a-chip using plasmonics and quantum cascade structures OPEN Benedikt Schwarz, Peter Reininger, Daniela Ristanić, Hermann Detz, Aaron Maxwell Andrews, Werner Schrenk and Gottfried Strasser Quantum cascade lasers and detectors enable photonic integration of semiconductor devices across a broad spectral range. Here, Schwarz et al. present a bi-functional laser and detector structure, monolithically integrated with plasmonic waveguides for mid-infrared chemical sensors on a chip. 06 June 2014 | doi: 10.1038/ncomms5085 Physical Sciences  Optical physics  Antigen capture and archiving by lymphatic endothelial cells following vaccination or viral infection Beth A. Tamburini, Matthew A. Burchill and Ross M. Kedl Viral antigens can persist within the secondary lymphoid tissues of the host for many weeks after resolution of the infection. Tamburini et al. demonstrate that antigens remaining following viral infection or vaccination can be captured and maintained for extended periods of time by lymphatic endothelial cells. 06 June 2014 | doi: 10.1038/ncomms4989 Biological Sciences  Immunology  Atomic Auger Doppler effects upon emission of fast photoelectrons Marc Simon, Ralph Püttner, Tatiana Marchenko, Renaud Guillemin, Rajesh K. Kushawaha, Loïc Journel, Gildas Goldsztejn, Maria Novella Piancastelli, James M. Ablett, Jean-Pascal Rueff and Denis Céolin During photoionization, the recoil of the atom or molecule due to the ejected electron can subtly alter the observed photoelectron and Auger spectra from expectations. Here, the authors study Auger emission from isolated neon atoms and see a Doppler shift in the spectrum resulting from translation recoil. 06 June 2014 | doi: 10.1038/ncomms5069 Physical Sciences  Atomic and molecular physics  Evidence of natural Wolbachia infections in field populations of Anopheles gambiae OPEN Francesco Baldini, Nicola Segata, Julien Pompon, Perrine Marcenac, W. Robert Shaw, Roch K. Dabiré, Abdoulaye Diabaté, Elena A. Levashina and Flaminia Catteruccia Wolbachia bacteria live within the cells of many insect species, manipulating their hosts' reproduction and immune responses. Here, the authors show that these microbes also infect wild populations of malaria-spreading Anopheles mosquitoes, supporting a potential use of Wolbachia to limit malaria transmission. 06 June 2014 | doi: 10.1038/ncomms4985 Biological Sciences  Microbiology  iPSC-derived neurons from GBA1-associated Parkinson's disease patients show autophagic defects and impaired calcium homeostasis David C. Schöndorf, Massimo Aureli, Fiona E. McAllister, Christopher J. Hindley, Florian Mayer, Benjamin Schmid, S. Pablo Sardi, Manuela Valsecchi, Susanna Hoffmann, Lukas Kristoffer Schwarz, Ulrike Hedrich, Daniela Berg, Lamya S. Shihabuddin, Jing Hu, Jan Pruszak, Steven P. Gygi, Sandro Sonnino, Thomas Gasser and Michela Deleidi Mutations in the gene, GBA1, cause Gaucher's disease, and are a strong risk factor for the development of Parkinson's disease. Here the authors use cells derived from Parkinson's patients with GBA1 mutations to model the disease, and reveal changes in cellular recycling systems that may promote neurodegeneration. 06 June 2014 | doi: 10.1038/ncomms5028 Biological Sciences  Cell biology  Medical research  Proliferation of neutral modes in fractional quantum Hall states Hiroyuki Inoue, Anna Grivnin, Yuval Ronen, Moty Heiblum, Vladimir Umansky and Diana Mahalu The accepted picture of transport in the fractional quantum Hall effect regime is that neutral modes are present only in hole-conjugate fractional states. Inoue et al. show the presence of upstream neutral modes and energy transport through the bulk in all tested non-hole-conjugate fractional states. 