Nature Communications - 06 May 2015

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Learn More: Transgenic Mouse & Stable Cell Line Services  Journal homepage Recommend to library Web feed     Latest Articles View all Articles     Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis Jurgen van Heemst, Diahann T. S. L. Jansen, Savvas Polydorides, Antonis K. Moustakas, Marieke Bax, Anouk L. Feitsma, Diënne G. Bontrop-Elferink, Martine Baarse, Diane van der Woude, Gert-Jan Wolbink, Theo Rispens, Frits Koning, René R. P. de Vries, George K. Papadopoulos, Georgios Archontis, Tom W. Huizinga and René E. Toes Autoantibodies targeting citrunillated proteins are common in rheumatoid arthritis patients. Here the authors show that vinculin (a human protein) and some microbial proteins are recognized by these antibodies and by CD4+ T cells, and this response is absent in patients carrying a protective HLA allele. 05 May 2015 | doi: 10.1038/ncomms7681 Biological Sciences  Immunology  Medical research  The oldest record of ornithuromorpha from the early cretaceous of China OPEN Min Wang, Xiaoting Zheng, Jingmai K. O’Connor, Graeme T. Lloyd, Xiaoli Wang, Yan Wang, Xiaomei Zhang and Zhonghe Zhou The origin and diversification of early birds remain unclear. Here, the authors report fossils from the oldest known ornithuromorph bird, recovered from the Huajiying Formation in China, which pushes the divergence of these and other early bird lineages back to the Jurassic–Cretaceous transition. 05 May 2015 | doi: 10.1038/ncomms7987 Biological Sciences  Palaeontology  Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds Graham D. Hamblin, Janane F. Rahbani and Hanadi F. Sleiman Assembling defined sequences of DNA is important for many applications, but the synthesis becomes more difficult as the target size increases. Here, the authors report a method for assembling DNA by combining smaller strands, with the final structure determined by the order of addition of the fragments. 05 May 2015 | doi: 10.1038/ncomms8065 Chemical Sciences  Molecular biology  Nanotechnology  Fast and bright spontaneous emission of Er3+ ions in metallic nanocavity OPEN Jung-Hwan Song, Jisu Kim, Hoon Jang, In Yong Kim, Indra Karnadi, Jonghwa Shin, Jung H. Shin and Yong-Hee Lee The Purcell effect predicts a spontaneous emission rate enhancement of several orders of magnitude, but experimental demonstrations have been much lower. Here, Song et al. show emission enhancement of Er3+ ions in a metallic nanocavity with a 170 Purcell factor at room temperature and 55% extraction efficiency. 05 May 2015 | doi: 10.1038/ncomms8080 Physical Sciences  Applied physics  Optical physics  Ultrahigh-capacity non-periodic photon sieves operating in visible light Kun Huang, Hong Liu, Francisco J. Garcia-Vidal, Minghui Hong, Boris Luk’yanchuk, Jinghua Teng and Cheng-Wei Qiu Miniaturization of optical structures allows light control in the nanoscale, but handling a large-scale device with aperiodic and random nanostructures is challenging. Here, Huang et al. design and fabricate a non-periodic photon sieve with control over amplitude, phase and polarization in visible light. 05 May 2015 | doi: 10.1038/ncomms8059 Physical Sciences  Applied physics  Nanotechnology  Optical physics  X-ray photonic microsystems for the manipulation of synchrotron light OPEN D. Mukhopadhyay, D. A. Walko, I. W. Jung, C. P. Schwartz, Jin Wang, D. López and G. K. Shenoy Microelectromechanical systems (MEMS) are essential in a wide range of photonics applications but have not been demonstrated for X-ray optics. Here, Mukhopadhyay et al. use single-crystal silicon to demonstrate a MEMS system that can preserve and manipulate the spatial, temporal and spectral correlations of the X-rays. 05 May 2015 | doi: 10.1038/ncomms8057 Physical Sciences  Applied physics  Nanotechnology  Optical physics  Magnetically induced forward scattering at visible wavelengths in silicon nanosphere oligomers OPEN J. H. Yan, P. Liu, Z. Y. Lin, H. Wang, H. J. Chen, C. X. Wang and G. W. Yang A weak and narrow electric dipole has limited the use of silicon nanospheres in nanophotonic applications requiring strong interaction between electric and magnetic modes. Here, Yan et al. demonstrate effective coupling between the magnetic resonance and the electric gap mode in nearly touching silicon nanospheres. 05 May 2015 | doi: 10.1038/ncomms8042 Physical Sciences  Applied physics  Materials science  Nanotechnology  Observation of laser-induced electronic structure in oriented polyatomic molecules OPEN P. M. Kraus, O. I. Tolstikhin, D. Baykusheva, A. Rupenyan, J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen and H. J. Wörner Although expected to have an influence, the effect of strong laser fields on molecules in high-harmonic generation in gases is rarely explored. Kraus et al. show that the laser modifies the electronic structure of large polyatomic molecules and present a new theoretical framework to model this. 05 May 2015 | doi: 10.1038/ncomms8039 Physical Sciences  Atomic and molecular physics  Physical chemistry  Theoretical physics  Tuning the acoustic frequency of a gold nanodisk through its adhesion layer Wei-Shun Chang, Fangfang Wen, Debadi Chakraborty, Man-Nung Su, Yue Zhang, Bo Shuang, Peter Nordlander, John E. Sader, Naomi J. Halas and Stephan Link The mechanical properties of metal nanostructures depend on nature of the adhesion layer attaching it to a substrate. Chang et al. find that the properties of phonons in gold nanodisks vary