Nature Communications - 2 July 2014

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Weekly Content Alert 02 July 2014  Featured image: Thorrold et al. show that Chilean devil rays dive to extreme depths to forage. Latest content: Review Articles Corrigendum Journal homepage Recommend to library Web feed   Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast on: Biomarker discovery: Translating proteomics into clinical diagnostics  Now available on demand  Sponsored by:         Latest Review View all Reviews     Systemic regulation of mammalian ageing and longevity by brain sirtuins Akiko Satoh and Shin-ichiro Imai Sirtuins have been implicated in the ageing process in a variety of organisms, but their role in mammalian ageing remains somewhat controversial. Here the authors discuss sirtuin proteins in the brain, providing an overview of their physiological functions as well as their implication in mammalian ageing. 26 June 2014 | doi: 10.1038/ncomms5211 Biological Sciences  Cell biology  Medical research        Latest Articles View all Articles     Offspring production with sperm grown in vitro from cryopreserved testis tissues Tetsuhiro Yokonishi, Takuya Sato, Mitsuru Komeya, Kumiko Katagiri, Yoshinobu Kubota, Kazuhiko Nakabayashi, Kenichiro Hata, Kimiko Inoue, Narumi Ogonuki, Atsuo Ogura and Takehiko Ogawa As the fertility of pre-pubertal male patients undergoing chemotherapy cannot be preserved using semen cryopreservation, alternative approaches are needed. Here the authors generate live mouse offspring via assisted reproduction technologies, using round spermatids or sperm derived from neonatal mouse cryopreserved testis tissues. 01 July 2014 | doi: 10.1038/ncomms5320 Biological Sciences  Developmental biology  Extreme diving behaviour in devil rays links surface waters and the deep ocean OPEN Simon R. Thorrold, Pedro Afonso, Jorge Fontes, Camrin D. Braun, Ricardo S. Santos, Gregory B. Skomal and Michael L. Berumen Many pelagic fishes and squids live at ocean depths below the euphotic zone but whether surface predators dive to these depths to feed on them is unclear. Here, the authors tag Chilean devil rays and demonstrate that they regularly make dives to at least 1,500 m, suggesting that the rays forage for food at these depths. 01 July 2014 | doi: 10.1038/ncomms5274 Biological Sciences  Zoology  Giant ultrafast photo-induced shear strain in ferroelectric BiFeO3 Mariusz Lejman, Gwenaelle Vaudel, Ingrid C. Infante, Pascale Gemeiner, Vitalyi E. Gusev, Brahim Dkhil and Pascal Ruello The generation of strain in a material using light is of relevance for ultrasonic devices. Here, the authors observe a large, ultrafast photo-induced shear strain in BiFeO3 at room temperature, suggesting promising uses of such oxides for high-frequency acoustic devices. 01 July 2014 | doi: 10.1038/ncomms5301 Physical Sciences  Condensed matter  Materials science  Origin of slow magnetic relaxation in Kramers ions with non-uniaxial anisotropy Silvia Gómez-Coca, Ainhoa Urtizberea, Eduard Cremades, Pablo J. Alonso, Agustín Camón, Eliseo Ruiz and Fernando Luis Transition metal ions with long-lived spin states represent the minimum size magnetic bit. Here, the authors study the spin–lattice relaxation of a cobalt(II) complex and demonstrate the role of time-reversal symmetry that hinders direct spin–phonon processes regardless of the sign of the magnetic anisotropy. 01 July 2014 | doi: 10.1038/ncomms5300 Chemical Sciences  Inorganic chemistry  Global relationship between phytoplankton diversity and productivity in the ocean OPEN S. M. Vallina, M. J. Follows, S. Dutkiewicz, J. M. Montoya, P. Cermeno and M. Loreau The mechanisms that determine the relationship between diversity and productivity in marine phytoplankton remain unclear. Here, Vallina et al. show that selective predation and transient competitive exclusion determine phytoplankton community composition. 01 July 2014 | doi: 10.1038/ncomms5299 Biological Sciences  Ecology  Opposing effects of target overexpression reveal drug mechanisms Adam C. Palmer and Roy Kishony Overexpression of a drug's molecular target increases drug resistance in some cases. Here the authors show that overexpressing antibiotic targets in Escherichia coli can cause positive and negative changes in drug resistance, depending on whether the drug induces harmful reactions involving its target. 01 July 2014 | doi: 10.1038/ncomms5296 Biological Sciences  Evolution  Genetics  Microbiology  An instant multi-responsive porous polymer actuator driven by solvent molecule sorption Qiang Zhao, John W. C. Dunlop, Xunlin Qiu, Feihe Huang, Zibin Zhang, Jan Heyda, Joachim Dzubiella, Markus Antonietti and Jiayin Yuan Soft actuators bearing rapid responsiveness and large-scale actuation are desirable for many biomimetic applications. Here, Zhao et al. build a polymer actuator with a porous architecture, which allows a fast bending response at a timescale of seconds through absorbing a variety of solvent vapours. 