Nature Communications - 18 May 2016

Advertisement Are you working on gene therapeutics? Have an innovative approach to AAV-mediated gene therapy with improved tissue targeting? If so, Boehringer Ingelheim invites you to enter their InnoCentive Challenge. A $15,000 award fund is available along with options for Research Collaborations. The deadline for submissions is June 5, 2016. See the full details and enter here.     Weekly Content Alert Nature Communications is now fully open access. Read more. 18 May 2016  Featured image: Karlas et al. screen for cellular factors that can modulate Chikungunya infection and identify new potential drug targets. Latest content: Correspondence Articles Corrigenda Errata Journal homepage Recommend to library Web feed   Advertisement Celebrating 10,000 articles published On the 20th April 2016, Nature Communications celebrated publishing its 10,000 article. To celebrate this milestone our editors have selected a sample of articles from each subject area published in the last five areas. 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Visit our open access funding page or contact openaccess@nature.com to learn more about APC funding.       Latest Correspondence     Correspondence: On the nature of strong piezoelectricity in graphene on SiO2 OPEN 17 May 2016 | doi: 10.1038/ncomms11570     Correspondence: Reply to ‘On the nature of strong piezoelectricity in graphene on SiO2’ OPEN 17 May 2016 | doi: 10.1038/ncomms11571     Correspondence: Reply to ‘Space-time asymmetry undermines water yield assessment’ OPEN 12 May 2016 | doi: 10.1038/ncomms11604     Correspondence: Space-time asymmetry undermines water yield assessment OPEN 12 May 2016 | doi: 10.1038/ncomms11603       Latest Articles View all Articles     Decimetre-scale multicellular eukaryotes from the 1.56-billion-year-old Gaoyuzhuang Formation in North China OPEN Shixing Zhu, Maoyan Zhu, Andrew H. Knoll, Zongjun Yin, Fangchen Zhao, Shufen Sun, Yuangao Qu, Min Shi and Huan Liu Macroscopic organisms are rare in the fossil record until the Ediacaran Period, beginning 635 million years ago. Here, Zhu et al. report the discovery of 1.56-billion-year-old carbonaceous compression fossils that provide evidence of the evolution of macroscopic, multicellular eukaryotes long before the Ediacaran Period. 17 May 2016 | doi: 10.1038/ncomms11500 Biological Sciences  Evolution  Palaeontology  Giraffe genome sequence reveals clues to its unique morphology and physiology OPEN Morris Agaba, Edson Ishengoma, Webb C. Miller, Barbara C. McGrath, Chelsea N. Hudson, Oscar C. Bedoya Reina, Aakrosh Ratan, Rico Burhans, Rayan Chikhi, Paul Medvedev, Craig A. Praul, Lan Wu-Cavener, Brendan Wood, Heather Robertson, Linda Penfold and Douglas R. Cavener Giraffe’s unique anatomy and physiology include its stature and associated cardiovascular adaptation. Here, Douglas Cavener and colleagues provide de novo genome assemblies of giraffe and its closest relative okapi and provide comparative analyses to infer insights into evolution and adaptation. 17 May 2016 | doi: 10.1038/ncomms11519 Biological Sciences  Evolution  Genetics  Zoology  Biological and physical controls in the Southern Ocean on past millennial-scale atmospheric CO2 changes OPEN Julia Gottschalk, Luke C. Skinner, Jörg Lippold, Hendrik Vogel, Norbert Frank, Samuel L. Jaccard and Claire Waelbroeck Direct proxy evidence for the many explanations for past millennial-scale atmospheric CO2 changes remains scarce. Here, the authors show that changes in the efficiency of respired carbon storage in the deep Southern Ocean were linked to variations in atmospheric CO2 over the last 65,000 years. 17 May 2016 | doi: 10.1038/ncomms11539 Earth Sciences  Climate science  Oceanography  Physiological constraints to climate warming in fish follow principles of plastic floors and concrete ceilings OPEN Erik Sandblom, Timothy D. Clark, Albin Gräns, Andreas Ekström, Jeroen Brijs, L. Fredrik Sundström, Anne Odelström, Anders Adill, Teija Aho and Fredrik Jutfelt Understanding climatic adaptation in fish is limited by a lack of large-scale, long term acclimation studies. Here, Sandblom et al. show that fish exposed to a 5-10 °C increase in water temperature next to a nuclear power plant display contrasting upper and lower cardiorespiratory thermal compensation limits. 17 May 2016 | doi: 10.1038/ncomms11447 Biological Sciences  Ecology  Zoology  ERK5 signalling rescues intestinal epithelial turnover and tumour cell proliferation upon ERK1/2 abrogation OPEN Petrus R. de Jong, Koji Taniguchi, Alexandra R. Harris, Samuel Bertin, Naoki Takahashi, Jen Duong, Alejandro D. Campos, Garth Powis, Maripat Corr, Michael Karin and Eyal Raz It is unclear how the extracellular signal-regulated kinases 1 and 2 (ERK1/2) pathways interact with other signals in intestinal epithelial cells. Here, the authors show that upon loss of Erk1/2, or pharmacological inhibition of MEK1/2, the ERK5 pathway is upregulated to maintain epithelial cell proliferation. 