Nature Communications - 15 January 2014

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Weekly Content Alert 15 January 2014  Featured image: Wang et al. sequence the locust genome and identify genes that may serve as potential targets for sustainable pest management. Latest content: Articles Erratum Journal homepage Recommend to library Web feed   Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast series: Drugging the Human Methylome   Two independent, but complimentary, webcasts and live Q & A's broadcasting on:   21 January    23 January    Sponsored by: Epizyme      Latest Articles View all Articles     The locust genome provides insight into swarm formation and long-distance flight OPEN Xianhui Wang, Xiaodong Fang, Pengcheng Yang, Xuanting Jiang, Feng Jiang, Dejian Zhao, Bolei Li, Feng Cui, Jianing Wei, Chuan Ma, Yundan Wang, Jing He, Yuan Luo, Zhifeng Wang, Xiaojiao Guo, Wei Guo, Xuesong Wang, Yi Zhang, Meiling Yang, Shuguang Hao et al. Locusts are destructive agricultural pests and serve as a model organism for studies of insects. Here, the authors report a draft genome sequence of the migratory locust, Locusta migratoria, and provide insight into genes associated with key survival traits such as phase-change, long-distance migration and feeding. 14 January 2014 | doi: 10.1038/ncomms3957 Biological Sciences  Evolution  Genetics  Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease Adil Mardinoglu, Rasmus Agren, Caroline Kampf, Anna Asplund, Mathias Uhlen and Jens Nielsen Alterations in hepatocyte metabolism can lead to disorders such as non-alcoholic steatohepatitis (NASH). Here the authors create a comprehensive model of hepatocyte metabolism and use it to identify metabolic pathways altered in disease, revealing that serine levels are reduced in patients with NASH. 14 January 2014 | doi: 10.1038/ncomms4083 Biological Sciences  Medical research  Systems biology  Imprintable membranes from incomplete chiral coalescence Mark J. Zakhary, Thomas Gibaud, C. Nadir Kaplan, Edward Barry, Rudolf Oldenbourg, Robert B. Meyer and Zvonimir Dogic Conventional coalescence at fluid drop and bubble interfaces follows the all-or-none rule. Zakhary et al. show that the coalescence between colloidal membranes composed of aligned rod-like viruses does not follow this rule, but exhibits an intermediate state induced by topological defects. 14 January 2014 | doi: 10.1038/ncomms4063 Physical Sciences  Condensed matter  Fluids and plasma physics  Topological zoo of free-standing knots in confined chiral nematic fluids David Seč, Simon Čopar and Slobodan Žumer Knotted structures can be stabilized in nematic liquid crystals using colloidal particles. Here the authors demonstrate theoretically and numerically that metastable free-standing knots can also be realized in cholesteric droplets, and their topology is determined by chirality and confinement conditions. 14 January 2014 | doi: 10.1038/ncomms4057 Physical Sciences  Condensed matter  Theoretical physics  Efficient genome engineering by targeted homologous recombination in mouse embryos using transcription activator-like effector nucleases Daniel Sommer, Annika Peters, Tristan Wirtz, Maren Mai, Justus Ackermann, Yasser Thabet, Jürgen Schmidt, Heike Weighardt, F. Thomas Wunderlich, Joachim Degen, Joachim L. Schultze and Marc Beyer Genetically engineered mice are an important aspect of human disease research. Here, the authors use artificial transcription activator-like effector-nucleases to generate a mouse line with a conditionally targeted allele and suggest that this method can be easily adapted to any gene in the mouse genome. 13 January 2014 | doi: 10.1038/ncomms4045 Biological Sciences  Biotechnology  Developmental biology  Guidance of subcellular tubulogenesis by actin under the control of a synaptotagmin-like protein and Moesin OPEN N. JayaNandanan, Renjith Mathew and Maria Leptin The terminal branches of the Drosophila tracheal network have intracellular tubules that grow through elongation of membrane invaginations. Here, the authors identify the synaptotagmin-like protein Bitesize as a regulator of actin-dependent luminal membrane morphogenesis. 