01 July 2014 | doi: 10.1038/ncomms5293 Physical Sciences  Condensed matter  Materials science  Direct observation of ultrafast long-range charge separation at polymer–fullerene heterojunctions Françoise Provencher, Nicolas Bérubé, Anthony W. Parker, Gregory M. Greetham, Michael Towrie, Christoph Hellmann, Michel Côté, Natalie Stingelin, Carlos Silva and Sophia C. Hayes Photocarrier generation at organic semiconductor heterojunctions is a crucial process, yet its mechanism and dynamics remain unclear. Here, Provencher et al. show little change in polymer structure following the charge-transfer process and interpret the observation in terms of unbounded electron-hole pairs. 01 July 2014 | doi: 10.1038/ncomms5288 Physical Sciences  Condensed matter  Materials science  Regulatory change at Physalis Organ Size 1 correlates to natural variation in tomatillo reproductive organ size Li Wang, Lingli He, Jing Li, Jing Zhao, Zhichao Li and Chaoying He The genetic basis of plant reproductive organ size is poorly understood. Here, the authors suggest that variation in the gene, Physalis Organ Size 1, regulates reproductive organ size in tomatillo and provides insight into the evolution of the genetic regulation of plant morphology. 01 July 2014 | doi: 10.1038/ncomms5271 Biological Sciences  Genetics  Plant sciences  Rag GTPases are cardioprotective by regulating lysosomal function Young Chul Kim, Hyun Woo Park, Sebastiano Sciarretta, Jung-Soon Mo, Jenna L. Jewell, Ryan C. Russell, Xiaohui Wu, Junichi Sadoshima and Kun-Liang Guan Rag family proteins control activation of the mTORC1 complex at the lysosome. Here the authors show that loss of RagA/B causes cardiac hypertrophy in mice, revealing an mTORC-independent function of Rag GTPAses as regulators of lysosome function and autophagic flux in cardiomyocytes. 01 July 2014 | doi: 10.1038/ncomms5241 Biological Sciences  Cell biology  Medical research  Theoretical prediction of a strongly correlated Dirac metal I. I. Mazin, Harald O. Jeschke, Frank Lechermann, Hunpyo Lee, Mario Fink, Ronny Thomale and Roser Valentí Herbertsmithite is a kagome material presumed to host a spin liquid phase with fractionalized excitations. Here, Mazin et al. study the crystallographic and electronic properties of gallium-substituted herbertsmithite, finding that it has symmetry-protected Dirac points at the Fermi level. 01 July 2014 | doi: 10.1038/ncomms5261 Physical Sciences  Condensed matter  Theoretical physics  Switchable imbibition in nanoporous gold OPEN Yahui Xue, Jürgen Markmann, Huiling Duan, Jörg Weissmüller and Patrick Huber The capillarity-driven uptake of liquids by porous solids can be experienced in daily life, e.g., when a sponge imbibes water. Here, the authors demonstrate that this process can be switched on and off reversibly when nanoporous gold takes the role of the sponge and an electric potential is used to control the surface tension. 01 July 2014 | doi: 10.1038/ncomms5237 Physical Sciences  Materials science  Nanotechnology  Physical chemistry  Approaching the limits of transparency and conductivity in graphitic materials through lithium intercalation Wenzhong Bao, Jiayu Wan, Xiaogang Han, Xinghan Cai, Hongli Zhu, Dohun Kim, Dakang Ma, Yunlu Xu, Jeremy N. Munday, H. Dennis Drew, Michael S. Fuhrer and Liangbing Hu Graphene-based materials have potential as transparent electrodes, but still fall short of desired performance goals. Here, Bao et al. report that upon intercalation of lithium into few-layer graphene, desired sheet resistance and optical transmittance may be achieved. 01 July 2014 | doi: 10.1038/ncomms5224 Physical Sciences  Materials science  Nanotechnology  Optical physics  Structural phase transitions in two-dimensional Mo- and W-dichalcogenide monolayers Karel-Alexander N. Duerloo, Yao Li and Evan J. Reed 2D transition metal dichalcogenide materials can potentially exist in more than one monolayer crystal structure, a feature likely to be useful for electronics that is absent in graphene. Here, the authors present calculations showing that such phase transitions may be readily accessible in MoTe2. 01 July 2014 | doi: 10.1038/ncomms5214 Physical Sciences  Materials science  Nanotechnology  TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease OPEN Yang-Lin Liu, Helen L. Reeves, Alastair D. Burt, Dina Tiniakos, Stuart McPherson, Julian B. S. Leathart, Michael E. D. Allison, Graeme J. Alexander, Anne-Christine Piguet, Rodolphe Anty, Peter Donaldson, Guruprasad P. Aithal, Sven Francque, Luc Van Gaal, Karine Clement, Vlad Ratziu, Jean-Francois Dufour, Christopher P. Day, Ann K. Daly and Quentin M. Anstee et al. Non-alcoholic fatty liver disease (NAFLD) is characterized by increased hepatic triglyceride content (HTGC) in the absence of high alcohol consumption. Here the authors show that a genetic variant in TM6SF2, which is known to be associated with HTGC, is a clinically relevant modifier of hepatic fibrogenesis and increases the risk of progressive NAFLD. 