17 May 2016 | doi: 10.1038/ncomms11551 Biological Sciences  Cancer  Cell biology  Negative magnetoresistance without well-defined chirality in the Weyl semimetal TaP OPEN Frank Arnold, Chandra Shekhar, Shu-Chun Wu, Yan Sun, Ricardo Donizeth dos Reis, Nitesh Kumar, Marcel Naumann, Mukkattu O. Ajeesh, Marcus Schmidt, Adolfo G. Grushin, Jens H. Bardarson, Michael Baenitz, Dmitry Sokolov, Horst Borrmann, Michael Nicklas, Claudia Felser, Elena Hassinger and Binghai Yan Magnetoresistance of topological semimetal shows unusual electron transport behaviour. Here, Arnold et al. demonstrate detailed Fermi surface topology of Weyl semimetal TaP and show that negative longitudinal magnetoresistance shows up without well-defined Weyl fermions. 17 May 2016 | doi: 10.1038/ncomms11615 Physical Sciences  Condensed matter  Materials science  Efficient and mechanically robust stretchable organic light-emitting devices by a laser-programmable buckling process OPEN Da Yin, Jing Feng, Rui Ma, Yue-Feng Liu, Yong-Lai Zhang, Xu-Lin Zhang, Yan-Gang Bi, Qi-Dai Chen and Hong-Bo Sun Highly stretchable organic light-emitting diodes tend to suffer from a lack of mechanical robustness. Here, Yin et al. fabricate ordered buckled films by laying flexible light-emitting diodes on laser-ablated, prestretched substrates. The devices exhibit good emission stability over 15,000 stretching cycles. 17 May 2016 | doi: 10.1038/ncomms11573 Physical Sciences  Applied physics  Materials science  Congruent pattern of accessibility identifies minimal pore gate in a non-symmetric voltage-gated sodium channel OPEN Kevin Oelstrom and Baron Chanda Gating of the central pore in voltage-dependent ion channels is mediated by changes in membrane potential. Here, the authors use substituted cysteine accessibility and metal cross-bridging to identify gate residues that form a physical occlusion when closed in a eukaryotic voltage-gated sodium channel. 17 May 2016 | doi: 10.1038/ncomms11608 Biological Sciences  Biochemistry  Synthesis of tetra- and octa-aurated heteroaryl complexes towards probing aromatic indoliums OPEN Jun Yuan, Tingting Sun, Xin He, Ke An, Jun Zhu and Liang Zhao Polymetalated aromatic compounds are challenging synthetic goals. Here, the authors describe the synthesis of tetra-aurated indole and octa-aurated benzodipyrrole complexes, in which incorporation of the aurated substituents at the nitrogen atoms leads to hyperconjugative aromaticity in the five-membered rings. 17 May 2016 | doi: 10.1038/ncomms11489 Chemical Sciences  Inorganic chemistry  Organic chemistry  Engineering electrocatalytic activity in nanosized perovskite cobaltite through surface spin-state transition OPEN Shiming Zhou, Xianbing Miao, Xu Zhao, Chao Ma, Yuhao Qiu, Zhenpeng Hu, Jiyin Zhao, Lei Shi and Jie Zeng The activity of electrocatalysts exhibits a strong dependence on their electronic structures. Here, the authors manipulate the eg filling of perovskite cobaltite LaCoO3 nanoparticles by changing particle size and show improved oxygen evolution activity with increased numbers of surface high-spin cobalt ions. 17 May 2016 | doi: 10.1038/ncomms11510 Chemical Sciences  Catalysis  Inorganic chemistry  Nanotechnology  Fast electronic resistance switching involving hidden charge density wave states OPEN I. Vaskivskyi, I. A. Mihailovic, S. Brazovskii, J. Gospodaric, T. Mertelj, D. Svetin, P. Sutar and D. Mihailovic The control of a material's state via external stimuli is the basis of modern information storage technology. Here, the authors use pulsed currents to induce fast switching between Mott insulator and metallic states in the charge density wave system 1T-TaS2, presenting an all-electronic storage mechanism. 16 May 2016 | doi: 10.1038/ncomms11442 Physical Sciences  Condensed matter  The elongation factor Spt5 facilitates transcription initiation for rapid induction of inflammatory-response genes OPEN Gil Diamant, Anat Bahat and Rivka Dikstein A subset of inflammatory-response NF-κB target genes is activated immediately after proinflammatory stimulation. Here, the authors show that in rapidly induced genes, depletion of the elongation factor Spt5 reduces transcription initiation and TFIID–promoter association without affecting the transcription elongation rate. 16 May 2016 | doi: 10.1038/ncomms11547 Biological Sciences  Immunology  Molecular biology  Data-driven magnetohydrodynamic modelling of a flux-emerging active region leading to solar eruption OPEN Chaowei Jiang, S. T. Wu, Xuesheng Feng and Qiang Hu Solar eruptions heavily influence space weather, but what are their causes remains an open question. Here the authors present a magnetohydrodynamic model of a solar eruption directly driven by solar magnetograms, following the transition from pre-eruptive to eruptive state. 