Nature Communications - 10 June 2015

Weekly Content Alert Nature Communications is now fully open access. Read more. 10 June 2015  Featured image: Deloulme et al. show a role for protein MAP6 in directing neuron elongation and brain development via the Semaphorin 3E pathway. Latest content: Articles Corrigendum Erratum Journal homepage Recommend to library Web feed   Advertisement Helmholtz Zentrum München and Nature Medicine are pleased to announce: THE 3RD ANNUAL HELMHOLTZ-NATURE MEDICINE DIABETES CONFERENCE September 19-21, 2015 | Munich, Germany  REGISTER NOW!      Nature Communications - now fully open access All new submissions, if accepted, will be published open access and an article processing charge (APC) will apply. For more information visit the website. Visit our open access funding page or contact openaccess@nature.com to learn more about APC funding.       Latest Articles View all Articles     Fibres and cellular structures preserved in 75-million–year-old dinosaur specimens OPEN Sergio Bertazzo, Susannah C. R. Maidment, Charalambos Kallepitis, Sarah Fearn, Molly M. Stevens and Hai-nan Xie Soft tissue from vertebrate fossils has previously been documented, but only in exceptionally preserved specimens. Here, Bertazzo et al. describe structures consistent with collagen fibres and red blood cells from eight Cretaceous dinosaur bones, none of which are exceptionally preserved. 09 June 2015 | doi: 10.1038/ncomms8352 Biological Sciences  Palaeontology  Extreme multifunctional proteins identified from a human protein interaction network OPEN Charles E. Chapple, Benoit Robisson, Lionel Spinelli, Céline Guien, Emmanuelle Becker and Christine Brun Proteins are sometimes implicated in separate and seemingly unrelated processes, so called moonlighting functions. Here the authors use bioinformatics tools to identify extreme multifunctional proteins and define a signature of extreme multifunctionality. 09 June 2015 | doi: 10.1038/ncomms8412 Biological Sciences  Bioinformatics  Systems biology  Macroscopic quantum tunnelling in spin filter ferromagnetic Josephson junctions OPEN D. Massarotti, A. Pal, G. Rotoli, L. Longobardi, M. G. Blamire and F. Tafuri Spin triplet superconductivity may benefit spintronics, providing dissipation-free spin-polarized currents. Here, the authors demonstrate macroscopic quantum tunnelling in spin filter Josephson junctions containing a ferromagnetic insulator barrier of GdN, evidencing unconventional superconductivity below 100 mK. 09 June 2015 | doi: 10.1038/ncomms8376 Physical Sciences  Applied physics  Condensed matter  Diffusion on networked systems is a question of time or structure Jean-Charles Delvenne, Renaud Lambiotte and Luis E. C. Rocha Structural patterns such as communities are used to understand the architecture of complex networks, but this is typically obtained for a purely static case. Here the authors introduce a generalized formalism that includes the statistical properties of the event timings. 09 June 2015 | doi: 10.1038/ncomms8366 Physical Sciences  Theoretical physics  Spatial modulation of light transmission through a single microcavity by coupling of photosynthetic complex excitations to surface plasmons Itai Carmeli, Moshik Cohen, Omri Heifler, Yigal Lilach, Zeev Zalevsky, Vladimiro Mujica and Shachar Richter The interaction between light and molecules can lead to hybrid quantum-physical states of light and matter. Here, the authors demonstrate one such effect, spatial modulation of light, with the protein photosystem I as a first demonstration of this quantum effect with such a biological molecule. 