30 June 2014 | doi: 10.1038/ncomms5309 Biological Sciences  Genetics  Isocitrate lyase mediates broad antibiotic tolerance in Mycobacterium tuberculosis Madhumitha Nandakumar, Carl Nathan and Kyu Y. Rhee Mycobacterium tuberculosis is intrinsically resistant to most antibiotics. Here, the authors show that the pathogen's tolerance to three antibiotics, each one targeting a distinct cellular process, is mediated by an antioxidant response that requires the activation of isocitrate lyases. 30 June 2014 | doi: 10.1038/ncomms5306 Biological Sciences  Biochemistry  Microbiology  Shp1 signalling is required to establish the long-lived bone marrow plasma cell pool OPEN Yan-Feng Li, Shengli Xu, Xijun Ou and Kong-Peng Lam SHP-1 signalling is required for the normal development of B lymphocytes but its role in the terminal differentiation of these cells has not been fully established. Here, the authors show that SHP-1 ablation impairs the establishment of long-lived bone marrow-resident plasma cells due to aberrant integrin activation. 30 June 2014 | doi: 10.1038/ncomms5273 Biological Sciences  Immunology  Wigner and Kondo physics in quantum point contacts revealed by scanning gate microscopy B. Brun, F. Martins, S. Faniel, B. Hackens, G. Bachelier, A. Cavanna, C. Ulysse, A. Ouerghi, U. Gennser, D. Mailly, S. Huant, V. Bayot, M. Sanquer and H. Sellier The electrical conductance across quantum point contacts shows quantum steps that are well understood except for some anomalies. Here, the authors are able to explain their origin in terms of spontaneously localized electron states by tuning the potential landscape of the contact with a scanning gate microscope. 30 June 2014 | doi: 10.1038/ncomms5290 Physical Sciences  Condensed matter  Nanotechnology  Molecular basis for bacterial peptidoglycan recognition by LysM domains OPEN Stéphane Mesnage, Mariano Dellarole, Nicola J. Baxter, Jean-Baptiste Rouget, Jordan D. Dimitrov, Ning Wang, Yukari Fujimoto, Andrea M. Hounslow, Sébastien Lacroix-Desmazes, Koichi Fukase, Simon J. Foster and Michael P. Williamson Proteins containing LysM domains recognize polysaccharides such as chitin and peptidoglycan, the main components of fungal and bacterial cell walls. Here the authors describe the molecular interactions between peptidoglycan and a LysM domain from the opportunistic bacterial pathogen Enterococcus faecalis. 30 June 2014 | doi: 10.1038/ncomms5269 Biological Sciences  Biochemistry  Microbiology  Regulating proton-coupled electron transfer for efficient water splitting by manganese oxides at neutral pH OPEN Akira Yamaguchi, Riko Inuzuka, Toshihiro Takashima, Toru Hayashi, Kazuhito Hashimoto and Ryuhei Nakamura Manganese oxides are extensively investigated as analogues of nature's oxygen-evolving complex, but they rarely function at neutral pH. Here, the authors investigate the induction and regulation of the proton-coupled electron-transfer mechanism involved in water oxidation by manganese oxides. 30 June 2014 | doi: 10.1038/ncomms5256 Chemical Sciences  Catalysis  Materials science  Reconfigurable microfluidic hanging drop network for multi-tissue interaction and analysis Olivier Frey, Patrick M. Misun, David A. Fluri, Jan G. Hengstler and Andreas Hierlemann Many tissues can be grown as 3D spheroid models in hanging drops of media. Here, Frey et al. develop a microfluidic, interconnected hanging drop network to facilitate inter-drop communication, and demonstrate that pro-drug conversion by liver spheroids can limit the growth of cancer spheroids in adjacent drops. 30 June 2014 | doi: 10.1038/ncomms5250 Biological Sciences  Biotechnology  Cell biology  Activity-dependent facilitation of Synaptojanin and synaptic vesicle recycling by the Minibrain kinase Chun-Kan Chen, Catherine Bregere, Jeremy Paluch, Jason F. Lu, Dion K. Dickman and Karen T. Chang Dysregulation of the kinase Mnb is implicated in autism spectrum disorder and Down's syndrome. Here the authors demonstrate that Mnb is required for correct synaptic morphology and synaptic vesicle endocytosis, which it achieves via phosphorylation of the synaptic endocytosis protein Synaptojanin. 30 June 2014 | doi: 10.1038/ncomms5246 Biological Sciences  Cell biology  Neuroscience  FOXO1 inhibition yields functional insulin-producing cells in human gut organoid cultures Ryotaro Bouchi, Kylie S. Foo, Haiqing Hua, Kyoichiro Tsuchiya, Yoshiaki Ohmura, P. Rodrigo Sandoval, Lloyd E. Ratner, Dieter Egli, Rudolph L. Leibel and Domenico Accili The transcription factor FOXO1 has been shown to control the differentiation of enteroendocrine cells in mice. Here the authors extend these findings to humans by showing that FOXO1-expressing cells also exist in the human gut, and that inhibition of FOXO1 generates insulin-secreting cells in human gut organoid cultures. 