16 May 2016 | doi: 10.1038/ncomms11522 Physical Sciences  Astronomy  The fast-recycling receptor Megalin defines the apical recycling pathway of epithelial cells OPEN Andres E. Perez Bay, Ryan Schreiner, Ignacio Benedicto, Maria Paz Marzolo, Jason Banfelder, Alan M. Weinstein and Enrique J. Rodriguez-Boulan Basolateral recycling and transcytotic pathways in epithelial cells are defined by specific markers, however the apical recycling pathway is poorly understood. Perez Bay et al. show that Megalin is a marker for this pathway, which intersects with the other routes in shared perinuclear recycling endosomes. 16 May 2016 | doi: 10.1038/ncomms11550 Biological Sciences  Cell biology  Critical phenomena of emergent magnetic monopoles in a chiral magnet OPEN N. Kanazawa, Y. Nii, X. -X. Zhang, A. S. Mishchenko, G. De Filippis, F. Kagawa, Y. Iwasa, N. Nagaosa and Y. Tokura Phase transitions in topologically non-trivial systems are characterized by changes of topological invariants, rather than conventional order parameters. Here, the authors propose a real-space topological phase transition upon pair annihilation of emergent monopoles inherent in chiral magnet MnGe. 16 May 2016 | doi: 10.1038/ncomms11622 Physical Sciences  Condensed matter  Giant edge state splitting at atomically precise graphene zigzag edges OPEN Shiyong Wang, Leopold Talirz, Carlo A. Pignedoli, Xinliang Feng, Klaus Müllen, Roman Fasel and Pascal Ruffieux The zigzag edges of graphene host edge-localized electronic states with aligned electron spins, but these states strongly interact with metallic substrates. Here, the authors measure the electronic structure of graphene nanoribbons after transferring them to an insulating support. 16 May 2016 | doi: 10.1038/ncomms11507 Physical Sciences  Materials science  Nanotechnology  A method for controlling the synthesis of stable twisted two-dimensional conjugated molecules OPEN Yongjun Li, Zhiyu Jia, Shengqiang Xiao, Huibiao Liu and Yuliang Li Polycyclic aromatic hydrocarbons with tunable optoelectronic properties promise applications in future high tech devices. Here, the authors demonstrate an efficient method for preparing a series of stable 2D twisted dibenzoterrylene-acenes, and investigate their electronic structures and geometries. 16 May 2016 | doi: 10.1038/ncomms11637 Chemical Sciences  Organic chemistry  Physical chemistry  Light-activated photocurrent degradation and self-healing in perovskite solar cells OPEN Wanyi Nie, Jean-Christophe Blancon, Amanda J. Neukirch, Kannatassen Appavoo, Hsinhan Tsai, Manish Chhowalla, Muhammad A. Alam, Matthew Y. Sfeir, Claudine Katan, Jacky Even, Sergei Tretiak, Jared J. Crochet, Gautam Gupta and Aditya D. Mohite Organometallic perovskite solar cells exhibit good efficiency but their photostability is still relatively poorly understood and controlled. Here the authors show that photo-degradation arises from the formation of light-activated meta-stable trap states, is reversible, and can be frozen at 0 °C. 16 May 2016 | doi: 10.1038/ncomms11574 Physical Sciences  Applied physics  Materials science  Pseudomonas aeruginosa elastase cleaves a C-terminal peptide from human thrombin that inhibits host inflammatory responses OPEN Mariena J. A. van der Plas, Ravi K. V. Bhongir, Sven Kjellström, Helena Siller, Gopinath Kasetty, Matthias Mörgelin and Artur Schmidtchen Neutrophil elastase cleaves thrombin generating anti-inflammatory peptides. Here the authors show that cleavage of thrombin by Pseudomonas aeruginosa elastase generates a peptide that prevents TLR dimerization and signaling, interfering with the inflammatory response to avoid host defense. 16 May 2016 | doi: 10.1038/ncomms11567 Biological Sciences  Immunology  Microbiology  Iso-acoustic focusing of cells for size-insensitive acousto-mechanical phenotyping OPEN Per Augustsson, Jonas T. Karlsen, Hao-Wei Su, Henrik Bruus and Joel Voldman Acoustophoresis, a method to manipulate individual cells based on their acoustic properties is confounded by a strong dependency on cell size. Here the authors present iso-acoustic focussing, a way to separate cells in a microfluidic chamber according to their effective acoustic impedance, independent of their size. 16 May 2016 | doi: 10.1038/ncomms11556 Biological Sciences  Biophysics  Biotechnology  Cytoplasmic cyclin D1 regulates cell invasion and metastasis through the phosphorylation of paxillin OPEN Noel P. Fusté, Rita Fernández-Hernández, Tània Cemeli, Cristina Mirantes, Neus Pedraza, Marta Rafel, Jordi Torres-Rosell, Neus Colomina, Francisco Ferrezuelo, Xavier Dolcet and Eloi Garí Previous studies suggest that Cyclin D1 may regulate cell adhesion and migration but the mechanisms underlying such regulation and the relevance to cancer development are unknown. Here, Fusté et al. show that Cyclin D1/Cdk4 phosphorylates paxillin and thereby promotes cellular migration and metastasis. 