Nature Communications - 19 November 2014

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	Weekly Content Alert 19 November 2014  Featured image: Kang et al. present an analytical system that can detect specific, single bacterial cells in blood within a few hours Latest content: Articles Corrigendum Errata Journal homepage Recommend to library Web feed   Advertisement Announcing the Nature Index: A global indicator of high-quality research The Nature Index tracks the affiliations of high-quality scientific articles. Updated monthly, the Nature Index presents research outputs by institution and country. Use the Nature Index to interrogate publication patterns and to benchmark research performance.  Access the Nature Index free online.        Latest Articles View all Articles     Evidence for henipavirus spillover into human populations in Africa OPEN Olivier Pernet, Bradley S. Schneider, Shannon M. Beaty, Matthew LeBreton, Tatyana E. Yun, Arnold Park, Trevor T. Zachariah, Thomas A. Bowden, Peta Hitchens, Christina M. Ramirez, Peter Daszak, Jonna Mazet, Alexander N. Freiberg, Nathan D. Wolfe and Benhur Lee Henipaviruses (HNVs) infect bats in Asia and Africa, but transmission to humans (often with lethal consequences) is known only in Asia. Here the authors show that 3% of human serum samples from certain areas in Cameroon contain antibodies against HNV, indicating spillover into the human population. 18 November 2014 | doi: 10.1038/ncomms6342 Biological Sciences  Medical research  Microbiology  Virology  Early life stress in fathers improves behavioural flexibility in their offspring Katharina Gapp, Saray Soldado-Magraner, María Alvarez-Sánchez, Johannes Bohacek, Gregoire Vernaz, Huan Shu, Tamara B. Franklin, David Wolfer and Isabelle M. Mansuy Traumatic events in one generation can affect the behaviour of their offspring. Here the authors subject male mouse pups to traumatic stress and find that their offspring display improved goal-directed behaviours associated with epigenetic changes of the mineralocorticoid receptor gene. 18 November 2014 | doi: 10.1038/ncomms6466 Biological Sciences  Neuroscience  Improving farming practices reduces the carbon footprint of spring wheat production OPEN Yantai Gan, Chang Liang, Qiang Chai, Reynald L. Lemke, Con A. Campbell and Robert P. Zentner Wheat is the world’s second most favoured food source, yet its production has climatic consequences. Here the authors quantify the carbon footprint of wheat production systems and evaluate potential alternative farming practices, with a reduced negative impact on climate. 18 November 2014 | doi: 10.1038/ncomms6012 Earth Sciences  Climate science  General incorporation of diverse components inside metal-organic framework thin films at room temperature Yiyin Mao, Junwei Li, Wei Cao, Yulong Ying, Pan Hu, Yu Liu, Luwei Sun, Hongtao Wang, Chuanhong Jin and Xinsheng Peng General methods to introduce functional components into metal-organic frameworks are challenging to develop. Here, the authors report a method for encapsulating a range of functional components, such as proteins and nanoparticles, into the structures with properties dependent on both the framework and the guest. 18 November 2014 | doi: 10.1038/ncomms6532 Chemical Sciences  Inorganic chemistry  Materials science  Oscillations emerging from noise-driven steady state in networks with electrical synapses and subthreshold resonance OPEN Tatjana Tchumatchenko and Claudia Clopath Oscillatory activity is ubiquitous in the brain and plays a critical role in cognitive processing. Tchumatchenko and Clopath present a model whereby oscillatory activity emerges through subthreshold resonance and electrical coupling between inhibitory interneurons. 18 November 2014 | doi: 10.1038/ncomms6512 Biological Sciences  Biophysics  Neuroscience  CpG island-mediated global gene regulatory modes in mouse embryonic stem cells OPEN Samuel Beck, Bum-Kyu Lee, Catherine Rhee, Jawon Song, Andrew J. Woo and Jonghwan Kim CpG islands are high GC content DNA elements that surround the majority of transcriptional start sites in eukaryotes. Here, the authors analyse over 200 genomic data sets to provide new insight into global CpG islands-dependent regulatory mechanisms in differentiated and pluripotent stem cells. 18 November 2014 | doi: 10.1038/ncomms6490 Biological Sciences  Bioinformatics  Cell biology  Systems biology  Modification of DBC1 by SUMO2/3 is crucial for p53-mediated apoptosis in response to DNA damage Jong Ho Park, Seong Won Lee, Seung Wook Yang, Hee Min Yoo, Jung Mi Park, Min Woo Seong, Seung Hyeun Ka, Kyu Hee Oh, Young Joo Jeon and Chin Ha Chung SIRT1 is a deacetylase that is negatively regulated by binding to DBC1. Here Park et al. show that DNA damage-induced SUMO2/3 conjugation of DBC1 promotes the SIRT1–DBC1 interaction, leading to an increase in acetylated p53 and induction of apoptosis. 18 November 2014 | doi: 10.1038/ncomms6483 Biological Sciences  Cell biology  Ciliary membrane proteins traffic through the Golgi via a Rabep1/GGA1/Arl3-dependent mechanism OPEN Hyunho Kim, Hangxue Xu, Qin Yao, Weizhe Li, Qiong Huang, Patricia Outeda, Valeriu Cebotaru, Marco Chiaravalli, Alessandra Boletta, Klaus Piontek, Gregory G. Germino, Edward J. Weinman, Terry Watnick and Feng Qian Polycystins (PC) 1 and 2 are large transmembrane proteins that play a vital role in the function of primary cilia. Here, Kim et al. identify the requirements for polycystin trafficking to the cilium, involving a PC1–PC2 interaction, PC1 proteolytic cleavage and a specific trafficking module at the trans-Golgi network. 18 November 2014 | doi: 10.1038/ncomms6482 Biological Sciences  Biochemistry  Cell biology  Synthesis of chiral heterocycles by ligand-controlled regiodivergent and enantiospecific Suzuki Miyaura cross-coupling Jinyue Ding, Taras Rybak and Dennis G. Hall Chiral heterocyclic compounds are highly valuable due to their biological and synthetic utility. Here the authors report a stereospecific cross-coupling methodology for the synthesis of non-aromatic heterocycles, giving products in high enantiomeric excess with control over the regioselectivity of bond formation. 