30 June 2014 | doi: 10.1038/ncomms5242 Biological Sciences  Medical research  Lineage-restricted function of the pluripotency factor NANOG in stratified epithelia Daniela Piazzolla, Adelaida R. Palla, Cristina Pantoja, Marta Cañamero, Ignacio Perez de Castro, Sagrario Ortega, Gonzalo Gómez-López, Orlando Dominguez, Diego Megías, Giovanna Roncador, Jose L. Luque-Garcia, Beatriz Fernandez-Tresguerres, Agustin F. Fernandez, Mario F. Fraga, Manuel Rodriguez-Justo, Miguel Manzanares, Marta Sánchez-Carbayo, Juana María García-Pedrero, Juan P. Rodrigo, Marcos Malumbres et al. The transcription factor Nanog regulates self-renewal in pluripotent stem cells and cancer stem cells. Here the authors show that Nanog is expressed in mouse adult stratified epithelia, and its overexpression increases proliferation and aneuploidy and activates pathways associated to mitosis. 30 June 2014 | doi: 10.1038/ncomms5226 Biological Sciences  Cancer  Structural and functional differences in medial prefrontal cortex underlie distractibility and suppression deficits in ageing James Z. Chadick, Theodore P. Zanto and Adam Gazzaley Brain-imaging studies have shown that compared with younger adults, older adults experience an increase in distractibility during working memory tasks. Here, the authors show that the increase in distractibility is in part due to reduced integrity and connectivity of the medial prefrontal cortex in older adults. 30 June 2014 | doi: 10.1038/ncomms5223 Biological Sciences  Neuroscience  Differentiation-dependent requirement of Tsix long non-coding RNA in imprinted X-chromosome inactivation Emily Maclary, Emily Buttigieg, Michael Hinten, Srimonta Gayen, Clair Harris, Mrinal Kumar Sarkar, Sonya Purushothaman and Sundeep Kalantry Imprinted mouse X-chromosome inactivation is controlled by two long non-coding RNAs, Tsix and Xist. Here, Maclary et al. demonstrate that Tsix is dispensable during the initiation and maintenance of X-inactivation in vivo and in vitro, but required to prevent Xist expression as trophectodermal progenitors differentiate. 30 June 2014 | doi: 10.1038/ncomms5209 Biological Sciences  Genetics  Water clustering on nanostructured iron oxide films Lindsay R. Merte, Ralf Bechstein, Guowen Peng, Felix Rieboldt, Carrie A. Farberow, Helene Zeuthen, Jan Knudsen, Erik Lægsgaard, Stefan Wendt, Manos Mavrikakis and Flemming Besenbacher It is not well-understood how nanoscale variations in surface structures impact the ordering of the first few wetting layers on oxide surfaces. Here, the authors employ a model surface, a hydroxylated iron oxide film, which allows direct probing of the impact of hydroxyl groups on the adsorbed water molecules. 30 June 2014 | doi: 10.1038/ncomms5193 Chemical Sciences  Materials science  Physical chemistry  The oil palm VIRESCENS gene controls fruit colour and encodes a R2R3-MYB OPEN Rajinder Singh, Eng-Ti Leslie Low, Leslie Cheng-Li Ooi, Meilina Ong-Abdullah, Rajanaidu Nookiah, Ngoot-Chin Ting, Marhalil Marjuni, Pek-Lan Chan, Maizura Ithnin, Mohd Arif Abdul Manaf, Jayanthi Nagappan, Kuang-Lim Chan, Rozana Rosli, Mohd Amin Halim, Norazah Azizi, Muhammad A. Budiman, Nathan Lakey, Blaire Bacher, Andrew Van Brunt, Chunyan Wang et al. Fruit colour is a trait that affects the harvesting, and therefore oil yield, of the economically important oil palm. Here, the authors identify a gene that may control fruit colour in the oil palm and suggest that selection for this gene during early development could advance the breeding potential of this important crop. 30 June 2014 | doi: 10.1038/ncomms5106 Biological Sciences  Genetics  Plant sciences  Anomalous piezoelectricity in two-dimensional graphene nitride nanosheets Matthew Zelisko, Yuranan Hanlumyuang, Shubin Yang, Yuanming Liu, Chihou Lei, Jiangyu Li, Pulickel M. Ajayan and Pradeep Sharma In piezoelectric materials, mechanical strain and electrical polarization are interlinked. Here, the authors find piezoelectricity in carbon nitride nanosheets, arising from the presence of holes in the two-dimensional sheets. 27 June 2014 | doi: 10.1038/ncomms5284 Physical Sciences  Condensed matter  Nanotechnology  Femtosecond X-ray-induced explosion of C60 at extreme intensity B. F. Murphy, T. Osipov, Z. Jurek, L. Fang, S.-K. Son, M. Mucke, J.H.D. Eland, V. Zhaunerchyk, R. Feifel, L. Avaldi, P. Bolognesi, C. Bostedt, J. D. Bozek, J. Grilj, M. Guehr, L. J. Frasinski, J. Glownia, D. T. Ha, K. Hoffmann, E. Kukk et al. Understanding the dynamics of molecules exposed to intense X-ray beams is crucial to ongoing efforts in biomolecular imaging with free-electron lasers. Here, the authors study C60 molecules interacting with femtosecond X-ray free-electron laser pulses and present a model based on classical and quantum physics. 27 June 2014 | doi: 10.1038/ncomms5281 Physical Sciences  Atomic and molecular physics  Physical chemistry  Legumain protease-activated TAT-liposome cargo for targeting tumours and their microenvironment Ze Liu, Min Xiong, Junbo Gong, Yan Zhang, Nan Bai, Yunping Luo, Luyuan Li, Yuquan Wei, Yanhua Liu, Xiaoyue Tan and Rong Xiang Legumain is a protease found expressed in tumour cells and may be useful in the specific targeting of chemotherapeutics to tumour cells. Here, the authors design nanoparticles that are loaded with doxorubicin and contain a legumain cleavage site; once the nanoparticles enter tumour cells legumain activity results in the release of doxorubicin. 