16 May 2016 | doi: 10.1038/ncomms11581 Biological Sciences  Cancer  Cell biology  Heterogeneity and clinical significance of ESR1 mutations in ER-positive metastatic breast cancer patients receiving fulvestrant OPEN Jill M. Spoerke, Steven Gendreau, Kimberly Walter, Jiaheng Qiu, Timothy R. Wilson, Heidi Savage, Junko Aimi, Mika K. Derynck, Meng Chen, Iris T. Chan, Lukas C. Amler, Garret M. Hampton, Stephen Johnston, Ian Krop, Peter Schmid and Mark R. Lackner Fulvestrant degrades the oestrogen receptor. Here, the authors report on a clinical trial using fulvestrant and show that mutations in the oestrogen receptor alpha gene are prevalent in circulating tumour DNA and do not influence the clinical outcome of patients to fulvestrant. 13 May 2016 | doi: 10.1038/ncomms11579 Biological Sciences  Cancer  Genetics  Medical research  Direct observation of narrow mid-infrared plasmon linewidths of single metal oxide nanocrystals OPEN Robert W. Johns, Hans A. Bechtel, Evan L. Runnerstrom, Ankit Agrawal, Sebastien D. Lounis and Delia J. Milliron Establishing the cause of inhomogeneous broadening would help to produce narrow ensemble localized surface plasmon resonance peaks, favourable for sensing applications. Here, Johns et al. use near field optics for enhancing signal contrast, enabling the measurement of mid-infrared spectra of single nanocrystals. 13 May 2016 | doi: 10.1038/ncomms11583 Physical Sciences  Materials science  Optical physics  Patient-specific factors influence somatic variation patterns in von Hippel–Lindau disease renal tumours OPEN Suzanne S. Fei, Asia D. Mitchell, Michael B. Heskett, Cathy D. Vocke, Christopher J. Ricketts, Myron Peto, Nicholas J. Wang, Kemal Sönmez, W. Marston Linehan and Paul T. Spellman Analysing multiple tumours from the same patient permits the study of the germline contribution to cancer. Here, the authors sequence multiple renal tumours from VHL patients and find that intra-patient tumours are clonally distinct but share some genetic features, suggesting that patient-specific factors influence tumour formation. 13 May 2016 | doi: 10.1038/ncomms11588 Biological Sciences  Cancer  Genetics  Van der Waals interactions and the limits of isolated atom models at interfaces OPEN Shigeki Kawai, Adam S. Foster, Torbjörn Björkman, Sylwia Nowakowska, Jonas Björk, Filippo Federici Canova, Lutz H. Gade, Thomas A. Jung and Ernst Meyer Van der Waals forces are individually weak, but on scale can drive many nano- and macroscopic processes. Here, Kawai et al. directly measure the van der Waals interactions between noble gas atom pairs and show how this changes with atom size and surface adsorption. 13 May 2016 | doi: 10.1038/ncomms11559 Physical Sciences  Applied physics  Nanotechnology  Physical chemistry  Fragmentation of magnetism in artificial kagome dipolar spin ice OPEN Benjamin Canals, Ioan-Augustin Chioar, Van-Dai Nguyen, Michel Hehn, Daniel Lacour, François Montaigne, Andrea Locatelli, Tevfik Onur Menteş, Benito Santos Burgos and Nicolas Rougemaille By nanofabricating arrays of dipolar-coupled bistable single-domain nanomagnets, artificial model systems exhibiting collective ordering may be realized. Here, the authors present signatures of spin fragmentation in low-energy states of an artificial kagome ice. 13 May 2016 | doi: 10.1038/ncomms11446 Physical Sciences  Condensed matter  Argonaute-associated short introns are a novel class of gene regulators OPEN Thomas B. Hansen, Morten T. Venø, Trine I. Jensen, Anne Schaefer, Christian K. Damgaard and Jørgen Kjems MicroRNAs are important small regulatory RNAs produced by sequential Drosha and Dicer cleavage. Here the authors describe 'agotrons', a subclass of small RNAs that bypass the canonical biogenesis machinery. 13 May 2016 | doi: 10.1038/ncomms11538 Biological Sciences  Molecular biology  Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly OPEN John M. A. Grime, James F. Dama, Barbie K. Ganser-Pornillos, Cora L. Woodward, Grant J. Jensen, Mark Yeager and Gregory A. Voth Significant morphological changes occur during the conversion of the immature HIV virion into a mature infectious form. Here the authors use coarse-grained molecular dynamics simulations to model HIV-1 capsid self-assembly and disassembly events that suggests several metastable capsid intermediates sensitive to local conditions. 