09 June 2015 | doi: 10.1038/ncomms8334 Physical Sciences  Biophysics  Optical physics  Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis OPEN Daniel C. Zielinski, Fabian V. Filipp, Aarash Bordbar, Kasper Jensen, Jeffrey W. Smith, Markus J. Herrgard, Monica L. Mo and Bernhard O. Palsson Adverse drug reactions are an important clinical problem. Here the authors combine information about drug-induced gene expression changes and genetic variability of patients with a genome-scale metabolic model to identify drug-induced changes in cellular metabolism that may be linked to drug side effects. 09 June 2015 | doi: 10.1038/ncomms8101 Biological Sciences  Bioinformatics  Medical research  Phasing of single DNA molecules by massively parallel barcoding OPEN Erik Borgström, David Redin, Sverker Lundin, Emelie Berglund, Anders F. Andersson and Afshin Ahmadian DNA phasing information — the determination of which specific sequences belong to the same DNA molecule—is not easily obtained from sequencing applications that rely on short reads. Here the authors develop a phasing method based on massively parallel barcoding of single DNA molecules. 09 June 2015 | doi: 10.1038/ncomms8173 Biological Sciences  Biotechnology  Genetics  Molecular biology  Site-specific processing of Ras and Rap1 Switch I by a MARTX toxin effector domain OPEN Irena Antic, Marco Biancucci, Yueming Zhu, David R. Gius and Karla J. F. Satchell V. vulnificus, a bacteria that cause life-threatening septicaemia following wound infections or tainted food consumption, utilizes MARTX toxins for toxic effector delivery. Here the authors show that the MARTX virulence factor DUF5 targets the cellular MAP kinase pathway as a Ras and Rap1 site-specific protease. 08 June 2015 | doi: 10.1038/ncomms8396 Biological Sciences  Biochemistry  Cell biology  Microbiology  Effective heritable gene knockdown in zebrafish using synthetic microRNAs OPEN Jean Giacomotto, Silke Rinkwitz and Thomas S. Becker Zebrafish is a model system for which for no reliable heritable gene silencing method is available. Here the authors provide a system for heritable miRNA-mediated knockdown and demonstrate tunable silencing of the smn1 gene that recapitulate different forms of spinal muscular atrophy. 08 June 2015 | doi: 10.1038/ncomms8378 Biological Sciences  Developmental biology  Genetics  Molecular biology  Direct characterization of photoinduced lattice dynamics in BaFe2As2 OPEN S. Gerber, K. W. Kim, Y. Zhang, D. Zhu, N. Plonka, M. Yi, G. L. Dakovski, D. Leuenberger, P.S. Kirchmann, R. G. Moore, M. Chollet, J. M. Glownia, Y. Feng, J.-S. Lee, A. Mehta, A. F. Kemper, T. Wolf, Y.-D. Chuang, Z. Hussain, C.-C. Kao et al. In BaFe2As2, the lattice couples strongly to the magnetic and electronic degrees of freedom, providing a way to control them. Here, by means of time-resolved X-ray scattering, the authors measure rapid lattice oscillations, which can induce changes in the material’s electronic and magnetic properties. 08 June 2015 | doi: 10.1038/ncomms8377 Physical Sciences  Condensed matter  Emergence of spin–orbit fields in magnetotransport of quasi-two-dimensional iron on gallium arsenide OPEN T. Hupfauer, A. Matos-Abiague, M. Gmitra, F. Schiller, J. Loher, D. Bougeard, C. H. Back, J. Fabian and D. Weiss Broken symmetry at material interfaces allows for novel spintronic functionality via emergent spin–orbit effects. Here, Hupfauer et al. follow the interface-to-bulk transition of ultra-thin epitaxial iron films on gallium arsenide via anisotropic magnetoresistance measurements and first-principle calculations. 08 June 2015 | doi: 10.1038/ncomms8374 Physical Sciences  Applied physics  Condensed matter  Robust quantum metrological schemes based on protection of quantum Fisher information Xiao-Ming Lu, Sixia Yu and C. H. Oh Quantum features such as entanglement can be used to improve metrological precision, but noise affects their performances. Here the authors construct schemes for exploiting quantum error correction to preserve the quantum Fisher information, thereby shielding quantum gain efficiently. 