27 June 2014 | doi: 10.1038/ncomms5280 Biological Sciences  Cancer  Engineering interlocking DNA rings with weak physical interactions Zai-Sheng Wu, Zhifa Shen, Kha Tram and Yingfu Li Catenanes are structures composed of interlocked supramolecular rings, and they have possible applications as molecular switches and nanomotors. Here, the authors present a catenane formed of interlocked DNA rings, and show how each ring can display independent functionalities. 27 June 2014 | doi: 10.1038/ncomms5279 Chemical Sciences  Nanotechnology  Degradable lipid nanoparticles with predictable in vivo siRNA delivery activity Kathryn A. Whitehead, J. Robert Dorkin, Arturo J. Vegas, Philip H. Chang, Omid Veiseh, Jonathan Matthews, Owen S. Fenton, Yunlong Zhang, Karsten T. Olejnik, Volkan Yesilyurt, Delai Chen, Scott Barros, Boris Klebanov, Tatiana Novobrantseva, Robert Langer and Daniel G. Anderson Robust and reliable structure–function relationships are valuable for the development of potent drug delivery systems. Here, the authors use a library of lipid-like materials to predict in vivo siRNA delivery efficacy without any biological testing. 27 June 2014 | doi: 10.1038/ncomms5277 Biological Sciences  Chemical biology  Nanotechnology  Sema3E/PlexinD1 regulates the migration of hem-derived Cajal-Retzius cells in developing cerebral cortex Ana Bribián, Sara Nocentini, Franc Llorens, Vanessa Gil, Erik Mire, Diego Reginensi, Yutaka Yoshida, Fanny Mann and José Antonio del Río In the developing cerebral cortex, early generated neurons, called Cajal-Retzius (CR) cells, migrate from their place of origin to the cortical surface. Here the authors show that the secreted axon guidance cue Semaphorin-3E and its receptor PlexinD1 regulate CR migration in mouse embryos. 27 June 2014 | doi: 10.1038/ncomms5265 Biological Sciences  Developmental biology  Neuroscience  Plant genomes enclose footprints of past infections by giant virus relatives OPEN Florian Maumus, Aline Epert, Fabien Nogué and Guillaume Blanc Nucleocytoplasmic large DNA viruses, NCLDVs, are eukaryotic viruses with large genomes, known to infect animals and diverse unicellular eukaryotes. Here, Maumus et al. find NCLDV-like sequences in two land plants and show that they are transcriptionally inactive and highly methylated. 27 June 2014 | doi: 10.1038/ncomms5268 Biological Sciences  Evolution  Genetics  DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes Junichi Yamamoto, Yuri Hagiwara, Kunitoshi Chiba, Tomoyasu Isobe, Takashi Narita, Hiroshi Handa and Yuki Yamaguchi The elongation factors DSIF and NELF have established roles in polymerase pausing, elongation and 3'-end processing of replication-dependent histone mRNAs. Here the authors demonstrate that DSIF and NELF form a complex with Integrator and allow proper 3'-processing of snRNA transcripts by preventing the recruitment of CstF. 27 June 2014 | doi: 10.1038/ncomms5263 Biological Sciences  Biochemistry  Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis OPEN Xiuying Liu, Yan Yin, Jinjun Wu and Zhenfeng Liu Cytidine-diphosphate diacylglycerol (CDP-DAG) is a central liponucleotide intermediate required for the biosynthesis of some phospholipids and is synthesized by CDP-DAG synthetase (Cds). Here, Liu et al. report the structure of a Cds that shows how it can accept hydrophilic and hydrophobic substrates, and suggest a mechanism that requires two metal ions. 27 June 2014 | doi: 10.1038/ncomms5244 Biological Sciences  Biochemistry  Ultra-high aspect ratio high-resolution nanofabrication for hard X-ray diffractive optics Chieh Chang and Anne Sakdinawat The increasing use of hard X-ray sources for scientific and biomedical imaging applications requires the development of suitable optical devices to focus and shape these high-energy beams. Here, Chang and Sakdinawat have fabricated ultra-high aspect ratio nanostructures for hard X-ray focusing. 27 June 2014 | doi: 10.1038/ncomms5243 Physical Sciences  Nanotechnology  Optical physics  Low-grade chromosomal mosaicism in human somatic and embryonic stem cell populations Kurt Jacobs, Afroditi Mertzanidou, Mieke Geens, Ha Thi Nguyen, Catherine Staessen and Claudia Spits De novo copy number variations are known to occur in somatic cell populations and pluripotent stem cells. Here the authors use single-cell array comparative genomic hybridization to identify copy number variations in individual human somatic and embryonic stem cells. 27 June 2014 | doi: 10.1038/ncomms5227 Biological Sciences  Developmental biology  Genetics  Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4 OPEN Yingqi Xu, Anna Plechanovová, Peter Simpson, Jan Marchant, Orsolya Leidecker, Sebastian Kraatz, Ronald T. Hay and Steve J. Matthews SUMO forms flexible polymeric chains that can interact with ubiquitin ligases, such as RNF4. Here Xu et al. have used NMR spectroscopy and biochemical experiments to investigate the interaction between SUMO and RNF4, and propose a mechanism for delivery of substrates to the ubiquitination machinery. 