13 May 2016 | doi: 10.1038/ncomms11568 Biological Sciences  Biophysics  Virology  Innate olfactory preferences for flowers matching proboscis length ensure optimal energy gain in a hawkmoth OPEN Alexander Haverkamp, Julia Bing, Elisa Badeke, Bill S. Hansson and Markus Knaden Foraging is energetically demanding for animals like hawkmoths that feed while flying. Here, Haverkamp et al. show that Manduca sexta has an innate preference for feeding on species of Nicotiana whose flower corolla length best matches the length of their proboscis, which allowed more efficient foraging and yielded the highest caloric gain. 13 May 2016 | doi: 10.1038/ncomms11644 Biological Sciences  Evolution  Zoology  Atomic-scale disproportionation in amorphous silicon monoxide OPEN Akihiko Hirata, Shinji Kohara, Toshihiro Asada, Masazumi Arao, Chihiro Yogi, Hideto Imai, Yongwen Tan, Takeshi Fujita and Mingwei Chen Amorphous silicon monoxide is known to undergo disproportionation to silicon- and silicon dioxide-like regions, however direct observation of the atomic-scale heterogeneity is still missing. Here, the authors use angstrom-beam electron diffraction to reveal precise structural details of this unusual material. 13 May 2016 | doi: 10.1038/ncomms11591 Chemical Sciences  Applied physics  Materials science  Physical chemistry  A single gene of a commensal microbe affects host susceptibility to enteric infection OPEN Mi Young Yoon, Kyung Bae Min, Kang-Mu Lee, Yujin Yoon, Yaeseul Kim, Young Taek Oh, Keehoon Lee, Jongsik Chun, Byung-Yong Kim, Seok-Hwan Yoon, Insuk Lee, Chan Yeong Kim and Sang Sun Yoon The interactions between gut bacteria and enteric pathogens are poorly understood. Here, Yoon et al. show that subinhibitory antibiotic treatment in a mouse model leads to overgrowth of an E. coli strain carrying a catalase-encoding gene that enhances infection with the human pathogen Vibrio cholerae. 13 May 2016 | doi: 10.1038/ncomms11606 Biological Sciences  Microbiology  Modelled drift patterns of fish larvae link coastal morphology to seabird colony distribution OPEN Hanno Sandvik, Robert T. Barrett, Kjell Einar Erikstad, Mari S. Myksvoll, Frode Vikebø, Nigel G. Yoccoz, Tycho Anker-Nilssen, Svein-Håkon Lorentsen, Tone K. Reiertsen, Jofrid Skarðhamar, Mette Skern-Mauritzen and Geir Helge Systad Seabirds breed in high density colonies, but the factors determining colony position aren't clear. Here, Sandvik et al. show that small-scale coastal topography is related to likely variation in fish larval abundance, which predicts the distribution of seabird colonies along the Norwegian coast. 13 May 2016 | doi: 10.1038/ncomms11599 Biological Sciences  Climate science  Ecology  Oceanography  An organelle-specific protein landscape identifies novel diseases and molecular mechanisms OPEN Karsten Boldt, Jeroen van Reeuwijk, Qianhao Lu, Konstantinos Koutroumpas, Thanh-Minh T. Nguyen, Yves Texier, Sylvia E. C. van Beersum, Nicola Horn, Jason R. Willer, Dorus A. Mans, Gerard Dougherty, Ideke J. C. Lamers, Karlien L. M. Coene, Heleen H. Arts, Matthew J. Betts, Tina Beyer, Emine Bolat, Christian Johannes Gloeckner, Khatera Haidari, Lisette Hetterschijt et al. Mutations in proteins that localize to primary cilia cause devastating diseases, yet the primary cilium is a poorly understood organelle. Here the authors use interaction proteomics to identify a network of human ciliary proteins that provides new insights into several biological processes and diseases. 13 May 2016 | doi: 10.1038/ncomms11491 Biological Sciences  Bioinformatics  Cell biology  Behavioural traits propagate across generations via segregated iterative-somatic and gametic epigenetic mechanisms OPEN Emma Mitchell, Shifra L. Klein, Kimon V. Argyropoulos, Ali Sharma, Robin B. Chan, Judit Gal Toth, Luendreo Barboza, Charlotte Bavley, Analia Bortolozzi, Qiuying Chen, Bingfang Liu, Joanne Ingenito, Willie Mark, Jarrod Dudakov, Steven Gross, Gilbert Di Paolo, Francesc Artigas, Marcel van den Brink and Miklos Toth Physiological effects of psychological stress and infection in mothers can increase the incidence of anxiety and psychiatric diseases in offsprings and in subsequent generation. Here, Miklos Toth and colleagues show that intergenerational inheritance of neurological traits is propagated across multiple generations independently by parallel non-genetic mechanisms involving independent segregation of epigenetic specific loci. 13 May 2016 | doi: 10.1038/ncomms11492 Biological Sciences  Genetics  Neuroscience  A combined computational and structural model of the full-length human prolactin receptor OPEN Katrine Bugge, Elena Papaleo, Gitte W. Haxholm, Jonathan T. S. Hopper, Carol V. Robinson, Johan G. Olsen, Kresten Lindorff-Larsen and Birthe B. Kragelund The prolactin receptor consists of a folded extracellular domain, a transmembrane domain and an intracellular intrinsically disordered domain. Here the authors use a combined experimental and computational approach to obtain a structure of a class I cytokine receptor, the human prolactin receptor. 