06 June 2014 | doi: 10.1038/ncomms5067 Physical Sciences  Applied physics  Condensed matter  Graphitic nanostripes in silicon carbide surfaces created by swift heavy ion irradiation Oliver Ochedowski, Orkhan Osmani, Martin Schade, Benedict Kleine Bussmann, Brigitte Ban-d'Etat, Henning Lebius and Marika Schleberger Defects alter the properties of silicon carbide structures, but the introduction of these defects in a controlled manner remains a challenge. Here, the authors show that swift heavy ions can create graphitic grooves if the irradiation is at grazing angles of incidence. 06 June 2014 | doi: 10.1038/ncomms4913 Physical Sciences  Materials science  A functional network perspective on response inhibition and attentional control OPEN Michelle Erika-Florence, Robert Leech and Adam Hampshire The right inferior frontal cortex has long been thought to house a neural module that inhibits dominant behaviours. Using brain imaging, Erika-Florence et al. demonstrate that this inhibition is in fact an emergent property of multiple neural networks that support broader classes of cognitive processes. 06 June 2014 | doi: 10.1038/ncomms5073 Biological Sciences  Neuroscience  Cortical representations of confidence in a visual perceptual decision Leopold Zizlsperger, Thomas Sauvigny, Barbara Händel and Thomas Haarmeier Visual attention is known to affect choice certainty, but exactly how is unclear. Here, the authors use electroencephalography in a visual motion discrimination task and identify neural correlates of choice certainty, which precede the decided action. 05 June 2014 | doi: 10.1038/ncomms4940 Biological Sciences  Neuroscience  Extreme surface propensity of halide ions in water Lukasz Piatkowski, Zhen Zhang, Ellen H. G. Backus, Huib J. Bakker and Mischa Bonn The surface chemistry of aqueous solutions plays a ubiquitous role in many chemical and biological processes. Here, the authors probe the surfaces of sodium halide solutions with surface-specific femtosecond vibrational spectroscopy, and observe surface concentrations of halide ions several times greater than in the bulk. 05 June 2014 | doi: 10.1038/ncomms5083 Chemical Sciences  Physical chemistry  Hybrid multiphoton volumetric functional imaging of large-scale bioengineered neuronal networks Hod Dana, Anat Marom, Shir Paluch, Roman Dvorkin, Inbar Brosh and Shy Shoham Three-dimensional neural networks are promising models of nervous tissues, which could aid our understanding of their structure and function. Here, the authors present advanced methods for studying volumetric activity in three-dimensional cultures of neural cells in hydrogels. 05 June 2014 | doi: 10.1038/ncomms4997 Biological Sciences  Neuroscience  Optical physics  Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses Rui Xu, Huaidong Jiang, Changyong Song, Jose A. Rodriguez, Zhifeng Huang, Chien-Chun Chen, Daewoong Nam, Jaehyun Park, Marcus Gallagher-Jones, Sangsoo Kim, Sunam Kim, Akihiro Suzuki, Yuki Takayama, Tomotaka Oroguchi, Yukio Takahashi, Jiadong Fan, Yunfei Zou, Takaki Hatsui, Yuichi Inubushi, Takashi Kameshima et al. Three-dimensional imaging is typically complex and time consuming. Here, the authors report the use of X-ray free-electron laser pulses for single-shot three-dimensional imaging of nanocrystals at ~5.5 nm resolution, using the symmetry in the nanocrystal and the curvature of the Ewald sphere. 05 June 2014 | doi: 10.1038/ncomms5061 Physical Sciences  Materials science  The PH gene determines fruit acidity and contributes to the evolution of sweet melons Shahar Cohen, Maxim Itkin, Yelena Yeselson, Galil Tzuri, Vitaly Portnoy, Rotem Harel-Baja, Shery Lev, Uzi Sa'ar, Rachel Davidovitz-Rikanati, Nadine Baranes, Einat Bar, Dalia Wolf, Marina Petreikov, Shmuel Shen, Shifra Ben-Dor, Ilana Rogachev, Asaph Aharoni, Tslil Ast, Maya Schuldiner, Eduard Belausov et al. Fruit acidity is an important factor affecting fleshy fruit taste. Here, the authors identify the PH gene that regulates fruit acidity in a number of species and report a mutation that is responsible for the diversification and evolution of the sweet melon. 