27 June 2014 | doi: 10.1038/ncomms5217 Biological Sciences  Biochemistry  Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate K. A. Modic, Tess E. Smidt, Itamar Kimchi, Nicholas P. Breznay, Alun Biffin, Sungkyun Choi, Roger D. Johnson, Radu Coldea, Pilanda Watkins-Curry, Gregory T. McCandless, Julia Y. Chan, Felipe Gandara, Z. Islam, Ashvin Vishwanath, Arkady Shekhter, Ross D. McDonald and James G. Analytis The spin–orbit interaction and the two-dimensional honeycomb structure of iridium-based oxides are promising for exotic electronic states. Here, the authors find an iridium oxide with a three-dimensional structure that preserves the features of the honeycomb systems, creating new material possibilities. 27 June 2014 | doi: 10.1038/ncomms5203 Physical Sciences  Condensed matter  Materials science  Destabilization of nucleophosmin mRNA by the HuR/KSRP complex is required for muscle fibre formation Anne Cammas, Brenda Janice Sanchez, Xian Jin Lian, Virginie Dormoy-Raclet, Kate van der Giessen, Isabel López de Silanes, Jennifer Ma, Carol Wilusz, John Richardson, Myriam Gorospe, Stefania Millevoi, Matteo Giovarelli, Roberto Gherzi, Sergio Di Marco and Imed-Eddine Gallouzi The expression of the nucleolar protein nucleophosmin (NPM) decreases during the differentiation of various cell types. Here, the authors show that the collaboration between the RNA-binding proteins, HuR and KSRP, reduces the stability of NPM mRNA in myoblasts, thereby allowing myogenesis. 27 June 2014 | doi: 10.1038/ncomms5190 Biological Sciences  Developmental biology  Molecular biology  Work extraction and thermodynamics for individual quantum systems Paul Skrzypczyk, Anthony J. Short and Sandu Popescu Traditionally, thermodynamics deals with the study of macroscopic systems comprised of a large number of particles. Skrzypczyk et al. present a framework—including a thermal bath and work-storage device—to extract the optimal amount of work from individual quantum systems. 27 June 2014 | doi: 10.1038/ncomms5185 Physical Sciences  Theoretical physics  Mild and selective hydrogenation of aromatic and aliphatic (di)nitriles with a well-defined iron pincer complex Christoph Bornschein, Svenja Werkmeister, Bianca Wendt, Haijun Jiao, Elisabetta Alberico, Wolfgang Baumann, Henrik Junge, Kathrin Junge and Matthias Beller Nitrile reduction is a simple method for the generation of amines, though successful catalysts use expensive precious metals such as ruthenium. Here, the authors use an iron complex, demonstrating its application in the hydrogenation of nitriles and dinitriles to primary amines. 27 June 2014 | doi: 10.1038/ncomms5111 Chemical Sciences  Catalysis  Organic chemistry  Differentiating moss from higher plants is critical in studying the carbon cycle of the boreal biome Wenping Yuan, Shuguang Liu, Wenjie Dong, Shunlin Liang, Shuqing Zhao, Jingming Chen, Wenfang Xu, Xianglan Li, Alan Barr, T. Andrew Black, Wende Yan, Mike L. Goulden, Liisa Kulmala, Anders Lindroth, Hank A. Margolis, Yojiro Matsuura, Eddy Moors, Michiel van der Molen, Takeshi Ohta, Kim Pilegaard et al. Satellite-derived indices used to estimate gross primary production and carbon cycling rarely differentiate between boreal mosses and vascular plants, despite differences in photosynthetic capacity. Here, the authors show that this may have led to an overestimation of the boreal carbon budget. 26 June 2014 | doi: 10.1038/ncomms5270 Earth Sciences  Biogeochemistry  Climate science  Character displacement of Cercopithecini primate visual signals William L. Allen, Martin Stevens and James P. Higham Visual signals that help individuals recognize their own species are predicted to be distinct from those of closely related sympatric species, but evidence for this pattern is scarce. Here, Allen et al. show guenon faces are distinctive, specifically from those of other guenon species they encounter. 26 June 2014 | doi: 10.1038/ncomms5266 Biological Sciences  Evolution  Zoology  The Barbier–Grignard-type arylation of aldehydes using unactivated aryl iodides in water Feng Zhou and Chao-Jun Li The Barbier–Grignard reaction is a commonly used method for forming carbon–carbon bonds, but for many substrates it is carried out in organic solvents. Here, the authors show a procedure for carrying out the reaction with unactivated aryl halides in water. 26 June 2014 | doi: 10.1038/ncomms5254 Chemical Sciences  Catalysis  Organic chemistry  Time-bin entangled photons from a quantum dot Harishankar Jayakumar, Ana Predojević, Thomas Kauten, Tobias Huber, Glenn S. Solomon and Gregor Weihs Future quantum technologies will need to be integrated with existing fibre networks, so compatible sources of photons are needed. Towards this aim, Jayakumar et al. present a source of time-bin entangled photons using biexciton–exciton cascade in quantum dots. 26 June 2014 | doi: 10.1038/ncomms5251 Physical Sciences  Nanotechnology  Optical physics  Facile scission of isonitrile carbon–nitrogen triple bond using a diborane(4) reagent OPEN Hiroki Asakawa, Ka-Ho Lee, Zhenyang Lin and Makoto Yamashita The cleavage of triple bonds can be achieved through the use of transition metal catalysts; however, it is less well explored for metal-free systems. Here, the authors show complete cleavage of a carbon–nitrogen triple bond under mild conditions through the use of a diborane(4) reagent. 