13 May 2016 | doi: 10.1038/ncomms11578 Biological Sciences  Biochemistry  Biophysics  miR-216b regulation of c-Jun mediates GADD153/CHOP-dependent apoptosis OPEN Zhenhua Xu, Yiwen Bu, Nilesh Chitnis, Costas Koumenis, Serge Y. Fuchs and J. Alan Diehl The transcription factor CHOP/GADD153 regulates apoptosis in response to the unfolded protein response. Here the authors show that CHOP/GADD153 regulates the expression of miR-216b, which targets c-Jun and sensitizes cells to ER stress-dependent apoptosis. 13 May 2016 | doi: 10.1038/ncomms11422 Biological Sciences  Cell biology  Molecular biology  Evidence that phytochrome functions as a protein kinase in plant light signalling OPEN Ah-Young Shin, Yun-Jeong Han, Ayoung Baek, Taeho Ahn, Soo Young Kim, Thai Son Nguyen, Minky Son, Keun Woo Lee, Yu Shen, Pill-Soon Song and Jeong-Il Kim Phytochromes regulate plant responses to environmental light conditions but despite extensive research the initial events in phytochrome signaling remain uncertain. Here, Shin et al. provide evidence that phytochrome phosphorylates target proteins via kinase activity in the N-terminal core domain. 13 May 2016 | doi: 10.1038/ncomms11545 Biological Sciences  Biochemistry  Plant sciences  Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks OPEN Rajiv K. Mishra, Sooyun Kim, Segundo J. Guzman and Peter Jonas STDP is dependent on the timing of pre- and post-synaptic activity. Here, the authors describe a symmetric STDP induction rule at CA3-CA3 synapses, which induces LTP over a broad range of paring intervals. Modelling suggests that this STDP rule may enhance storage capacity and pattern completion in the CA3 cell network. 13 May 2016 | doi: 10.1038/ncomms11552 Biological Sciences  Neuroscience  Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly OPEN Marjetka Podobnik, Peter Savory, Nejc Rojko, Matic Kisovec, Neil Wood, Richard Hambley, Jonathan Pugh, E. Jayne Wallace, Luke McNeill, Mark Bruce, Idlir Liko, Timothy M. Allison, Shahid Mehmood, Neval Yilmaz, Toshihide Kobayashi, Robert J. C. Gilbert, Carol V. Robinson, Lakmal Jayasinghe and Gregor Anderluh Pore-forming toxins act by forming oligomeric pores in lipid membranes. Here the authors report the crystal structure of the lysenin pore, providing insights into the assembly and function of the pore in addition to suggesting that its properties make lysenin potentially well-suited for nanopore sensing applications. 12 May 2016 | doi: 10.1038/ncomms11598 Biological Sciences  Biophysics  Nanotechnology  A human genome-wide loss-of-function screen identifies effective chikungunya antiviral drugs OPEN Alexander Karlas, Stefano Berre, Thérèse Couderc, Margus Varjak, Peter Braun, Michael Meyer, Nicolas Gangneux, Liis Karo-Astover, Friderike Weege, Martin Raftery, Günther Schönrich, Uwe Klemm, Anne Wurzlbauer, Franz Bracher, Andres Merits, Thomas F. Meyer and Marc Lecuit Chikungunya virus is a mosquito transmitted untreatable emergent pathogen that causes joint pain and fever. Here the authors perform a host genome-wide loss-of-function screen to identify targets for chikungunya antiviral drugs and validate hits using a mouse model of chikungunya infection. 12 May 2016 | doi: 10.1038/ncomms11320 Biological Sciences  Medical research  Virology  Deep-reaching thermocline mixing in the equatorial pacific cold tongue OPEN Chuanyu Liu, Armin Köhl, Zhiyu Liu, Fan Wang and Detlef Stammer The role of thermocline mixing in the Pacific cold tongue in the propagation of ENSO remains uncertain. Here, Liu et al. show a persistent occurrence of mixing events in the middle and lower parts of the thermocline, particularly during tropical instability waves and under La Niña conditions. 12 May 2016 | doi: 10.1038/ncomms11576 Earth Sciences  Climate science  Oceanography  Revealing the mechanism of passive transport in lipid bilayers via phonon-mediated nanometre-scale density fluctuations OPEN Mikhail Zhernenkov, Dima Bolmatov, Dmitry Soloviov, Kirill Zhernenkov, Boris P. Toperverg, Alessandro Cunsolo, Alexey Bosak and Yong Q. Cai The molecular transport through bio-membranes of cells heavily relies on the dynamics of lipids, but the related mechanism remains unknown. Here, Zhernenkov et al. observe the propagating transverse phonon mode with a finite band gap and suggest its connection to short-lived local lipid clustering. 