05 June 2014 | doi: 10.1038/ncomms5026 Biological Sciences  Evolution  Genetics  ADAM metalloproteases promote a developmental switch in responsiveness to the axonal repellant Sema3A Erez Romi, Irena Gokhman, Eitan Wong, Niv Antonovsky, Andreas Ludwig, Irit Sagi, Paul Saftig, Marc Tessier-Lavigne and Avraham Yaron The basic axonal wiring of the vertebrate nervous system is set up during embryonic development, and during this process axons gain or lose sensitivity to guidance cues. Here the authors show that in proprioceptive axons, two members of the ADAM metalloproteinase family promote loss of responsiveness to Sema3A, via cleavage of its receptor Neuropilin-1. 05 June 2014 | doi: 10.1038/ncomms5058 Biological Sciences  Developmental biology  Neuroscience  Overproduction of stomatal lineage cells in Arabidopsis mutants defective in active DNA demethylation Chizuko Yamamuro, Daisuke Miki, Zhimin Zheng, Jun Ma, Jing Wang, Zhenbiao Yang, Juan Dong and Jian-Kang Zhu Loss of active DNA demethylation increases DNA methylation at numerous loci in plant vegetative tissues; however, resulting developmental phenotypes have not been observed. Yamamuro et al. show that mutation of the 5-methylcytosine DNA glycosylase ROS1 results in overproduction of stomatal lineage cells in Arabidopsis. 05 June 2014 | doi: 10.1038/ncomms5062 Biological Sciences  Developmental biology  Molecular biology  Plant sciences  Distinct roles for BAI1 and TIM-4 in the engulfment of dying neurons by microglia Fargol Mazaheri, Oksana Breus, Sevi Durdu, Petra Haas, Jochen Wittbrodt, Darren Gilmour and Francesca Peri The removal of dying neurons by microglia plays a key role in both vertebrate nervous system development and several diseases. Here, the authors use a quantitative live imaging approach to investigate neuronal-microglial interactions at single-cell resolution and establish the functions of the phosphatidylserine receptors, TIM-4 and BAI1, in neuronal engulfment. 05 June 2014 | doi: 10.1038/ncomms5046 Biological Sciences  Developmental biology  Neuroscience  All-printable band-edge modulated ZnO nanowire photodetectors with ultra-high detectivity OPEN Xi Liu, Leilei Gu, Qianpeng Zhang, Jiyuan Wu, Yunze Long and Zhiyong Fan Nanowire photodetectors offer a high sensitivity arising from their geometry that makes them of interest for optoelectronic devices. Here, the authors demonstrate the printable fabrication of ZnO nanowires with high detectivity, making them suitable for high-performance flexible electronics applications. 05 June 2014 | doi: 10.1038/ncomms5007 Physical Sciences  Nanotechnology  Optical physics  Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences Bo Cao, Chao Chen, Michael S. DeMott, Qiuxiang Cheng, Tyson A. Clark, Xiaolin Xiong, Xiaoqing Zheng, Vincent Butty, Stuart S. Levine, George Yuan, Matthew Boitano, Khai Luong, Yi Song, Xiufen Zhou, Zixin Deng, Stephen W. Turner, Jonas Korlach, Delin You, Lianrong Wang, Shi Chen et al. Phosphorothioate (PT) DNA modifications are widespread in bacteria and play a critical role in cell physiology. Here, the authors develop two sequence-based technologies to map PT modifications across bacterial genomes. 05 June 2014 | doi: 10.1038/ncomms4951 Biological Sciences  Cell biology  Genetics  Design amphiphilic dipolar π-systems for stimuli-responsive luminescent materials using metastable states Shiki Yagai, Satoru Okamura, Yujiro Nakano, Mitsuaki Yamauchi, Keiki Kishikawa, Takashi Karatsu, Akihide Kitamura, Akira Ueno, Daiki Kuzuhara, Hiroko Yamada, Tomohiro Seki and Hajime Ito Some π-conjugated molecules exhibit tunable luminescence—a property that is useful for the next generation of optical devices. Yagai et al. propose a strategy to design these materials on a molecular level, which tailors the emission colour via structural changes in response to mechanical stimuli. 