26 June 2014 | doi: 10.1038/ncomms5245 Chemical Sciences  Inorganic chemistry  Organic chemistry  Allele-specific genome editing and correction of disease-associated phenotypes in rats using the CRISPR–Cas platform OPEN K. Yoshimi, T. Kaneko, B. Voigt and T. Mashimo The bacterial CRISPR–Cas system is increasingly used for genome editing in animal models. Here the authors utilize this system to target and edit specific coat colour alleles in rats and demonstrate the potential of this technology for the creation of genetically engineered animal models. 26 June 2014 | doi: 10.1038/ncomms5240 Biological Sciences  Biotechnology  Genetics  A mortise–tenon joint in the transmembrane domain modulates autotransporter assembly into bacterial outer membranes Denisse L. Leyton, Matthew D. Johnson, Rajiv Thapa, Gerard H.M. Huysmans, Rhys A. Dunstan, Nermin Celik, Hsin-Hui Shen, Dorothy Loo, Matthew J. Belousoff, Anthony W. Purcell, Ian R. Henderson, Travis Beddoe, Jamie Rossjohn, Lisandra L. Martin, Richard A. Strugnell and Trevor Lithgow Bacterial autotransporters are folded in a process that entraps segments of their N-terminal passenger domain. Here, Leyton et al. identify glycine-aromatic mortise and tenon motifs that mediate the passenger domain's translocation to the bacterial cell surface, and show that the motifs are evolutionarily conserved. 26 June 2014 | doi: 10.1038/ncomms5239 Biological Sciences  Biochemistry  Microbiology  Human symptoms–disease network XueZhong Zhou, Jörg Menche, Albert-László Barabási and Amitabh Sharma Unravelling the relationships between disease symptoms and underlying molecular origins is an important task in biomedical research. Here, Zhou et al. link diseases via their symptom overlap, and show that similar phenotypes are mirrored in networks that connect diseases with common genes or protein interactions. 26 June 2014 | doi: 10.1038/ncomms5212 Biological Sciences  Medical research  An artificial primitive mimic of the Gramicidin-A channel Mihail Barboiu, Yann Le Duc, Arnaud Gilles, Pierre-André Cazade, Mathieu Michau, Yves Marie Legrand, Arie van der Lee, Benoît Coasne, Paria Parvizi, Joshua Post and Thomas Fyles Gramicidin A pores are important natural structures for the transport of ions through biological membranes. Here, the authors show that this functionality can be mimicked using an artificial transmembrane channel formed of synthetic pore-forming compounds. 26 June 2014 | doi: 10.1038/ncomms5142 Biological Sciences  Biochemistry  Natural occurring epialleles determine vitamin E accumulation in tomato fruits Leandro Quadrana, Juliana Almeida, Ramon Asís, Tomás Duffy, Pia Guadalupe Dominguez, Luisa Bermúdez, Gabriela Conti, Junia V. Corrêa da Silva, Iris E. Peralta, Vincent Colot, Sebastian Asurmendi, Alisdair R. Fernie, Magdalena Rossi and Fernando Carrari Selecting for varieties of commercial crops with enhanced nutritional quality is important in agriculture. Here, the authors identify alleles of a gene in tomatoes that give rise to increased levels of vitamin E and find that the promoter of the gene is differentially methylated. 26 June 2014 | doi: 10.1038/ncomms5027 Biological Sciences  Genetics  Plant sciences  Diverse matrix metalloproteinase functions regulate cancer amoeboid migration Jose L. Orgaz, Pahini Pandya, Rimple Dalmeida, Panagiotis Karagiannis, Berta Sanchez-Laorden, Amaya Viros, Jean Albrengues, Frank O. Nestle, Anne J. Ridley, Cedric Gaggioli, Richard Marais, Sophia N. Karagiannis and Victoria Sanz-Moreno Migrating cancer cells are round or elongated, and it is thought that the differently shaped cells invade surrounding tissue using different mechanisms. Here, Orgaz et al. show that the round cells secrete matrix metalloproteinases, which allow them to degrade surrounding connective tissue more effectively than elongated cells. 25 June 2014 | doi: 10.1038/ncomms5255 Biological Sciences  Cancer  Cell biology  Porous aromatic frameworks with anion-templated pore apertures serving as polymeric sieves Ye Yuan, Fuxing Sun, Lina Li, Peng Cui and Guangshan Zhu Porous materials for gas separation are industrially important. Here, the authors show that the pores of an aromatic framework can be tuned by the incorporation of counter ions, and that this can direct the interaction with gas molecules of various sizes, allowing separation of complex gas mixtures. 