13 January 2014 | doi: 10.1038/ncomms4036 Biological Sciences  Cell biology  Developmental biology  Hydrogen-free graphene edges Kuang He, Gun-Do Lee, Alex W. Robertson, Euijoon Yoon and Jamie H. Warner The local coordination of the edge atoms of graphene may affect its electronic or magnetic properties. Here the authors experimentally demonstrate that non-functionalized graphene edges can exist in vacuum, contrary to some previous theoretical predictions 13 January 2014 | doi: 10.1038/ncomms4040 Chemical Sciences  Materials science  Nanotechnology  Structural basis for microtubule recognition by the human kinetochore Ska complex OPEN Maria Alba Abad, Bethan Medina, Anna Santamaria, Juan Zou, Carla Plasberg-Hill, Arumugam Madhumalar, Uma Jayachandran, Patrick Marc Redli, Juri Rappsilber, Erich A. Nigg and A. Arockia Jeyaprakash Kinetochores must interact with both polymerizing (straight) and depolymerizing (curved) microtubules to ensure correct mitotic chromosome segregation. Abad et al. reveal how this flexibility is achieved through structural characterization of the interactions between microtubules and the kinetochore protein Ska1. 13 January 2014 | doi: 10.1038/ncomms3964 Biological Sciences  Cell biology  Structure of the mammalian oligosaccharyl-transferase complex in the native ER protein translocon Stefan Pfeffer, Johanna Dudek, Marko Gogala, Stefan Schorr, Johannes Linxweiler, Sven Lang, Thomas Becker, Roland Beckmann, Richard Zimmermann and Friedrich Förster Proteins that are translocated across the endoplasmic reticulum (ER) membrane may be subject to glycosylation during transport. Using cryoelectron microscopy of native ER membranes, Pfeffer et al. map the location of oligosaccharyl-transferase within the translocon, providing insight into how these processes are coupled. 10 January 2014 | doi: 10.1038/ncomms4072 Biological Sciences  Biochemistry  Cell biology  A fluorinated dendrimer achieves excellent gene transfection efficacy at extremely low nitrogen to phosphorus ratios Mingming Wang, Hongmei Liu, Lei Li and Yiyun Cheng Polymers represent promising gene vectors due to their high efficiency and low cytotoxicity. Here, the authors show that fluorination increases gene transfection efficacy, while reducing cytotoxicity, and suggest an important role for this strategy in the design of efficient gene vectors. 10 January 2014 | doi: 10.1038/ncomms4053 Biological Sciences  Biotechnology  Eye position information is used to compensate the consequences of ocular torsion on V1 receptive fields N. Daddaoua, P. W. Dicke and P. Thier The receptive fields of neurons in the primary visual cortex are generally believed to be activated by eye movement-induced retinal stimulation. In this study, the authors show that a substantial proportion of primary visual cortex neurons are in fact responsive to head movements. 10 January 2014 | doi: 10.1038/ncomms4047 Biological Sciences  Neuroscience  Mia40 targets cysteines in a hydrophobic environment to direct oxidative protein folding in the mitochondria Johanna R. Koch and Franz X. Schmid Proteins containing multiple disulphide bonds fold more efficiently if these bonds are formed in a defined order. Koch et al. find that the mitochondrial thiol oxidase Mia40 achieves this by preferentially targeting cysteine residues within a hydrophobic context. 10 January 2014 | doi: 10.1038/ncomms4041 Biological Sciences  Cell biology  A fully genetically encoded protein architecture for optical control of peptide ligand concentration Daniel Schmidt, Paul W. Tillberg, Fei Chen and Edward S. Boyden The design of optogenetic tools to control ion channel function typically requires careful consideration of channel structure. Schmidt et al. present a modular strategy to engineer light sensitivity in several K+ channels, which functions independently of exogenous chemical modulators. 