18 November 2014 | doi: 10.1038/ncomms6474 Chemical Sciences  Catalysis  Organic chemistry  Redox-responsive branched-bottlebrush polymers for in vivo MRI and fluorescence imaging Molly A. Sowers, Jessica R. McCombs, Ying Wang, Joseph T. Paletta, Stephen W. Morton, Erik C. Dreaden, Michael D. Boska, M. Francesca Ottaviani, Paula T. Hammond, Andrzej Rajca and Jeremiah A. Johnson Multimodal and stimuli-responsive imaging agents can yield more biological information than more typical single-mode or inert imaging probes. Here, the authors have made a dual-modal MRI-fluorescence probe and demonstrate its ability to image redox status in vivo. 18 November 2014 | doi: 10.1038/ncomms6460 Biological Sciences  Chemical biology  Quantitative profiling of peptides from RNAs classified as noncoding Sudhakaran Prabakaran, Martin Hemberg, Ruchi Chauhan, Dominic Winter, Ry Y. Tweedie-Cullen, Christian Dittrich, Elizabeth Hong, Jeremy Gunawardena, Hanno Steen, Gabriel Kreiman and Judith A. Steen A large portion of the transcribed genome—such as introns and noncoding RNAs—is believed to not be translated into protein products. Here, the authors provide evidence for the existence of regulated peptide products that are translated from transcribed sequences generally characterized as noncoding. 18 November 2014 | doi: 10.1038/ncomms6429 Biological Sciences  Bioinformatics  Molecular biology  Structure and function of a spectrin-like regulator of bacterial cytokinesis OPEN Robert M. Cleverley, Jeffrey R. Barrett, Arnaud Baslé, Nhat Khai Bui, Lorraine Hewitt, Alexandra Solovyova, Zhi-Qiang Xu, Richard A. Daniel, Nicholas E. Dixon, Elizabeth J. Harry, Aaron J. Oakley, Waldemar Vollmer and Richard J. Lewis EzrA regulates the polymerization of FtsZ, a tubulin-like protein and main component of the Z-ring, which drives cell division in bacteria. Here the authors describe the crystal structure of EzrA and demonstrate that it shares structural and functional properties with eukaryotic spectrins. 18 November 2014 | doi: 10.1038/ncomms6421 Biological Sciences  Biochemistry  Biophysics  Microbiology  MNKs act as a regulatory switch for eIF4E1 and eIF4E3 driven mRNA translation in DLBCL OPEN Ari L. Landon, Parameswary A. Muniandy, Amol C. Shetty, Elin Lehrmann, Laurent Volpon, Simone Houng, Yongqing Zhang, Bojie Dai, Raymond Peroutka, Krystyna Mazan-Mamczarz, James Steinhardt, Anup Mahurkar, Kevin G. Becker, Katherine L. Borden and Ronald B. Gartenhaus Diffuse large B-cell lymphoma (DLBCL) is a highly aggressive and heterogeneous type of non-Hodgkin’s lymphoma. Here the authors demonstrate that the differential regulation of eIF4E1 and eIF4E3 by the MAPK-interacting kinases is involved in DLBCL aetiology through modification of the cellular translatome. 18 November 2014 | doi: 10.1038/ncomms6413 Biological Sciences  Biochemistry  Cancer  Molecular biology  Hepatitis C virus genetics affects miR-122 requirements and response to miR-122 inhibitors Benjamin Israelow, Gavriel Mullokandov, Judith Agudo, Marion Sourisseau, Ali Bashir, Andres Y. Maldonado, Arvin C. Dar, Brian D. Brown and Matthew J. Evans Replication of the hepatitis C virus (HCV) requires a host RNA molecule, miR-122, whose transient inhibition is being explored as an antiviral therapy. Here, the authors study the interaction between miR-122 and HCV, and identify mutations in HCV strains that affect susceptibility to miR-122 inhibition. 18 November 2014 | doi: 10.1038/ncomms6408 Biological Sciences  Molecular biology  Virology  The DUSP–Ubl domain of USP4 enhances its catalytic efficiency by promoting ubiquitin exchange OPEN Marcello Clerici, Mark P. A. Luna-Vargas, Alex C. Faesen and Titia K. Sixma Ubiquitin-specific protease USP4 regulates several cellular signalling pathways. Here, Clerici et al. show that the DUSP–Ubl domain of USP4 is required for full catalytic activity, by enhancing the release of ubiquitin from the catalytic site after substrate hydrolysis. 18 November 2014 | doi: 10.1038/ncomms6399 Biological Sciences  Biochemistry  Tuning charge–discharge induced unit cell breathing in layer-structured cathode materials for lithium-ion batteries Yong-Ning Zhou, Jun Ma, Enyuan Hu, Xiqian Yu, Lin Gu, Kyung-Wan Nam, Liquan Chen, Zhaoxiang Wang and Xiao-Qing Yang Battery cycling induces various changes in the electrode. Here, the authors propose a generalized hypothesis based on metal–metal bonding to rationalize the lattice changes of layer-structured cathode materials including lithium molybdenum trioxide which exhibits abnormal lattice change behaviour. 18 November 2014 | doi: 10.1038/ncomms6381 Chemical Sciences  Materials science  Physical chemistry  Age-related variations in the methylome associated with gene expression in human monocytes and T cells Lindsay M. Reynolds, Jackson R. Taylor, Jingzhong Ding, Kurt Lohman, Craig Johnson, David Siscovick, Gregory Burke, Wendy Post, Steven Shea, David R. Jacobs Jr., Hendrik Stunnenberg, Stephen B. Kritchevsky, Ina Hoeschele, Charles E. McCall, David M. Herrington, Russell P. Tracy and Yongmei Liu The functional relevance of age-related variation in DNA methylation is unclear. Here, Reynolds et al. analyze how patterns of genome-wide gene expression and DNA methylation data vary with age in circulating monocytes and T cells, and report age-associated methylation signals that are correlated with cis-gene expression and vascular aging. 18 November 2014 | doi: 10.1038/ncomms6366 Biological Sciences  Genetics  Catalytic activation of pre-substrates via dynamic fragment assembly on protein templates Edyta Burda and Jörg Rademann The identification of protein-binding fragments during drug development can be hampered by poor binding affinities before optimization. Here, the authors have designed pre-substrates to release fluorescent signals whenever a nucleophile fragment binds next to the active site of the enzyme. 