12 May 2016 | doi: 10.1038/ncomms11575 Biological Sciences  Biochemistry  Biophysics  Materials science  A high-resolution strain-gauge nanolaser OPEN Jae-Hyuck Choi, You-Shin No, Jae-Pil So, Jung Min Lee, Kyoung-Ho Kim, Min-Soo Hwang, Soon-Hong Kwon and Hong-Gyu Park Flexible, millimetre-scale systems and devices require embedded, reliable micrometre-scale components, which can be challenging to achieve for optical sensors. Here, the authors design a photonic crystal nanolaser and demonstrate its use in measuring strain. 12 May 2016 | doi: 10.1038/ncomms11569 Physical Sciences  Materials science  Optical physics  Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock OPEN Pauline L. Kamath, Jeffrey T. Foster, Kevin P. Drees, Gordon Luikart, Christine Quance, Neil J. Anderson, P. Ryan Clarke, Eric K. Cole, Mark L. Drew, William H. Edwards, Jack C. Rhyan, John J. Treanor, Rick L. Wallen, Patrick J. White, Suelee Robbe-Austerman and Paul C. Cross The role of wild elk in the spread and persistence of bovine brucellosis in the Great Yellowstone area is unclear. Here, Kamath et al. analyse the genomic sequences of 245 Brucella abortus isolates from elk, bison and cattle, supporting the idea that elk is an important reservoir and source of livestock infections. 11 May 2016 | doi: 10.1038/ncomms11448 Biological Sciences  Ecology  Genetics  Microbiology  0.5-keV Soft X-ray attosecond continua OPEN S. M. Teichmann, F. Silva, S. L. Cousin, M. Hemmer and J. Biegert Attosecond soft X-ray pulses hold promise for probing electronic dynamics in real time, but it is challenging to achieve element sensitivity while maintaining temporal resolution. Teichmann et al. report the cover of carbon, nitrogen and oxygen absorption edges with an isolated pulse supporting 13 as duration. 11 May 2016 | doi: 10.1038/ncomms11493 Physical Sciences  Atomic and molecular physics  Optical physics  Caloric restriction blocks neuropathology and motor deficits in Machado–Joseph disease mouse models through SIRT1 pathway OPEN Janete Cunha-Santos, Joana Duarte-Neves, Vitor Carmona, Leonard Guarente, Luís Pereira de Almeida and Cláudia Cavadas SIRTs have been reported to provide neuroprotective actions in polyglutamine diseases, and are linked to the beneficial effects of caloric restrictive diets. Here, the authors show caloric restriction improves behavioural and neuropathological deficits in MJD model mice, an effect dependent on SIRT1 activity. 11 May 2016 | doi: 10.1038/ncomms11445 Biological Sciences  Neuroscience  Synthesis of acetic acid via methanol hydrocarboxylation with CO2 and H2 OPEN Qingli Qian, Jingjing Zhang, Meng Cui and Buxing Han Industrial routes to acetic acid use carbon monoxide for the carbonylation of methanol. Here, the authors report a hydrocarboxylation method that instead uses carbon dioxide and hydrogen for the conversion of methanol into acetic acid. 11 May 2016 | doi: 10.1038/ncomms11481 Chemical Sciences  Catalysis  Inorganic chemistry  Organic chemistry  Mapping quantum state dynamics in spontaneous emission OPEN M. Naghiloo, N. Foroozani, D. Tan, A. Jadbabaie and K. W. Murch The evolution of a quantum state undergoing radiative decay depends on how the emission is detected. Here, the authors demonstrate how continuous field detection, as opposed to the more common detection of energy quanta, allows control of the back-action on the emitter’s state. 11 May 2016 | doi: 10.1038/ncomms11527 Physical Sciences  Optical physics  Theoretical physics  Superior thermoelasticity and shape-memory nanopores in a porous supramolecular organic framework OPEN You-Gui Huang, Yoshihito Shiota, Ming-Yan Wu, Sheng-Qun Su, Zi-Shuo Yao, Soonchul Kang, Shinji Kanegawa, Guo-Ling Li, Shu-Qi Wu, Takashi Kamachi, Kazunari Yoshizawa, Katsuhiko Ariga, Mao-Chun Hong and Osamu Sato Designing porous materials with empty shape-switchable pores remains a formidable challenge. Here, the authors fabricate a supramolecular organic framework possessing empty shape-memory nanopores which operates via a ferroelastic transition, endowing it with switchable sorption properties. 11 May 2016 | doi: 10.1038/ncomms11564 Chemical Sciences  Inorganic chemistry  Materials science  Nucleation and spreading of a heterochromatic domain in fission yeast OPEN Michaela J. Obersriebnig, Emil M. H. Pallesen, Kim Sneppen, Ala Trusina and Geneviève Thon Chromosomes contain large heterochromatin domains. Here, the authors measure the kinetics of heterochromatin formation in fission yeast and show both global and local feedbacks by nucleosome-bound enzymes are important for formation and stability of the large heterochromatin domains. 11 May 2016 | doi: 10.1038/ncomms11518 Biological Sciences  Cell biology  Molecular biology  A microfluidics-based in vitro model of the gastrointestinal human–microbe interface OPEN Pranjul Shah, Joëlle V. Fritz, Enrico Glaab, Mahesh S. Desai, Kacy Greenhalgh, Audrey Frachet, Magdalena Niegowska, Matthew Estes, Christian Jäger, Carole Seguin-Devaux, Frederic Zenhausern and Paul Wilmes Research on the interactions between the gut microbiota and human cells would greatly benefit from improved in vitro models. Here, Shah et al. present a modular microfluidics-based model that allows co-culture of human and microbial cells followed by 'omic' molecular analyses of the two cell contingents. 