10 January 2014 | doi: 10.1038/ncomms4019 Biological Sciences  Biochemistry  Biophysics  Neuroscience  Multiple recent horizontal transfers of a large genomic region in cheese making fungi OPEN Kevin Cheeseman, Jeanne Ropars, Pierre Renault, Joëlle Dupont, Jérôme Gouzy, Antoine Branca, Anne-Laure Abraham, Maurizio Ceppi, Emmanuel Conseiller, Robert Debuchy, Fabienne Malagnac, Anne Goarin, Philippe Silar, Sandrine Lacoste, Erika Sallet, Aaron Bensimon, Tatiana Giraud and Yves Brygoo Horizontal gene transfers are known to play an important role in prokaryote evolution but their impact and prevalence in eukaryotes is less clear. Here, the authors sequence the genomes of cheese making fungi P. roqueforti and P. camemberti, and provide evidence for recent horizontal transfers of a large genomic region. 10 January 2014 | doi: 10.1038/ncomms3876 Biological Sciences  Evolution  Genetics  Quantifying interface and bulk contributions to spin–orbit torque in magnetic bilayers Xin Fan, Halise Celik, Jun Wu, Chaoying Ni, Kyung-Jin Lee, Virginia O. Lorenz and John Q. Xiao Spin–orbit-driven effects are of great interest for spintronic applications but the underlying mechanisms are challenging to probe. Here, the authors develop a sensitive spin–orbit torque magnetometer to quantify the interface and bulk contributions to the spin–orbit torques in magnetic bilayers. 09 January 2014 | doi: 10.1038/ncomms4042 Physical Sciences  Applied physics  Condensed matter  Nanotechnology  Snail1-dependent control of embryonic stem cell pluripotency and lineage commitment Yongshun Lin, Xiao-Yan Li, Amanda L. Willis, Chengyu Liu, Guokai Chen and Stephen J. Weiss Factors inducing epithelial to mesenchymal transition, such as the transcriptional repressor Snail1, have been implicated in cancer stem cell development and function. Here Lin et al. report that endogenous Snail1 is not required for embryonic stem cell pluripotency and self-renewal, but rather regulates Wnt-induced epiblast differentiation. 09 January 2014 | doi: 10.1038/ncomms4070 Biological Sciences  Developmental biology  Evidence for spin selectivity of triplet pairs in superconducting spin valves N. Banerjee, C. B. Smiet, R. G. J. Smits, A. Ozaeta, F. S. Bergeret, M. G. Blamire and J. W. A. Robinson Ferromagnets are an integral part of spintronics because of their spin selectivity, but in combination with superconductors selectivity between different Cooper pairs is required. Here, the authors find evidence for this selectivity in a ferromagnet–superconductor–ferromagnet spin valve. 09 January 2014 | doi: 10.1038/ncomms4048 Physical Sciences  Applied physics  Condensed matter  Manipulating surface reactions in lithium–sulphur batteries using hybrid anode structures Cheng Huang, Jie Xiao, Yuyan Shao, Jianming Zheng, Wendy D. Bennett, Dongping Lu, Saraf V. Laxmikant, Mark Engelhard, Liwen Ji, Jiguang Zhang, Xiaolin Li, Gordon L. Graff and Jun Liu Operation of lithium–sulphur batteries suffers from uncontrolled lithium polysulphide formation and corrosion at the anode. Huang et al. design an integrated anode structure composed of electrically connected graphite and lithium metal, which alleviates the problems and leads to high battery performance. 09 January 2014 | doi: 10.1038/ncomms4015 Chemical Sciences  Materials science  Physical chemistry  Non-classicality of the molecular vibrations assisting exciton energy transfer at room temperature OPEN Edward J. O'Reilly and Alexandra Olaya-Castro Understanding the possible role of quantum effects in biological systems requires identification of their non-classical features. Here, the authors study prototype dimers in photosynthetic antennae and find that vibration-assisted processes benefit from non-classical fluctuations of their collective motions. 