18 November 2014 | doi: 10.1038/ncomms6170 Chemical Sciences  Chemical biology  Medicinal chemistry  Strain and structure heterogeneity in MoS2 atomic layers grown by chemical vapour deposition Zheng Liu, Matin Amani, Sina Najmaei, Quan Xu, Xiaolong Zou, Wu Zhou, Ting Yu, Caiyu Qiu, A. Glen Birdwell, Frank J. Crowne, Robert Vajtai, Boris I. Yakobson, Zhenhai Xia, Madan Dubey, Pulickel M. Ajayan and Jun Lou Large-size monolayer molybdenum disulfide (MoS2) has recently been produced via chemical vapour deposition (CVD), yet its structures and physical properties are yet to be fully explored. Here, the authors study the growth-induced strain in CVD-grown MoS2 and strain-based bandgap engineering of MoS2. 18 November 2014 | doi: 10.1038/ncomms6246 Physical Sciences  Materials science  Nanotechnology  Sub-optical wavelength acoustic wave modulation of integrated photonic resonators at microwave frequencies Semere Ayalew Tadesse and Mo Li Acousto-optic modulators use acoustic waves to control light on a chip. Here, the authors achieve modulation in nanophotonic resonators using microwave frequency surface acoustic waves with wavelength smaller than the optical wavelength towards highly integrated devices on silicon. 17 November 2014 | doi: 10.1038/ncomms6402 Physical Sciences  Applied physics  Nanotechnology  Optical physics  A photon thermal diode Zhen Chen, Carlaton Wong, Sean Lubner, Shannon Yee, John Miller, Wanyoung Jang, Corey Hardin, Anthony Fong, Javier E. Garay and Chris Dames A thermal diode is the heat transfer analogue of an electrical diode: it favours the flow of energy carriers such as photons, phonons or electrons in one direction. Here, the authors demonstrate a photon thermal diode that uses pyramidal reflectors to asymmetrically scatter the photons. 17 November 2014 | doi: 10.1038/ncomms6446 Physical Sciences  Applied physics  Biting disrupts integration to spur skull evolution in eels David C. Collar, Peter C. Wainwright, Michael E. Alfaro, Liam J. Revell and Rita S. Mehta Functional integration limits the potential for morphological differences to evolve. Here, the authors show an association between changes in skull morphology and evolutionary integration with feeding behaviour in eels. 17 November 2014 | doi: 10.1038/ncomms6505 Biological Sciences  Evolution  Localized light-induced protein dimerization in living cells using a photocaged dimerizer Edward R. Ballister, Chanat Aonbangkhen, Alyssa M. Mayo, Michael A. Lampson and David M. Chenoweth Protein localization in cells can yield much information about the spatial arrangement of cellular processes and the participating groups. Here, the authors present a membrane-permeable and photoactive agent for localized protein dimerization in cells. 17 November 2014 | doi: 10.1038/ncomms6475 Biological Sciences  Cell biology  Separate neural representations for physical pain and social rejection Choong-Wan Woo, Leonie Koban, Ethan Kross, Martin A. Lindquist, Marie T. Banich, Luka Ruzic, Jessica R. Andrews-Hanna and Tor D. Wager Physical pain and social rejection are believed to be processed by common neural substrates in the brain. Here Woo et al. combine brain imaging with pattern analysis to show that, in fact, pain and rejection are processed by distinct neural substrates that are located in similar anatomical brain regions. 17 November 2014 | doi: 10.1038/ncomms6380 Biological Sciences  Neuroscience  Targeting TopBP1 at a convergent point of multiple oncogenic pathways for cancer therapy Pinki Chowdhury, Gregory E. Lin, Kang Liu, Yongcheng Song, Fang-Tsyr Lin and Weei-Chin Lin Topoisomerase IIß-binding protein 1 (TopBP1) is known to suppress apoptosis in cancer and to mediate effects of p53 mutations. Here the authors identify calcein as a lead compound to inhibit TopBP1 and show that calcein has anti-tumour activity in mouse cancer models. 17 November 2014 | doi: 10.1038/ncomms6476 Biological Sciences  Cancer  Nondispersive optical activity of meshed helical metamaterials Hyun Sung Park, Teun-Teun Kim, Hyeon-Don Kim, Kyungjin Kim and Bumki Min Metamaterials manipulate light to deliver tailored optical functionalities, like nonlinearity and optical activity. By exploiting the Drude response and four-fold rotational symmetries, Park et al. show that meshed helical metallic structures can produce a strong and broadband nondispersive optical activity. 17 November 2014 | doi: 10.1038/ncomms6435 Physical Sciences  Applied physics  Concentration and chemical-state profiles at heterogeneous interfaces with sub-nm accuracy from standing-wave ambient-pressure photoemission Slavomír Nemšák, Andrey Shavorskiy, Osman Karslioglu, Ioannis Zegkinoglou, Arunothai Rattanachata, Catherine S. Conlon, Armela Keqi, Peter K. Greene, Edward C. Burks, Farhad Salmassi, Eric M. Gullikson, See-Hun Yang, Kai Liu, Hendrik Bluhm and Charles S. Fadley Heterogeneous chemical processes are vital for many applications, but the crucial interfaces involved are difficult to probe experimentally with elemental and chemical-state specificity. Here, the authors present a photoelectron spectroscopy-based method for studying such interfaces with sub-nanometre accuracy and under realistic pressure conditions 17 November 2014 | doi: 10.1038/ncomms6441 Chemical Sciences  Analytical chemistry  Materials science  Spatial mapping of multimode Brownian motions in high-frequency silicon carbide microdisk resonators Zenghui Wang, Jaesung Lee and Philip X. -L. Feng Identifying and manipulating high-order modes in mechanical resonators remains a challenge. Here, the authors provide an experimental demonstration of the mapping of such modes in a silicon carbide microdisk resonator, identifying intrinsic Brownian vibrations up to the ninth flexural mode. 17 November 2014 | doi: 10.1038/ncomms6158 Physical Sciences  Materials science  Nanotechnology  Omega-1 knockdown in Schistosoma mansoni eggs by lentivirus transduction reduces granuloma size in vivo OPEN Jana Hagen, Neil D. Young, Alison L. Every, Charles N. Pagel, Corinna Schnoeller, Jean-Pierre Y. Scheerlinck, Robin B. Gasser and Bernd H. Kalinna Schistosomiasis, a neglected tropical disease, is caused by flatworms such as Schistosoma mansoni. Here, Hagen et al. describe a lentivirus-based transduction system to deliver microRNA-adapted small hairpin RNAs into S. mansoni to inhibit transcription of selected genes implicated in the disease process. 