08 June 2015 | doi: 10.1038/ncomms8282 Physical Sciences  Theoretical physics  Chirality- and sequence-selective successive self-sorting via specific homo- and complementary-duplex formations OPEN Wataru Makiguchi, Junki Tanabe, Hidekazu Yamada, Hiroki Iida, Daisuke Taura, Naoki Ousaka and Eiji Yashima The recognition and self-sorting of chiral molecules is a vital feature of many biomolecules. Here, the authors report chirality- and sequence-specific self-sorting of organic strands containing carboxylic acid or amidine groups, leading to selective duplex formation. 08 June 2015 | doi: 10.1038/ncomms8236 Chemical Sciences  Organic chemistry  Signal-sequence induced conformational changes in the signal recognition particle OPEN Tobias Hainzl and A. Elisabeth Sauer-Eriksson The signal recognition particle plays a key role in the co-translational protein targeting of membrane and secretory proteins. Here the authors report a crystal structure of the ternary SRP complex in signal sequence bound and unbound forms, providing insight into how signal sequence binding is coupled to SRP receptor interaction. 08 June 2015 | doi: 10.1038/ncomms8163 Biological Sciences  Biochemistry  Biophysics  TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport OPEN Miriam Schmidts, Yuqing Hou, Claudio R. Cortés, Dorus A. Mans, Celine Huber, Karsten Boldt, Mitali Patel, Jeroen van Reeuwijk, Jean-Marc Plaza, Sylvia E. C. van Beersum, Zhi Min Yap, Stef J. F. Letteboer, S. Paige Taylor, Warren Herridge, Colin A. Johnson, Peter J. Scambler, Marius Ueffing, Hulya Kayserili, Deborah Krakow, Stephen M. King et al. Severe congenital development defects such as Jeune syndrome can result from the malfunction of primary cilia and dynein. Here Schmidts et al. report unique biallelic null mutations in a gene encoding a dynein light chain, helping to explain the nature of ciliopathies in human patients. 05 June 2015 | doi: 10.1038/ncomms8074 Biological Sciences  Cell biology  Genetics  Phase stability and dynamics of entangled polymer–nanoparticle composites OPEN Rahul Mangal, Samanvaya Srivastava and Lynden A. Archer The lowering of polymer viscosity upon addition of small amounts of nanoparticles is counter-intuitive and has puzzled researchers. Here, Mangal et al. explain this intriguing phenomenon using a model polymer–nanocomposite system comprised of well-dispersed nanoparticles in an entangled polymer melt. 05 June 2015 | doi: 10.1038/ncomms8198 Physical Sciences  Fluids and plasma physics  Materials science  Nanotechnology  Phase and composition controllable synthesis of cobalt manganese spinel nanoparticles towards efficient oxygen electrocatalysis OPEN Chun Li, Xiaopeng Han, Fangyi Cheng, Yuxiang Hu, Chengcheng Chen and Jun Chen It is challenging to synthesize cobalt manganese spinels with controlled phase and composition. Here the authors present a solution-based synthesis method for the spinels, which show potential in catalysing oxygen reduction reactions. 04 June 2015 | doi: 10.1038/ncomms8345 Chemical Sciences  Materials science  Nanotechnology  Evolutionary analysis of the female-specific avian W chromosome OPEN Linnéa Smeds, Vera Warmuth, Paulina Bolivar, Severin Uebbing, Reto Burri, Alexander Suh, Alexander Nater, Stanislav Bureš, Laszlo Z. Garamszegi, Silje Hogner, Juan Moreno, Anna Qvarnström, Milan Ružić, Stein-Are Sæther, Glenn-Peter Sætre, Janos Török and Hans Ellegren The evolution of non-recombining chromosomes is poorly understood. Here, the authors sequence the collared flycatcher female-specific W chromosome and show nonrandom survival of genes during W chromosome degeneration which is due to selection for maintaining gene dose and expression levels of essential genes. 