09 January 2014 | doi: 10.1038/ncomms4012 Physical Sciences  Atomic and molecular physics  Biophysics  Theoretical physics  Structural analysis of human 2'-O-ribose methyltransferases involved in mRNA cap structure formation OPEN Miroslaw Smietanski, Maria Werner, Elzbieta Purta, Katarzyna H. Kaminska, Janusz Stepinski, Edward Darzynkiewicz, Marcin Nowotny and Janusz M. Bujnicki Human mRNA transcripts possess a 5' cap structure that is modified by methylation. Here, Smietanski et al. present the structures of human methyltransferases responsible for this reaction, revealing key differences to their viral counterparts and thereby providing a framework for targeted drug design. 09 January 2014 | doi: 10.1038/ncomms4004 Biological Sciences  Molecular biology  Hydrogen evolution from a copper(I) oxide photocathode coated with an amorphous molybdenum sulphide catalyst Carlos G. Morales-Guio, S. David Tilley, Heron Vrubel, Michael Grätzel and Xile Hu Photoelectrochemical water splitting may be used to produce hydrogen using abundant solar energy. Here, the authors fabricate layered films of amorphous molybdenum sulphide on copper(I) oxide and demonstrate the catalytic activity and enhanced stability of these devices made from earth-abundant materials. 08 January 2014 | doi: 10.1038/ncomms4059 Chemical Sciences  Catalysis  Inorganic chemistry  Materials science  Broadband terahertz generation from metamaterials Liang Luo, Ioannis Chatzakis, Jigang Wang, Fabian B. P. Niesler, Martin Wegener, Thomas Koschny and Costas M. Soukoulis Finding broadband terahertz emitters and detectors is key to developing practical terahertz technologies and to exploring fundamental nonlinear optics. Luo et al. show that split-ring-resonator metamaterials of a few tens of nanometres thickness can efficiently generate terahertz pulses up to 4 THz. 08 January 2014 | doi: 10.1038/ncomms4055 Physical Sciences  Applied physics  Optical physics  Natural wetland emissions of methylated trace elements Bas Vriens, Markus Lenz, Laurent Charlet, Michael Berg and Lenny H.E. Winkel Methane emission occurs in natural wetlands on a large scale, but the corresponding trace element emissions have not been studied. Here, the authors study selenium and arsenic emission in a pristine peatland and show that this causes large amounts of those trace elements to enter the biogeochemical cycle. 08 January 2014 | doi: 10.1038/ncomms4035 Earth Sciences  Biogeochemistry  Climate science  Reversible cyclic deformation mechanism of gold nanowires by twinning–detwinning transition evidenced from in situ TEM Subin Lee, Jiseong Im, Youngdong Yoo, Erik Bitzek, Daniel Kiener, Gunther Richter, Bongsoo Kim and Sang Ho Oh In situ studies of deformation in metal nanowires have yielded interesting results. Here, the authors perform cyclic loading on gold nanowires and observe twinning and detwinning phenomena, respectively caused by tensile and compressive loading, and elucidate the underpinning mechanism by molecular dynamics simulations. 08 January 2014 | doi: 10.1038/ncomms4033 Physical Sciences  Materials science  Dynamic heterogeneity controls diffusion and viscosity near biological interfaces Sander Pronk, Erik Lindahl and Peter M. Kasson Many biological reactions typically occur in a fluid that is near to a surface. Here, the authors apply theory used to describe glassy systems to quantitatively understand these effects, finding that correlated particle motion near the interface leads to an increase in fluid viscosity. 08 January 2014 | doi: 10.1038/ncomms4034 Physical Sciences  Materials science  Ferroelectric translational antiphase boundaries in nonpolar materials OPEN Xian-Kui Wei, Alexander K. Tagantsev, Alexander Kvasov, Krystian Roleder, Chun-Lin Jia and Nava Setter In ferroelectrics, the domain walls can have different properties than the domains themselves. Here, Wei et al. show that certain domain walls in antiferroelectric materials are ferroelectric, which makes them interesting candidates for new non-volatile memory concepts. 