17 November 2014 | doi: 10.1038/ncomms6375 Biological Sciences  Cell biology  FCA mediates thermal adaptation of stem growth by attenuating auxin action in Arabidopsis Hyo-Jun Lee, Jae-Hoon Jung, Lucas Cortés Llorca, Sang-Gyu Kim, Sangmin Lee, Ian T. Baldwin and Chung-Mo Park The PIF4 transcription factor promotes stem elongation by inducing auxin biosynthesis at elevated temperature in Arabidopsis. Here, Lee et al. show that the RNA-binding protein FCA attenuates PIF4 activity by promoting its dissociation from the promoter of a gene encoding an auxin biosynthetic enzyme. 17 November 2014 | doi: 10.1038/ncomms6473 Biological Sciences  Plant sciences  Nanoscale visualization of redox activity at lithium-ion battery cathodes Yasufumi Takahashi, Akichika Kumatani, Hirokazu Munakata, Hirotaka Inomata, Komachi Ito, Kosuke Ino, Hitoshi Shiku, Patrick R. Unwin, Yuri E. Korchev, Kiyoshi Kanamura and Tomokazu Matsue It is important as well as challenging to map out redox activity at battery electrodes. Here, the authors present a scanning electrochemical cell microscope approach, which allows redox activity and ion flux processes at battery electrodes to be visualized with high space and time resolution. 17 November 2014 | doi: 10.1038/ncomms6450 Chemical Sciences  Analytical chemistry  Coccolithophore calcification response to past ocean acidification and climate change OPEN Sarah A. O’Dea, Samantha J. Gibbs, Paul R. Bown, Jeremy R. Young, Alex J. Poulton, Cherry Newsam and Paul A. Wilson Calcifying organisms such as planktonic coccolithophores may be particularly vulnerable to increased ocean acidification. Here, O’Dea et al. show that two fossil coccolithophore species exhibited reduced calcification rates during a global warming acidification event 56 million years ago. 17 November 2014 | doi: 10.1038/ncomms6363 Biological Sciences  Ecology  Palaeontology  Giant electrode effect on tunnelling electroresistance in ferroelectric tunnel junctions Rohit Soni, Adrian Petraru, Paul Meuffels, Ondrej Vavra, Martin Ziegler, Seong Keun Kim, Doo Seok Jeong, Nikolay A. Pertsev and Hermann Kohlstedt The electroresistance displayed by ferroelectric tunnel junctions could be used for non-volatile computer memories and other computing applications. Here, the authors show that effects from ferroelectric–electrode interfaces can have a strong positive impact on the electroresistance in such junctions. 17 November 2014 | doi: 10.1038/ncomms6414 Physical Sciences  Nanotechnology  BRCA1 haploinsufficiency for replication stress suppression in primary cells OPEN Shailja Pathania, Sangeeta Bade, Morwenna Le Guillou, Karly Burke, Rachel Reed, Christian Bowman-Colin, Ying Su, David T. Ting, Kornelia Polyak, Andrea L. Richardson, Jean Feunteun, Judy E. Garber and David M. Livingston BRCA1 is a key breast and ovarian cancer suppressor involved in DSB repair. Here, the authors show that cells heterozygous for several BRCA1 mutations are universally defective in the response to replication stress, which could contribute to the BRCA1 breast cancer development pathway. 17 November 2014 | doi: 10.1038/ncomms6496 Biological Sciences  Cancer  Genetics  Molecular biology  TRF2 and lamin A/C interact to facilitate the functional organization of chromosome ends OPEN Ashley M. Wood, Jannie M. Rendtlew Danielsen, Catherine A. Lucas, Ellen L. Rice, David Scalzo, Takeshi Shimi, Robert D. Goldman, Erica D. Smith, Michelle M. Le Beau and Steven T. Kosak The shortening of telomeres—a structure that protects chromosome ends—is associated with cellular aging. Here, Wood et al. present evidence that interaction between the telomere-binding protein TRF2 and lamin A/C facilitates the formation of interstitial t-loops and stabilizes telomeres. 17 November 2014 | doi: 10.1038/ncomms6467 Biological Sciences  Cell biology  Structural and functional conservation of fungal MatA and human SRY sex-determining proteins Wioletta Czaja, Karen Y. Miller, Michael K. Skinner and Bruce L. Miller Genes involved in sex determination show sequence conservation between mammals and fungi. Here the authors show that human sex determinant, SRY protein, is able to functionally replace the fungal mating type determinant MatA, which suggests that sex determination factors are functionally conserved. 17 November 2014 | doi: 10.1038/ncomms6434 Biological Sciences  Evolution  Genetics  The SH2 domain of Abl kinases regulates kinase autophosphorylation by controlling activation loop accessibility Allan Joaquim Lamontanara, Sandrine Georgeon, Giancarlo Tria, Dmitri I. Svergun and Oliver Hantschel Abl is a cytoplasmic tyrosine kinase important for growth, whose hyper activation is associated with several types of cancers. Here, the authors use recombinant Abl protein to uncover the molecular mechanism underlying allosteric activation of Abl by its SH2 domain through the regulation of autophosphorylation. 17 November 2014 | doi: 10.1038/ncomms6470 Biological Sciences  Biochemistry  Biophysics  Formation and maintenance of neuronal assemblies through synaptic plasticity Ashok Litwin-Kumar and Brent Doiron Connectivity patterns between neurons in the brain store recent sensory experiences, but how these patterns form is unclear. Here, the authors provide a model describing the process through which synaptic plasticity combined with homeostatic mechanisms allow stable neuronal assemblies to form. 14 November 2014 | doi: 10.1038/ncomms6319 Biological Sciences  Neuroscience  Histone H3.3 and its proteolytically processed form drive a cellular senescence programme Luis F. Duarte, Andrew R. J. Young, Zichen Wang, Hsan-Au Wu, Taniya Panda, Yan Kou, Avnish Kapoor, Dan Hasson, Nicholas R. Mills, Avi Ma’ayan, Masashi Narita and Emily Bernstein Cellular senescence involves extensive structural changes to chromatin, but the role of histone variants and histone cleavage is unknown. Here, Duarte et al. identify histone variant H3.3 and its proteolytically processed form lacking a portion of the N-terminal tail as key regulators of senescence. 