05 June 2014 | doi: 10.1038/ncomms5013 Chemical Sciences  Materials science  Optical physics  Organic chemistry  Mapping polarization induced surface band bending on the Rashba semiconductor BiTeI OPEN Christopher John Butler, Hung-Hsiang Yang, Jhen-Yong Hong, Shih-Hao Hsu, Raman Sankar, Chun-I Lu, Hsin-Yu Lu, Kui-Hon Ou Yang, Hung-Wei Shiu, Chia-Hao Chen, Chao-Cheng Kaun, Guo-Jiun Shu, Fang-Cheng Chou and Minn-Tsong Lin Surfaces of semiconductors exhibiting large Rasha effect are of great interest for spintronics applications. Here, Butler et al. present the spectroscopic observation and microscopic mapping of termination-dependent band-bending at the surface of Rashba semiconductor BiTeI. 05 June 2014 | doi: 10.1038/ncomms5066 Physical Sciences  Applied physics  Condensed matter  Lateralized enhancement of auditory cortex activity and increased sensitivity to self-generated sounds Daniel Reznik, Yael Henkin, Noa Schadel and Roy Mukamel Self-generated sounds and externally generated sounds are both processed in the auditory cortex, but it is unclear how. Daniel et al. find that compared to externally generated sounds, self-generated sounds produce enhanced responses in the auditory cortex that are due to motor cortex corollary discharges. 05 June 2014 | doi: 10.1038/ncomms5059 Biological Sciences  Neuroscience  Intramuscular adipogenesis is inhibited by myo-endothelial progenitors with functioning Bmpr1a signalling Ping Huang, Tim J. Schulz, Ariane Beauvais, Yu-Hua Tseng and Emanuela Gussoni Bmp signalling is required for adult muscle maintenance and growth. Here, the authors show that ablating the expression of Bmp receptor 1a in mouse myo-endothelial cells increases intramuscular adipogenesis. 05 June 2014 | doi: 10.1038/ncomms5063 Biological Sciences  Developmental biology  A Snail1/Notch1 signalling axis controls embryonic vascular development Zhao-Qiu Wu, R. Grant Rowe, Kim-Chew Lim, Yongshun Lin, Amanda Willis, Yi Tang, Xiao-Yan Li, Jacques E. Nor, Ivan Maillard and Stephen J. Weiss Notch1 signalling and the dosage of the Notch1 ligand, Dll4, are critical for vascular development. Here the authors show that the transcriptional repressor, Snail1, is expressed in endothelial cells, where it regulates vascular development by downregulating Dll4 levels and Notch1 signalling during mouse embryogenesis. 04 June 2014 | doi: 10.1038/ncomms4998 Biological Sciences  Developmental biology  Halogen-bonded mesogens direct polymer self-assemblies up to millimetre length scale OPEN Nikolay Houbenov, Roberto Milani, Mikko Poutanen, Johannes Haataja, Valentina Dichiarante, Jani Sainio, Janne Ruokolainen, Giuseppe Resnati, Pierangelo Metrangolo and Olli Ikkala Achieving polymeric self-assemblies that are macroscopically aligned up to millimetre length scale remains challenging. Here, Houbenov et al. tackle this problem in a model polymer system, which exhibits an efficient spontaneous organization guided by halogen bonding without external stimuli. 04 June 2014 | doi: 10.1038/ncomms5043 Chemical Sciences  Materials science  Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action Dominic Birth, Wei-Chun Kao and Carola Hunte Atovaquone is an antimalarial drug that inhibits a crucial enzyme, cytochrome bc1 complex, within the parasite's mitochondria. Here the authors report the crystal structure of the enzyme with bound atovaquone, opening the way for rational development of improved antimalarial drugs. 04 June 2014 | doi: 10.1038/ncomms5029 Biological Sciences  Biochemistry  Chemical biology  Molecular biology  Dicke-type phase transition in a spin-orbit-coupled Bose–Einstein condensate Chris Hamner, Chunlei Qu, Yongping Zhang, JiaJia Chang, Ming Gong, Chuanwei Zhang and Peter Engels Spin-orbit coupling in a Bose–Einstein condensate provides an additional degree of freedom to explore interesting phenomena. Hamner et al. study the ground state of such a system and show that it exhibits a transition between normal and superradiant phases that can be described by the Dicke model. 