11 May 2016 | doi: 10.1038/ncomms11535 Biological Sciences  Cell biology  Microbiology  Systems biology  Timescales of methane seepage on the Norwegian margin following collapse of the Scandinavian Ice Sheet OPEN Antoine Crémière, Aivo Lepland, Shyam Chand, Diana Sahy, Daniel J. Condon, Stephen R. Noble, Tõnu Martma, Terje Thorsnes, Simone Sauer and Harald Brunstad Understanding the timescales of gas hydrate dissociation and methane release are critical to gauge the potential climate impact. Here, the authors report a methane efflux chronology from five sites in Barents and Norwegian seas and show methane release coincident with the release of ice sheet-induced pressure. 11 May 2016 | doi: 10.1038/ncomms11509 Earth Sciences  Climate science  Geology and geophysics    Nature Communications JOBS of the week Postdoctoral Fellow The Scripps Research Institute (TSRI) Post Doctoral Fellow University of Toronto Postdoctoral Research Assistant University of Dundee Research Associate Robert Koch Institute (RKI) Post-Doctoral Fellow University of Oklahoma Health Sciences Center Postdoctoral Fellow Baylor College of Medicine (BCM) Post Doctoral Fellow – Gabrilovich Lab The Wistar Institute Team leader Life sience Institute of Physiology of the CAS Postdoctoral Associate Yale University Max Planck Research Group Leader Max Planck Institute for Chemical Ecology More Science jobs from Nature Communications EVENT Genomic Medicine Conference 08.08.16 Huntsville, USA More science events from       Latest Corrigenda     Corrigendum: High yield and ultrafast sources of electrically triggered entangled-photon pairs based on strain-tunable quantum dots OPEN Jiaxiang Zhang, Johannes S. Wildmann, Fei Ding, Rinaldo Trotta, Yongheng Huo, Eugenio Zallo, Daniel Huber, Armando Rastelli and Oliver G. Schmidt 11 May 2016 | doi: 10.1038/ncomms11681 Physical Sciences  Condensed matter  Materials science  Optical physics      Corrigendum: A coral-on-a-chip microfluidic platform enabling live-imaging microscopy of reef-building corals OPEN Orr H. Shapiro, Esti Kramarsky-Winter, Assaf R. Gavish, Roman Stocker and Assaf Vardi 11 May 2016 | doi: 10.1038/ncomms11680 Biological Sciences  Biotechnology  Microbiology      Corrigendum: HSP90 regulates temperature-dependent seedling growth in Arabidopsis by stabilizing the auxin co-receptor F-box protein TIR1 OPEN Renhou Wang, Yi Zhang, Martin Kieffer, Hong Yu, Stefan Kepinski and Mark Estelle 11 May 2016 | doi: 10.1038/ncomms11677 Biological Sciences  Plant sciences      Corrigendum: Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan OPEN Markus Schosserer, Nadege Minois, Tina B. Angerer, Manuela Amring, Hanna Dellago, Eva Harreither, Alfonso Calle-Perez, Andreas Pircher, Matthias Peter Gerstl, Sigrid Pfeifenberger, Clemens Brandl, Markus Sonntagbauer, Albert Kriegner, Angela Linder, Andreas Weinhäusel, Thomas Mohr, Matthias Steiger, Diethard Mattanovich, Mark Rinnerthaler, Thomas Karl et al. 11 May 2016 | doi: 10.1038/ncomms11530 Biological Sciences  Medical research  Molecular biology        Latest Errata     Erratum: Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression OPEN André Franz, Paul A. Pirson, Domenic Pilger, Swagata Halder, Divya Achuthankutty, Hamid Kashkar, Kristijan Ramadan and Thorsten Hoppe 17 May 2016 | doi: 10.1038/ncomms11593 Biological Sciences  Molecular biology      Erratum: Magnetic droplet nucleation boundary in orthogonal spin-torque nano-oscillators OPEN Sunjae Chung, Anders Eklund, Ezio Iacocca, Seyed Majid Mohseni, Sohrab R. Sani, Lake Bookman, Mark A. Hoefer, Randy K. Dumas and Johan Åkerman 12 May 2016 | doi: 10.1038/ncomms11699 Physical Sciences  Condensed matter      Advertisement Nature Collection: Computational Biology Advances in technology across all areas of science have ushered in an era of big data, providing researchers with unprecedented opportunities to understand how biological systems function and interact. Access this collection free online for six months Produced with support from: IBM Research & IBM Watson Health   Advertisement Nature Outlook: Research commercialization Universities need to deliver more value for research outlay. Companies are facing competition in the search for the next business-sustaining product. These sectors have their own objectives, but are locked in a synergistic embrace that is fuelling a push to extract commercial value from academic research. 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