14 November 2014 | doi: 10.1038/ncomms6210 Biological Sciences  Cell biology  Genomic landscape of metastatic colorectal cancer OPEN Josien C. Haan, Mariette Labots, Christian Rausch, Miriam Koopman, Jolien Tol, Leonie J. M. Mekenkamp, Mark A. van de Wiel, Danielle Israeli, Hendrik F. van Essen, Nicole C. T. van Grieken, Quirinus J. M. Voorham, Linda J. W. Bosch, Xueping Qu, Omar Kabbarah, Henk M. W. Verheul, Iris D. Nagtegaal, Cornelis J. A. Punt, Bauke Ylstra and Gerrit A. Meijer Response to drug therapy in colorectal cancer (CRC) patients has been associated with tumour heterogeneity. Here the authors analyse DNA copy number aberrations in primary tumours from CRC patients and identify genetic variants that influence drug response. 14 November 2014 | doi: 10.1038/ncomms6457 Biological Sciences  Cancer  Genetics  The structure of apo-kinesin bound to tubulin links the nucleotide cycle to movement Luyan Cao, Weiyi Wang, Qiyang Jiang, Chunguang Wang, Marcel Knossow and Benoît Gigant A complete description of how the motor protein kinesin-1 walks along microtubules is missing because of the lack of a key structure. Here, Cao et al. solve the apo-kinesin:microtubule structure, completing the structure set and permitting the description of the structural changes that occur during the nucleotide cycle and their functional consequences. 14 November 2014 | doi: 10.1038/ncomms6364 Biological Sciences  Biochemistry  Polarity of bacterial magnetotaxis is controlled by aerotaxis through a common sensory pathway Felix Popp, Judith P. Armitage and Dirk Schüler Magnetotactic bacteria sense and migrate along the geomagnetic field, but the molecular mechanism for directed motion is not known. Here, Popp et al. show that M. gryphiswaldense displays swimming polarity in an oxygen gradient sensed by the chemotactic sensory pathway CheOp1, revealing a link between aerotactic sensing and magnetotactic polarity. 14 November 2014 | doi: 10.1038/ncomms6398 Biological Sciences  Microbiology  Structural basis for LAR-RPTP/Slitrk complex-mediated synaptic adhesion Ji Won Um, Kee Hun Kim, Beom Seok Park, Yeonsoo Choi, Doyoun Kim, Cha Yeon Kim, Soo Jin Kim, Minhye Kim, Ji Seung Ko, Seong-Gyu Lee, Gayoung Choii, Jungyong Nam, Won Do Heo, Eunjoon Kim, Jie-Oh Lee, Jaewon Ko and Ho Min Kim The presynaptic LAR-RPTPs interact with postsynaptic Slitrks and this contributes to regulating synapse formation. Here, the authors identified the minimal binding regions and determined the crystal structure of the resulting complex and performed functional analysis in cells to determine LAR-RPTP/Slitrk complex-mediated synapse formation. 14 November 2014 | doi: 10.1038/ncomms6423 Biological Sciences  Cell biology  Neuroscience  Explaining why simple liquids are quasi-universal Andreas K. Bacher, Thomas B. Schrøder and Jeppe C. Dyre Researchers refer to the approximate invariance in the structure and dynamics of simple liquids among different pair models as quasi-universality, while little is known about its origin. Here, Becher et al. show that the pair potential as a sum of exponential terms fulfils the quasuniversality. 14 November 2014 | doi: 10.1038/ncomms6424 Physical Sciences  Fluids and plasma physics  Theoretical physics  Interlaced crystals having a perfect Bravais lattice and complex chemical order revealed by real-space crystallography Xiao Shen, Emil A. Hernández-Pagan, Wu Zhou, Yevgeniy S. Puzyrev, Juan-Carlos Idrobo, Janet E. Macdonald, Stephen J. Pennycook and Sokrates T. Pantelides Ternary nanoparticles have shown uses in areas such as thermoelectric devices. Here, the authors synthesise such nanoparticles and observe a crystalline ordering consisting of a global Bravais lattice, wherein the cation sublattice displays a range of interlaced chemical ordering. 14 November 2014 | doi: 10.1038/ncomms6431 Chemical Sciences  Materials science  Nanotechnology  Real-time estimation and biofeedback of single-neuron firing rates using local field potentials OPEN Thomas M. Hall, Kianoush Nazarpour and Andrew Jackson The use of local field potential (LFP) brain signals may allow development of more efficient and robust neural prosthetic devices. Here, Hall et al. develop a method for estimation and biofeedback control of single-neuron firing rates using signals extracted from multiple low-frequency LFPs. 14 November 2014 | doi: 10.1038/ncomms6462 Biological Sciences  Neuroscience  CSN6 drives carcinogenesis by positively regulating Myc stability Jian Chen, Ji-Hyun Shin, Ruiying Zhao, Liem Phan, Hua Wang, Yuwen Xue, Sean M. Post, Hyun Ho Choi, Jiun-Sheng Chen, Edward Wang, Zhongguo Zhou, Chieh Tseng, Christopher Gully, Guermarie Velazquez-Torres, Enrique Fuentes-Mattei, Giselle Yeung, Yi Qiao, Ping-Chieh Chou, Chun-Hui Su, Yun-Chih Hsieh et al. The COP9 signalosome (CSN) is a protein complex involved in protein degradation and tumorigenesis. Here the authors show that the CSN6 subunit antagonizes the deneddylation function of CSN5 towards ubiquitin ligase Cullin-1, resulting in Fbxw7 ubiquitin ligase degradation and thereby stabilization of the Fbxw7 target Myc. 14 November 2014 | doi: 10.1038/ncomms6384 Biological Sciences  Cancer  Molecular biology  Decreased tumorigenesis in mice with a Kras point mutation at C118 Lu Huang, John Carney, Diana M. Cardona and Christopher M. Counter The Ras family of proteins is frequently mutated in cancer, and free radical oxidants can also activate these proteins via modifications at cysteine 118 (C118). Here the authors introduce a C118S mutant Kras gene into mice and show that this mutant allele results in a reduction in lung tumorigenesis. 