08 January 2014 | doi: 10.1038/ncomms4031 Physical Sciences  Applied physics  Condensed matter  Materials science  slanDCs selectively accumulate in carcinoma-draining lymph nodes and marginate metastatic cells William Vermi, Alessandra Micheletti, Silvia Lonardi, Claudio Costantini, Federica Calzetti, Riccardo Nascimbeni, Mattia Bugatti, Manuela Codazzi, Patrick C. Pinter, Knut Schäkel, Nicola Tamassia and Marco A. Cassatella slanDCs represent a population of dendritic cells whose role in cancer immune surveillance is not known. Here, the authors reveal that in cancer patients, slanDCs accumulate in the metastatic tumour-draining lymph nodes but not primary carcinoma sites, suggesting their involvement in nodal immune responses to cancer cells. 08 January 2014 | doi: 10.1038/ncomms4029 Biological Sciences  Cancer  Immunology  Medical research  A Diels–Alder super diene breaking benzene into C2H2 and C4H4 units OPEN Yusuke Inagaki, Masaaki Nakamoto and Akira Sekiguchi The stability of the benzene molecule reduces its tendency to react in ways that perturb the aromaticity–for example, in Diels–Alder reactions. Here the authors report a diene capable of not only inducing benzene to react under mild conditions but also of breaking apart the ring system itself. 08 January 2014 | doi: 10.1038/ncomms4018 Chemical Sciences  Organic chemistry  High efficiency cell-specific targeting of cytokine activity Geneviève Garcin, Franciane Paul, Markus Staufenbiel, Yann Bordat, José Van der Heyden, Stephan Wilmes, Guillaume Cartron, Florence Apparailly, Stefaan De Koker, Jacob Piehler, Jan Tavernier and Gilles Uzé Despite their clinical potential, cytokines can often be highly toxic in patients, due to their systemic activity. Here, the authors present a strategy to engineer immunocytokines with very high targeting efficacies using mutant cytokines linked to nanobodies that only become active when bound to a specific cell marker. 08 January 2014 | doi: 10.1038/ncomms4016 Biological Sciences  Biotechnology  Immunology  Predicting network functions with nested patterns Mathias Ganter, Hans-Michael Kaltenbach and Jörg Stelling Identifying functionally important features of complex biological networks is computationally challenging. Ganter et al. develop a probabilistic framework that uses recurrent metabolite patterns to predict the properties and existence of reactions within a genome-scale metabolic network. 08 January 2014 | doi: 10.1038/ncomms4006 Physical Sciences  Systems biology  Theoretical physics  Ultra-high mobility transparent organic thin film transistors grown by an off-centre spin-coating method Yongbo Yuan, Gaurav Giri, Alexander L. Ayzner, Arjan P. Zoombelt, Stefan C. B. Mannsfeld, Jihua Chen, Dennis Nordlund, Michael F. Toney, Jinsong Huang and Zhenan Bao One of the advantages of organic over inorganic semiconductors is they can be grown from solution, but their electrical mobility is often poor. Yuan et al. report a technique for fabricating organic transistors with mobilities far beyond that of amorphous silicon and close to that of polycrystalline silicon. 08 January 2014 | doi: 10.1038/ncomms4005 Physical Sciences  Applied physics  Materials science    Nature Communications JOBS of the week Post Doctoral Research Fellow University College Dublin Post-Doctoral Scientist The George Washington University Postdoctoral Associate University of Florida Post-doctoral Scientist Cambridge Institute for Medical Research (CIMR) Post-doctoral Research Associate Masaryk University Research Fellow National Cancer Center Singapore Phd Student (M / F) German Cancer Research Center (DKFZ) Postdoctoral Research Associate University of Oxford Research Associate University of Glasgow Postdoctoral research scholar University of Iowa More Science jobs from Nature Communications EVENT Pancreatic Cancer 18.05.14 New Orleans, USA More science events from       Latest Erratum     Erratum: Louisville seamount subduction and its implication on mantle flow beneath the central Tonga–Kermadec arc Christian Timm, Daniel Bassett, Ian J. 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