04 June 2015 | doi: 10.1038/ncomms8330 Biological Sciences  Evolution  Genetics  Microporous metal–organic framework with dual functionalities for highly efficient removal of acetylene from ethylene/acetylene mixtures OPEN Tong-Liang Hu, Hailong Wang, Bin Li, Rajamani Krishna, Hui Wu, Wei Zhou, Yunfeng Zhao, Yu Han, Xue Wang, Weidong Zhu, Zizhu Yao, Shengchang Xiang and Banglin Chen The removal of acetylene from ethylene/acetylene mixtures is an industrially important but challenging task. Here the authors report a microporous metal–organic framework with optimized pore/cage space design and chemical functionalization, capable of removing acetylene from low concentration mixtures. 04 June 2015 | doi: 10.1038/ncomms8328 Chemical Sciences  Inorganic chemistry  Materials science  High-performance ternary blend polymer solar cells involving both energy transfer and hole relay processes OPEN Luyao Lu, Wei Chen, Tao Xu and Luping Yu Ternary blend solar cells offer the potential for high-power conversion efficiencies (PCEs); however their performances can be limited by design complexity. Here, the authors integrate multiple materials into a single junction device with 9.2% PCE and elucidate the mechanisms of enhancement at play. 04 June 2015 | doi: 10.1038/ncomms8327 Physical Sciences  Applied physics  Materials science  Optical physics  A network comprising short and long noncoding RNAs and RNA helicase controls mouse retina architecture OPEN Jacek Krol, Ilona Krol, Claudia Patricia Patino Alvarez, Michele Fiscella, Andreas Hierlemann, Botond Roska and Witold Filipowicz The mammalian retina is a modular brain region, in which cell layers are of uniform thickness but the molecular mechanism controlling this process is not well understood. Here the authors identify a regulatory network consisting of the long noncoding RNA Rncr4, RNA helicase Ddx3x and miR-183/96/182 that controls the even distribution of cells across layers. 04 June 2015 | doi: 10.1038/ncomms8305 Biological Sciences  Developmental biology  Neuroscience  Molecular architecture of native fibronectin fibrils OPEN Susanna Maria Früh, Ingmar Schoen, Jonas Ries and Viola Vogel Fibronectin fibres are an important component of the extracellular matrix, supporting cell adhesion, growth and migration. Here the authors combine site-specific protein labelling with single-molecule localization microscopy to provide detailed insights into the molecular organization of native fibronectin fibrils. 04 June 2015 | doi: 10.1038/ncomms8275 Biological Sciences  Biophysics  Cell biology  Circadian control of bile acid synthesis by a KLF15-Fgf15 axis OPEN Sean (Shuxin) Han, Rongli Zhang, Rajan Jain, Hong Shi, Lilei Zhang, Guangjin Zhou, Panjamaporn Sangwung, Derin Tugal, G. Brandon Atkins, Domenick A. Prosdocimo, Yuan Lu, Xiaonan Han, Patrick Tso, Xudong Liao, Jonathan A. Epstein and Mukesh K. Jain Bile acids are important for the absorption of nutrients. Here the authors provide a molecular explanation for the oscillatory release of bile acids, showing that diurnal expression of the transcription factor KLF15 regulates FGF15 secretion from enterocytes, which then inhibits bile acid synthesis in the liver. 04 June 2015 | doi: 10.1038/ncomms8231 Biological Sciences  Medical research  Imaging screw dislocations at atomic resolution by aberration-corrected electron optical sectioning OPEN H. Yang, J. G. Lozano, T. J. Pennycook, L. Jones, P. B. Hirsch and P. D. Nellist Although screw dislocations impact on the properties of various engineering materials, their investigation on the atomic scale has been challenging. Here, the authors use optical sectioning in a scanning transmission electron microscope to achieve direct imaging of screw displacements around a screw dislocation core in GaN. 04 June 2015 | doi: 10.1038/ncomms8266 Physical Sciences  Materials science  Nanotechnology  Biomimetic mineralization of metal-organic frameworks as protective coatings for biomacromolecules OPEN Kang Liang, Raffaele Ricco, Cara M. Doherty, Mark J. Styles, Stephen Bell, Nigel Kirby, Stephen Mudie, David Haylock, Anita J. Hill, Christian J. Doonan and Paolo Falcaro Robust biomacromolecules