04 June 2014 | doi: 10.1038/ncomms5023 Physical Sciences  Atomic and molecular physics  Optical physics  Synaptic recruitment of gephyrin regulates surface GABAA receptor dynamics for the expression of inhibitory LTP OPEN Enrica Maria Petrini, Tiziana Ravasenga, Torben J. Hausrat, Giuliano Iurilli, Umberto Olcese, Victor Racine, Jean-Baptiste Sibarita, Tija C. Jacob, Stephen J. Moss, Fabio Benfenati, Paolo Medini, Matthias Kneussel and Andrea Barberis GABA receptors are implicated in neuronal postsynaptic long-term potentiation of inhibition (iLTP). Here, Petrini et al. show that iLTP depends on recruitment of the scaffold protein gephyrin at synapses, which is enhanced by CaMKII-dependent phosphorylation of a specific residue on GABAA receptors. 04 June 2014 | doi: 10.1038/ncomms4921 Biological Sciences  Neuroscience  Orbitofrontal neurons infer the value and identity of predicted outcomes Thomas A. Stalnaker, Nisha K. Cooch, Michael A. McDannald, Tzu-Lan Liu, Heather Wied and Geoffrey Schoenbaum Orbitofrontal cortex neuronal activity is thought to represent expected outcomes based on inferred states. Here, the authors show definitively that orbitofrontal cortex activity represents features of expected outcomes through inferred rather than experienced information, which is not dependent on the outcome value. 04 June 2014 | doi: 10.1038/ncomms4926 Biological Sciences  Neuroscience  Cathepsin K-mediated notch1 activation contributes to neovascularization in response to hypoxia Haiying Jiang, Xian Wu Cheng, Guo-Ping Shi, Lina Hu, Aiko Inoue, Yumiko Yamamura, Hongxian Wu, Kyosuke Takeshita, Xiang Li, Zhe Huang, Haizhen Song, Masashi Asai, Chang-Ning Hao, Kazumasa Unno, Teruhiro Koike, Yoshiharu Oshida, Kenji Okumura, Toyoaki Murohara and Masafumi Kuzuya The cathepsin family of proteases cleaves intracellular as well as extracellular proteins. Here the authors implicate cathepsin K in ischaemia-induced neovascularization by showing that cathepsin K increases the levels of cleaved Notch1 and downstream Notch signalling in endothelial cells. 04 June 2014 | doi: 10.1038/ncomms4838 Biological Sciences  Medical research  Tailoring gadolinium-doped ceria-based solid oxide fuel cells to achieve 2 Wcm-2 at 550 °C Jin Goo Lee, Jeong Ho Park and Yong Gun Shul In low-temperature solid oxide fuel cells, power losses due to large ohmic resistances and activation barriers of ion transport are a common problem. Here, Lee et al. report a gadolinium-doped ceria-based solid oxide fuel cell, which overcomes the problem and achieves a power density of 2 Wcm-2. 04 June 2014 | doi: 10.1038/ncomms5045 Chemical Sciences  Inorganic chemistry  Materials science  Light-inducible receptor tyrosine kinases that regulate neurotrophin signalling Ki-Young Chang, Doyeon Woo, Hyunjin Jung, Sangkyu Lee, Sungsoo Kim, Joungha Won, Taeyoon Kyung, Hyerim Park, Nury Kim, Hee Won Yang, Jae-Yong Park, Eun Mi Hwang, Daesoo Kim and Won Do Heo Optogenetic tools allow fine spatial control of signalling pathways using light. Chang et al. present a strategy for constructing light-sensitive receptor tyrosine kinases and demonstrate that optogenetic stimulation of Trk receptors in neurons promotes neurite outgrowth. 04 June 2014 | doi: 10.1038/ncomms5057 Biological Sciences  Bioengineering  Cell biology  Expanded graphite as superior anode for sodium-ion batteries Yang Wen, Kai He, Yujie Zhu, Fudong Han, Yunhua Xu, Isamu Matsuda, Yoshitaka Ishii, John Cumings and Chunsheng Wang Graphite is a common anode material for lithium-ion batteries, but small interlayer spacing makes it unsuitable for sodium-ion batteries. Here, Wen et al. synthesize a graphite material with expanded layer distances, which could be a promising anodic material for sodium-ion batteries. 04 June 2014 | doi: 10.1038/ncomms5033 Chemical Sciences  Materials science  Physical chemistry  Ulk1-mediated Atg5-independent macroautophagy mediates elimination of mitochondria from embryonic reticulocytes Shinya Honda, Satoko Arakawa, Yuya Nishida, Hirofumi Yamaguchi, Eiichi Ishii and Shigeomi Shimizu An alternative form of autophagy that operates independently of Atg5 has been described; however, its physiological significance remains unclear. Honda et al. show that Atg5-independent autophagy is required for the efficient removal of mitochondria from reticulocytes in both embryonic and stress-induced erythropoiesis. 