25 June 2014 | doi: 10.1038/ncomms5260 Chemical Sciences  Inorganic chemistry  Materials science  Rotated waveplates in integrated waveguide optics OPEN Giacomo Corrielli, Andrea Crespi, Riccardo Geremia, Roberta Ramponi, Linda Sansoni, Andrea Santinelli, Paolo Mataloni, Fabio Sciarrino and Roberto Osellame Integrated photonic circuits with arbitrary control over the light polarization state are important in quantum information applications. Corrielli et al. realize compact quantum state tomography of polarization-entangled photons using waveguide-integrated waveplates fabricated by femtosecond laser inscription. 25 June 2014 | doi: 10.1038/ncomms5249 Physical Sciences  Applied physics  Optical physics  Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation OPEN Chris S. Clarkson, David Weetman, John Essandoh, Alexander E. Yawson, Gareth Maslen, Magnus Manske, Stuart G. Field, Mark Webster, Tiago Antão, Bronwyn MacInnis, Dominic Kwiatkowski and Martin J. Donnelly Highly divergent genomic islands segregate between a species pair of the mosquito, Anopheles gambiae. Here Clarkson et al. show that loss of one of the largest islands, driven by adaptive introgression of an insecticide-resistance mutation, had no impact on reproductive isolation. 25 June 2014 | doi: 10.1038/ncomms5248 Biological Sciences  Evolution  Genetics  Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics Yuwei Zhang, Ping Song, Qiang Fu, Mingbo Ruan and Weilin Xu Chemical reactions are typically composed of a number of elementary steps, but elucidating these steps is a challenge, particularly in the condensed phase. Here, the authors use quantum chemical calculations and single-molecule spectroscopy to unravel the details of a reversible redox process. 25 June 2014 | doi: 10.1038/ncomms5238 Chemical Sciences  Catalysis  Organic chemistry  Physical chemistry  Made-to-order metal-organic frameworks for trace carbon dioxide removal and air capture OPEN Osama Shekhah, Youssef Belmabkhout, Zhijie Chen, Vincent Guillerm, Amy Cairns, Karim Adil and Mohamed Eddaoudi The capture and removal of low-concentration carbon dioxide from air is appealing. Here, the authors report a metal-organic framework with a precisely tuned network of pores and optimal charge density, which is capable of carbon dioxide uptake at very low partial pressures relevant to direct air capture. 25 June 2014 | doi: 10.1038/ncomms5228 Chemical Sciences  Inorganic chemistry  Materials science  Development of oculomotor circuitry independent of hox3 genes Leung-Hang Ma, Charlotte L. Grove and Robert Baker Hox genes have been implicated in the development and functioning of neural circuits in vertebrates. Here, the authors show that although hox3 genes are not required for overall neural circuit development, they do appear to be necessary to prevent the formation of specific aberrant neuronal connections. 25 June 2014 | doi: 10.1038/ncomms5221 Biological Sciences  Developmental biology  Neuroscience  Self-assembled nanoscale coordination polymers with trigger release properties for effective anticancer therapy Demin Liu, Christopher Poon, Kuangda Lu, Chunbai He and Wenbin Lin Nanoscale coordination polymers are promising materials for use as drug delivery nanoparticles, as their structural properties can be easily and precisely controlled to influence drug loading and release. Here, the authors present such a structure for effective in vivo anticancer therapy. 25 June 2014 | doi: 10.1038/ncomms5182 Biological Sciences  Cancer  Nanotechnology  High-strength carbon nanotube fibre-like ribbon with high ductility and high electrical conductivity J. N. Wang, X. G. Luo, T. Wu and Y. Chen There is strong interest in carbon nanotube assemblies for a variety of applications, many of which require combined high mechanical and electrical properties. Here, the authors demonstrate a rolling technique for performance improvement, reporting tensile strength of 4.34 GPa, ductility of 10% and electrical conductivity of 2.0 × 104 S cm-1. 25 June 2014 | doi: 10.1038/ncomms4848 Physical Sciences  Materials science    Nature Communications JOBS of the week PhD Student University of Oxford Postdoctoral fellow University of Maryland at Baltimore PhD position Lund University Senior Research Fellow University College Cork PhD student Goethe-Universität Frankfurt am Main Research Assistant I The Scripps Research Institute (TSRI) Postdoctoral Research Associate University of Liverpool Research Associate Cardiff University Research Associate King's College London PhD Positions Institute for Stroke and Dementia Research (ISD) More Science jobs from Nature Communications EVENT Genomic Medicine for Clinicians 28.01.15 Cambridge, UK More science events from       Latest Corrigendum     Corrigendum: Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden J. -B. Cazier, S. R. Rao, C. M. McLean, A. L. Walker, B. J. Wright, E. E. M. Jaeger, C. Kartsonaki, L. Marsden, C. Yau, C. Camps, P. Kaisaki, J. Taylor, J. W. Catto, I. P. M. Tomlinson, A. E. Kiltie and F. C. Hamdy 26 June 2014 | doi: 10.1038/ncomms5264 Biological Sciences  Cancer  Genetics        Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com  More Nature Events You have been sent this Table of Contents Alert because you have opted in to receive it. 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