14 November 2014 | doi: 10.1038/ncomms6410 Biological Sciences  Cancer  The role of maternal-specific H3K9me3 modification in establishing imprinted X-chromosome inactivation and embryogenesis in mice OPEN Atsushi Fukuda, Junko Tomikawa, Takumi Miura, Kenichiro Hata, Kazuhiko Nakabayashi, Kevin Eggan, Hidenori Akutsu and Akihiro Umezawa During mouse preimplantation phases, a repressive imprint is imposed on the maternal allele of Xist, which encodes a large non-coding RNA required for X-chromosome inactivation. Here the authors show that trimethylation of histone H3 at lysine 9 on Xist promoter chromatin is responsible for the maternally determined Xist repression. 14 November 2014 | doi: 10.1038/ncomms6464 Biological Sciences  Developmental biology  Molecular biology  Crown ethers in graphene Junjie Guo, Jaekwang Lee, Cristian I. Contescu, Nidia C. Gallego, Sokrates T. Pantelides, Stephen J. Pennycook, Bruce A. Moyer and Matthew F. Chisholm Crown ethers have been used as strong and selective binders for alkali metals and other cations since their discovery. Here the authors observe crown ether type structures in partially oxidized graphene and through simulations predict that they have similar abilities to selectively bind cations. 13 November 2014 | doi: 10.1038/ncomms6389 Chemical Sciences  Materials science  Nanotechnology  Ostwald’s rule of stages governs structural transitions and morphology of dipeptide supramolecular polymers Aviad Levin, Thomas O. Mason, Lihi Adler-Abramovich, Alexander K. Buell, George Meisl, Celine Galvagnion, Yaron Bram, Samuel A. Stratford, Christopher M. Dobson, Tuomas P. J. Knowles and Ehud Gazit Suparmolecular polymers are built by monomers via non-covalent bonds, whilst the pathway of their nucleation processes is not yet clear. Here, Levin et al. show that the self-assembly of monomers proceeds through a series of metastable states, which are energetically governed by Ostwald’s rule of stages. 13 November 2014 | doi: 10.1038/ncomms6219 Chemical Sciences  Materials science  Organic chemistry  Physical chemistry  Seismic reflection data support episodic and simultaneous growth of the Tibetan Plateau since 25 Myr Xiao-Dian Jiang and Zheng-Xiang Li How the Tibetan Plateau arrived at its present size and elevation remains a topic of debate. Here, the authors use drill-hole and seismic data from the Tarim basin and conclude that plateau extension was episodic and synchronous along eastern and northern margins, likely occurring via brittle thickening of the upper crust. 13 November 2014 | doi: 10.1038/ncomms6453 Earth Sciences  Geology and geophysics  Ion antiport accelerates photosynthetic acclimation in fluctuating light environments OPEN Ute Armbruster, L. Ruby Carrillo, Kees Venema, Lazar Pavlovic, Elisabeth Schmidtmann, Ari Kornfeld, Peter Jahns, Joseph A. Berry, David M. Kramer and Martin C. Jonikas Plants must respond rapidly to unpredictable variations in light intensity to maximize photosynthetic efficiency. Here Armbruster et al. identify a potassium antiporter that is critical for accelerating proton fluxes across thylakoid membranes and minimizing energy loss in fluctuating light conditions. 13 November 2014 | doi: 10.1038/ncomms6439 Biological Sciences  Plant sciences  Chlamydia infection depends on a functional MDM2-p53 axis OPEN Erik González, Marion Rother, Markus C. Kerr, Munir A. Al-Zeer, Mohammad Abu-Lubad, Mirjana Kessler, Volker Brinkmann, Alexander Loewer and Thomas F. Meyer Protein p53 plays key roles in cellular stress responses and is frequently deregulated in cancer. Here the authors show that infection with chlamydiae activates the ubiquitin ligase MDM2 in infected cells, leading to proteasomal degradation of p53 and thus promoting apoptosis resistance. 13 November 2014 | doi: 10.1038/ncomms6201 Biological Sciences  Cancer  Cell biology  Microbiology  Inhibition of osteoclastogenesis and inflammatory bone resorption by targeting BET proteins and epigenetic regulation Kyung-Hyun Park-Min, Elisha Lim, Min Joon Lee, Sung Ho Park, Eugenia Giannopoulou, Anna Yarilina, Marjolein van der Meulen, Baohong Zhao, Nicholas Smithers, Jason Witherington, Kevin Lee, Paul P. Tak, Rab K. Prinjha and Lionel B Ivashkiv Epigenetic changes during the differentiation of bone-resorbing cells have important implications in bone remodelling. Here the authors target this pathway with I-BET151, an inhibitor of bromo and extra-terminal proteins that inhibits expression of the MYC-NFAT axis and suppresses bone loss in multiple mouse models. 13 November 2014 | doi: 10.1038/ncomms6418 Biological Sciences  Cancer  Immunology  Fc gamma receptor-TLR cross-talk elicits pro-inflammatory cytokine production by human M2 macrophages OPEN Lisa T. C. Vogelpoel, Ivo S. Hansen, Theo Rispens, Femke J. M. Muller, Toni M. M. van Capel, Maureen C. Turina, Joost B. Vos, Dominique L. P. Baeten, Martien L. Kapsenberg, Esther C. de Jong and Jeroen den Dunnen M2-polarized macrophages are generally considered anti-inflammatory, but whether polarization markers always reflect functional states remains debatable. Here the authors show that complexed IgG and TLR co-stimulation, observed in infections or rheumatoid arthritis, elicits an inflammatory response in M2 macrophages. 13 November 2014 | doi: 10.1038/ncomms6444 Biological Sciences  Immunology  Spin–orbit coupling in surface plasmon scattering by nanostructures D. O’Connor, P. Ginzburg, F. J. Rodríguez-Fortuño, G. A. Wurtz and A. V. Zayats The polarization state of light is analogous to the spin state of electrons, enabling equivalent phenomena to be explored in optics as in the solid state. Here, the authors study directional scattering of light from nanostructured surfaces, arising from a spin-orbit coupling effect for surface plasmon waves. 13 November 2014 | doi: 10.1038/ncomms6327 Physical Sciences  Nanotechnology  Optical physics  Large-scale analysis of lysine SUMOylation by SUMO remnant immunoaffinity profiling Frédéric Lamoliatte, Danielle Caron, Chantal Durette, Louiza Mahrouche, Mohamed Ali Maroui, Olivier Caron-Lizotte, Eric Bonneil, Mounira K. Chelbi-Alix and Pierre Thibault Protein SUMOylation plays an important role in regulation of many cellular processes. Lamoliatte et al. use a monoclonal antibody specific for SUMO3 tryptic peptides to enhance proteomic identification of SUMOylated proteins, and dramatically expand the number of sites known to be modified by SUMO3. 