04 June 2014 | doi: 10.1038/ncomms5004 Biological Sciences  Cell biology  The FAM3 superfamily member ILEI ameliorates Alzheimer's disease-like pathology by destabilizing the penultimate amyloid-β precursor Hiroshi Hasegawa, Lei Liu, Ikuo Tooyama, Shigeo Murayama and Masaki Nishimura γ-secretase is a major target for treating Alzheimer's disease (AD). Here, the authors screen various binding proteins against the γ-secretase complex and find that the evolutionarily conserved secretory protein ILEI interferes with γ-secretase-dependent production of β-amyloid, which is implicated in AD. 04 June 2014 | doi: 10.1038/ncomms4917 Biological Sciences  Medical research  Neuroscience  Ultrafast acousto-plasmonic control and sensing in complex nanostructures Kevin O'Brien, N. D. Lanzillotti-Kimura, Junsuk Rho, Haim Suchowski, Xiaobo Yin and Xiang Zhang The nanometre length scale of plasmonic structures leads to vibrational dynamics at high frequencies, which could be exploited for sensitive optical detectors. O'Brien et al. show that they can detect spatial properties of phonon modes in multimodal plasmonic structures, revealing complex nanomechanical dynamics. 04 June 2014 | doi: 10.1038/ncomms5042 Physical Sciences  Nanotechnology  Optical physics  Homeostatic control of polo-like kinase-1 engenders non-genetic heterogeneity in G2 checkpoint fidelity and timing OPEN Hongqing Liang, Alessandro Esposito, Siddharth De, Suzan Ber, Philippe Collin, Uttam Surana and Ashok R. Venkitaraman Cells exposed to DNA damage delay mitotic entry to allow repair. Liang et al. unexpectedly find that the duration of arrest and the completeness of repair vary from cell to cell, determined by progressively increasing polo-like kinase-1 activity, which must pass a threshold to trigger mitosis. 04 June 2014 | doi: 10.1038/ncomms5048 Biological Sciences  Cell biology  Two-way traffic of glycoside hydrolase family 18 processive chitinases on crystalline chitin Kiyohiko Igarashi, Takayuki Uchihashi, Taku Uchiyama, Hayuki Sugimoto, Masahisa Wada, Kazushi Suzuki, Shohei Sakuda, Toshio Ando, Takeshi Watanabe and Masahiro Samejima The degradation of chitin and cellulose is dependent on the processivity of degrading enzymes. Here, Igarashi et al. use high-speed atomic force microscopy to visualize the movement of two chitinases (ChiA and ChiB) and show them to move in opposite directions, allowing a molecular mechanism to be proposed. 04 June 2014 | doi: 10.1038/ncomms4975 Biological Sciences  Biochemistry  Biophysics  Tailoring magnetic skyrmions in ultra-thin transition metal films Bertrand Dupé, Markus Hoffmann, Charles Paillard and Stefan Heinze Skyrmions—magnetic vortices that can behave like particles—have recently been observed in ultra-thin transition metal films. Dupé et al. show how the structure and composition of the interface influence the size and stability of the skyrmions. 04 June 2014 | doi: 10.1038/ncomms5030 Physical Sciences  Condensed matter    Nature Communications JOBS of the week Research Technician University of Bristol Research Associate Imperial College London PhD Fellowships Universität Konstanz Postdoctoral Scholar University of Chicago Postdoctoral Associate Sanford Bunrham Medical Research Institute Post Doctoral Scientist The George Washington University Postdoctoral Research Scientist University of Oxford PhD Position Philipps-Universität Marburg Senior Research Assistant The Babraham Institute PhD Student Position University of Twente (UT) More Science jobs from Nature Communications EVENT International Study Group for Systems Biology 2014: From Cell to Organism 02.09.14 Durham, UK More science events from     Advertisement   A new online open access multi-and interdisciplinary journal dedicated to publishing the finest research on microbial biofilms and microbiomes. 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