could be used for a wide range of biotechnological applications. Here the authors report a biomimetic mineralization process, in which biomolecules are encapsulated within metal-organic frameworks, and their stability is subsequently increased without significant bioactivity loss. 04 June 2015 | doi: 10.1038/ncomms8240 Chemical Sciences  Inorganic chemistry  Nanotechnology  Structural insights into the translational infidelity mechanism OPEN Alexey Rozov, Natalia Demeshkina, Eric Westhof, Marat Yusupov and Gulnara Yusupova Translation of mRNA into proteins is the least accurate process during genetic information transfer. Here the authors suggest—based on 11 high-resolution ribosome crystal structures—that the origin of protein missense errors involves molecular mimicry via tautomerism or ionization. 03 June 2015 | doi: 10.1038/ncomms8251 Biological Sciences  Biophysics  Microtubule-associated protein 6 mediates neuronal connectivity through Semaphorin 3E-dependent signalling for axonal growth OPEN Jean-Christophe Deloulme, Sylvie Gory-Fauré, Franck Mauconduit, Sophie Chauvet, Julie Jonckheere, Benoit Boulan, Erik Mire, Jing Xue, Marion Jany, Caroline Maucler, Agathe A. Deparis, Olivier Montigon, Alexia Daoust, Emmanuel L. Barbier, Christophe Bosc, Nicole Deglon, Jacques Brocard, Eric Denarier, Isabelle Le Brun, Karin Pernet-Gallay et al. Loss of the structural microtubule-associated protein 6 (MAP6) leads to neuronal differentiation defects that are independent of MAP6’s microtubule-binding properties. Here the authors establish a functional link between MAP6 and Semaphorin 3E signalling for proper formation of the fornix of the brain. 03 June 2015 | doi: 10.1038/ncomms8246 Biological Sciences  Cell biology  Developmental biology  Neuroscience  CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1 Ling Zhu, Qingyun Bu, Xiaosa Xu, Inyup Paik, Xi Huang, Ute Hoecker, Xing Wang Deng and Enamul Huq Light exposure to plants initiates a developmental programme known as photomorphogenesis, which is triggered by repression of PIF transcription factors. Here Zhu et al. identify an E3 ubiquitin ligase complex that contributes to photomorphogenesis and is required for the degradation of PIF1. 03 June 2015 | doi: 10.1038/ncomms8245 Biological Sciences  Plant sciences  Total synthesis of tetraacylated phosphatidylinositol hexamannoside and evaluation of its immunomodulatory activity OPEN Pratap S. Patil, Ting-Jen Rachel Cheng, Medel Manuel L. Zulueta, Shih-Ting Yang, Larry S. Lico and Shang-Cheng Hung Phosphatidylinositol mannosides are cell envelope components vital for the survival of M. tuberculosis. Here, the authors report an elegant and convergent total synthesis of the complex glycolipid tetraacylated phosphatidylinositol hexamannoside (Ac2PIM6) and study the immunological effects in mice. 03 June 2015 | doi: 10.1038/ncomms8239 Chemical Sciences  Chemical biology  Medicinal chemistry  Organic chemistry    Nature Communications JOBS of the week Research Fellow Queen's University Belfast Postdoctoral Fellow Massachusetts General Hospital Postdoctoral Research Assistant University of Bristol Post-Doctoral Fellow University of Oslo Research Fellow in Neuroscience University of Leeds Postdoctoral Research Scientist Cancer Research UK Beatson Institute in Glasgow Research Associate University of Minnesota Post-Doctoral Fellow Position National Institute of Child Health Tenure Track Faculty Position University of California Los Angeles Research Associate University College London (UCL) More Science jobs from Nature Communications EVENT SMODIA "Statistical Methods for Omics Data Integration and Analysis 2015" 14.09.15 Valencia, Spain More science events from       Latest Corrigendum     Corrigendum: The mitochondrial uniporter controls fight or flight heart rate increases Yuejin Wu, Tyler P. 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