13 November 2014 | doi: 10.1038/ncomms6409 Biological Sciences  Biochemistry  Thickness sorting of two-dimensional transition metal dichalcogenides via copolymer-assisted density gradient ultracentrifugation Joohoon Kang, Jung-Woo T. Seo, Diego Alducin, Arturo Ponce, Miguel Jose Yacaman and Mark C. Hersam Transition metal dichalcogenides are emerging two-dimensional materials, yet monodisperse and stoichiometrically pristine sample production is challenging. Here, the authors employ a block copolymer to control buoyant density for isopycnic density gradient ultracentrifugation, allowing thickness sorting of the material. 13 November 2014 | doi: 10.1038/ncomms6478 Chemical Sciences  Applied physics  Materials science  Nanotechnology  Rapid detection of single bacteria in unprocessed blood using Integrated Comprehensive Droplet Digital Detection OPEN Dong-Ku Kang, M. Monsur Ali, Kaixiang Zhang, Susan S. Huang, Ellena Peterson, Michelle A. Digman, Enrico Gratton and Weian Zhao Early detection of blood stream infections is essential for providing effective treatments. Here the authors present a system integrating DNAzyme sensors, droplet microfluidics and a high-throughput 3D particle counter that can detect specific, single bacterial cells in blood within a few hours. 13 November 2014 | doi: 10.1038/ncomms6427 Biological Sciences  Analytical chemistry  Biotechnology  Microbiology  Nuclear stability and transcriptional directionality separate functionally distinct RNA species Robin Andersson, Peter Refsing Andersen, Eivind Valen, Leighton J. Core, Jette Bornholdt, Mette Boyd, Torben Heick Jensen and Albin Sandelin Despite our growing understanding of their complexity, different types of RNA are still classified using technical rather than functional criteria. Andersson et al. show that categorization of RNAs based on stability and direction of transcription is an effective means of functional classification. 12 November 2014 | doi: 10.1038/ncomms6336 Biological Sciences  Bioinformatics  Molecular biology  Suppression of the FOXM1 transcriptional programme via novel small molecule inhibition Michael V. Gormally, Thomas S. Dexheimer, Giovanni Marsico, Deborah A. Sanders, Christopher Lowe, Dijana Matak-Vinković, Sam Michael, Ajit Jadhav, Ganesha Rai, David J. Maloney, Anton Simeonov and Shankar Balasubramanian Overexpression of the FOXM1 transcription factor occurs in several cancer and correlates with poor prognoses. Here, the authors identify a novel small molecule capable of displacing FOXM1 from its DNA consensus motif in vitro, displace it from target promoters and downregulate the expression of its target genes cancer cells. 12 November 2014 | doi: 10.1038/ncomms6165 Biological Sciences  Cancer  Chemical biology  A glutamatergic reward input from the dorsal raphe to ventral tegmental area dopamine neurons Jia Qi, Shiliang Zhang, Hui-Ling Wang, Huikun Wang, Jose de Jesus Aceves Buendia, Alexander F. Hoffman, Carl R. Lupica, Rebecca P. Seal and Marisela Morales Glutamatergic neurons project from the dorsal raphe to the ventral tegmental area, two brain areas strongly associated with addictive behaviour, however the functional significance of this connection remains unclear. Qi et al. show that optogenetic activation of this pathway conveys reward in mice. 12 November 2014 | doi: 10.1038/ncomms6390 Biological Sciences  Neuroscience  Lysophospholipids secreted by splenic macrophages induce chemotherapy resistance via interference with the DNA damage response Julia M. Houthuijzen, Laura G. M. Daenen, Jeanine M. L. Roodhart, Ilse Oosterom, Marijn T. M. van Jaarsveld, Klaas M. Govaert, Michelle E. Smith, Sahar J. Sadatmand, Hilde Rosing, Fabian Kruse, Bernd J. Helms, Nico van Rooijen, Jos H. Beijnen, Bodduluri Haribabu, Chris H. A. van de Lest and Emile E Voest It is known that mesenchymal stem cells contribute to chemotherapy resistance by secreting polyunsaturated fatty acids. Here the authors show that macrophages in the spleen secrete lysophosphatidylcholines and contribute to chemotherapy resistance by altering the tumour's DNA damage response. 12 November 2014 | doi: 10.1038/ncomms6275 Biological Sciences  Cancer  Immunology  Electrically tunable optical polarization rotation on a silicon chip using Berry’s phase Qiang Xu, Li Chen, Michael G. Wood, Peng Sun and Ronald M. Reano Integrated optical devices require complete control of the polarization of light, but this is difficult to realize. By exploiting Berry’s phase, Xu et al. show out-of-plane guiding of light on a silicon chip and dynamic tuning of the optical polarization by application of electric fields. 12 November 2014 | doi: 10.1038/ncomms6337 Physical Sciences  Applied physics  Nanotechnology  Optical physics  Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster Michael D. Valentino, Abigail Manson McGuire, Jason W. Rosch, Paulo J. M. Bispo, Corinna Burnham, Christine M. Sanfilippo, Robert A. Carter, Michael E. Zegans, Bernard Beall, Ashlee M. Earl, Elaine I. Tuomanen, Timothy W. Morris, Wolfgang Haas and Michael S. Gilmore Pneumococci can cause a variety of bacterial infections including conjunctivitis. Here, Valentino et al. show that most conjunctivitis-causing pneumococci belong to a closely related group of strains that possess a unique set of putative virulence factors. 12 November 2014 | doi: 10.1038/ncomms6411 Biological Sciences  Microbiology  Structure-guided mutational analysis reveals the functional requirements for product specificity of DOT1 enzymes Gülcin Dindar, Andreas M. Anger, Christine Mehlhorn, Sandra B. Hake and Christian J. Janzen DOT1A and DOT1B are African trypanosome homologues of the enzyme DOT1 methyltransferase, which is involved in the methylation of the histone H3K79. In this study, the authors identify specific residues that modulate the specificity of these enzymes for different forms of methylation. 12 November 2014 | doi: 10.1038/ncomms6313 Biological Sciences  Biochemistry  Molecular biology  Cytoplasmic parafibromin/hCdc73 targets and destabilizes p53 mRNA to control p53-mediated apoptosis Jay-Hyun Jo, Tae-Moon Chung, Hyewon Youn and Joo-Yeon Yoo Mutations of hCdc73, a component of the PAFc complex that regulates RNA polymerase II-dependent transcription, have been associated with parathyroid carcinoma. Here the authors show that hCdc73 regulates the mRNA stability of p53 through the interaction with eEF1Bγ, a translation elongation complex subunit, and hSki8, a component of mRNA decay complex. 12 November 2014 | doi: 10.1038/ncomms6433 Biological Sciences  Cancer  Molecular biology  Microwave purification of large-area horizontally aligned arrays of single-walled carbon nanotubes Xu Xie, Sung Hun Jin, Muhammad A. Wahab, Ahmad E. Islam, Chenxi Zhang, Frank Du, Eric Seabron, Tianjian Lu, Simon N. Dunham, Hou In Cheong, Yen-Chu Tu, Zhilin Guo, Ha Uk Chung, Yuhang Li, Yuhao Liu, Jong-Ho Lee, Jizhou Song, Yonggang Huang, Muhammad A. Alam, William L. Wilson et al. Creating large-area horizontally aligned arrays of purely semiconducting tubes is one of the most daunting technical challenges in carbon nanotube electronics. Here, the authors introduce an approach using microwave radiation with microstrip antenna structures and demonstrate its effectiveness. 12 November 2014 | doi: 10.1038/ncomms6332 Physical Sciences  Materials science  PP2A and Aurora differentially modify Cdc13 to promote telomerase release from telomeres at G2/M phase Zih-Jie Shen, Pang-Hung Hsu, Yu-Tai Su, Chia-Wei Yang, Li Kao, Shun-Fu Tseng, Ming-Daw Tsai and Shu-Chun Teng Telomere maintenance requires proper termination of telomere replication at G2/M cell cycle stage. Here, Shen et al. show that termination of telomere replication requires PP2A phosphatase and Aurora kinase, which work independently but additively to remove active telomerase from telomeres. 12 November 2014 | doi: 10.1038/ncomms6312 Biological Sciences  Cell biology  Molecular biology  Bacterial effector modulation of host E3 ligase activity suppresses PAMP-triggered immunity in rice Kazuya Ishikawa, Koji Yamaguchi, Kazuaki Sakamoto, Satomi Yoshimura, Kento Inoue, Seiji Tsuge, Chojiro Kojima and Tsutomu Kawasaki The mechanisms by which pathogen effector proteins target host defence responses remain poorly understood. Here, Ishikawa et al. show that XopPXoo, a rice pathogen effector, suppresses host plant immunity by inhibiting the activity of an E3 ubiquitin ligase. 12 November 2014 | doi: 10.1038/ncomms6430 Biological Sciences  Plant sciences  Silicon nanofin grating as a miniature chirality-distinguishing beam-splitter Mohammadreza Khorasaninejad and Kenneth B. Crozier There is a need for micro- and nanostructures capable of polarization control to cope with the increasing miniaturization of optics devices. Here, the authors propose a beam-splitter consisting of amorphous silicon nanofins on glass that reflect left- and right-circularly polarized light in different directions. 12 November 2014 | doi: 10.1038/ncomms6386 Physical Sciences  Applied physics  Materials science  Optical physics  Enhanced second-harmonic generation from metal-integrated semiconductor nanowires via highly confined whispering gallery modes Ming-Liang Ren, Wenjing Liu, Carlos O. Aspetti, Liaoxin Sun and Ritesh Agarwal Nanoscale light sources using nonlinearities are needed in many applications but their small size leads to very low efficiencies. Here, Ren et al. exploit the highly confined whispering gallery modes in metal-coated nanowires to achieve enhanced second-harmonic generation with minimal Ohmic losses. 12 November 2014 | doi: 10.1038/ncomms6432 Physical Sciences  Applied physics  Nanotechnology  Optical physics  Target control of complex networks OPEN Jianxi Gao, Yang-Yu Liu, Raissa M. D'Souza and Albert-László Barabási Network controllability has numerous applications in natural and technological systems. Here, Gao et al. develop a theoretical approach and a greedy algorithm to study target control—the ability to efficiently control a preselected subset of nodes—in complex networks. 12 November 2014 | doi: 10.1038/ncomms6415 Physical Sciences  Theoretical physics    Nature Communications JOBS of the week Research Fellow The University of Warwick Research Associate / Senior Research Associate x 2 University College London (UCL) Project leader position in Proteomics (m / f) Leibniz-Institut für Analytische Wissenschaften ISAS e.V. Research Technician de Duve Institute Postdoctoral Fellowship Wayne State University Rice Scholar Postdoctoral Program. Rice University Postdoctoral Research Fellow University of Edinburgh Group Leader Position IMBA-Institute of Molecular Biotechnology Medical Statistician University of Oxford More Science jobs from Nature Communications EVENT 2015 IMB Conference "DNA Repair & Genome Stability in a Chromatin Environment 04.06.15 Mainz, Germany More science events from       Latest Corrigendum     Corrigendum: Atomically resolved imaging of highly ordered alternating fluorinated graphene Reza J. Kashtiban, M. Adam Dyson, Rahul R. Nair, Recep Zan, Swee L. Wong, Quentin Ramasse, Andre K. Geim, Ursel Bangert and Jeremy Sloan 12 November 2014 | doi: 10.1038/ncomms6545 Physical Sciences  Materials science  Nanotechnology        Latest Errata     Erratum: Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion Sungwook Woo and Paul W. K. Rothemund 18 November 2014 | doi: 10.1038/ncomms6610 Chemical Sciences  Biophysics  Nanotechnology      Erratum: In situ nanoindentation study on plasticity and work hardening in aluminium with incoherent twin boundaries D. Bufford, Y. Liu, J. Wang, H. Wang and X. Zhang 17 November 2014 | doi: 10.1038/ncomms6546 Physical Sciences  Materials science
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