with adhesion layer thickness, and that this response can act as a probe of the metallic composition of the disk. 05 May 2015 | doi: 10.1038/ncomms8022 Physical Sciences  Nanotechnology  Optical physics  Enhanced meta-analysis and replication studies identify five new psoriasis susceptibility loci Lam C. Tsoi, Sarah L. Spain, Eva Ellinghaus, Philip E. Stuart, Francesca Capon, Jo Knight, Trilokraj Tejasvi, Hyun M. Kang, Michael H. Allen, Sylviane Lambert, Stefan W. Stoll, Stephan Weidinger, Johann E. Gudjonsson, Sulev Koks, Külli Kingo, Tonu Esko, Sayantan Das, Andres Metspalu, Michael Weichenthal, Charlotta Enerback et al. About 2% of the population are affected by psoriasis, a chronic skin disease with complex genetics. Here Tsoi et al. conduct a meta-analysis of several genome-wide association studies and identify five novel loci, helping to further our understanding of the biology behind this condition. 05 May 2015 | doi: 10.1038/ncomms8001 Biological Sciences  Genetics  High-power multi-megahertz source of waveform-stabilized few-cycle light OPEN O. Pronin, M. Seidel, F. Lücking, J. Brons, E. Fedulova, M. Trubetskov, V. Pervak, A. Apolonski, Th. Udem and F. Krausz Frequency combs have revolutionized the study of electronic structures and dynamics of matter but currently used lasers systems are limited in terms of achievable pulse energies. Here, Pronin et al. demonstrate few cycle pulse emission from a thin-disk laser with 150 nJ pulse energy and 7.7 fs pulse duration. 05 May 2015 | doi: 10.1038/ncomms7988 Physical Sciences  Optical physics  Rubrene crystal field-effect mobility modulation via conducting channel wrinkling OPEN Marcos A. Reyes-Martinez, Alfred J. Crosby and Alejandro L. Briseno Building flexible electronic devices demands an understanding of how mechanical deformation affects the active materials. Here, the authors observe and quantify the effects of local strains generated by the wrinkling instability in the conducting channel of rubrene crystal thin-film transistors. 05 May 2015 | doi: 10.1038/ncomms7948 Physical Sciences  Applied physics  Materials science  Dynamic interplay between catalytic and lectin domains of GalNAc-transferases modulates protein O-glycosylation OPEN Erandi Lira-Navarrete, Matilde de las Rivas, Ismael Compañón, María Carmen Pallarés, Yun Kong, Javier Iglesias-Fernández, Gonçalo J. L. Bernardes, Jesús M. Peregrina, Carme Rovira, Pau Bernadó, Pierpaolo Bruscolini, Henrik Clausen, Anabel Lostao, Francisco Corzana and Ramon Hurtado-Guerrero Polypeptide GalNAc-transferases decorate proteins with dense arrays of O-glycans, which in the case of mucins are essential for their barrier functions. Here the authors present comprehensive structural studies that shed light on the molecular attributes that allow GalNAc-T2 to efficiently carry out dense O-glycosylation. 05 May 2015 | doi: 10.1038/ncomms7937 Biological Sciences  Biochemistry  Biophysics  Two susceptibility loci identified for prostate cancer aggressiveness Sonja I. Berndt, Zhaoming Wang, Meredith Yeager, Michael C. Alavanja, Demetrius Albanes, Laufey Amundadottir, Gerald Andriole, Laura Beane Freeman, Daniele Campa, Geraldine Cancel-Tassin, Federico Canzian, Jean-Nicolas Cornu, Olivier Cussenot, W. Ryan Diver, Susan M. Gapstur, Henrik Grönberg, Christopher A. Haiman, Brian Henderson, Amy Hutchinson, David J. Hunter et al. Prostate cancer often does not progress to invasive disease and thus markers predicting the course of the disease progression are critical for optimal treatment choices. Here the authors show that variants at two genetic loci correlate with the aggressiveness of prostate cancer. 05 May 2015 | doi: 10.1038/ncomms7889 Biological Sciences  Cancer  Genetics  Structural basis for binding of human IgG1 to its high-affinity human receptor FcγRI OPEN Masato Kiyoshi, Jose M.M. Caaveiro, Takeaki Kawai, Shinya Tashiro, Teruhiko Ide, Yoshiharu Asaoka, Kouta Hatayama and Kouhei Tsumoto FcγRs are cell-surface receptors for IgGs that play key roles in the humoral and cellular immune response to infection. Here, the authors present a high-resolution crystal structure of the hFcγRI-Fc complex to reveal the molecular mechanisms underlying the high specificity of this important immunological interaction. 30 April 2015 | doi: 10.1038/ncomms7866 Biological Sciences  Biochemistry  Immunology  Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes Rachel D. Melamed, Kevin J. Emmett, Chioma Madubata, Andrey Rzhetsky and Raul Rabadan Historically, Mendelian disorders were used to provide the first insight into cancer-associated genes. Here Melamed et al. use the unprecedented scope of electronic health records to explore genetic relationships and uncover potentially new drivers of cancer. 30 April 2015 | doi: 10.1038/ncomms8033 Biological Sciences  Cancer  Genetics  Emerging land use practices rapidly increase soil organic matter Megan B. Machmuller, Marc G. Kramer, Taylor K. Cyle, Nick Hill, Dennis Hancock and Aaron Thompson Agricultural practices can degrade soil conditions through the loss of organic matter, a situation that will be exacerbated with growing populations. Here, the authors show that converting cropland to management intensive grazing can rapidly improve soil quality and increase organic matter concentrations. 30 April 2015 | doi: 10.1038/ncomms7995 Earth Sciences  Biogeochemistry  Plant sciences  Tumour-derived SPARC drives vascular permeability and extravasation through endothelial VCAM1 signalling to promote metastasis Mélanie Tichet, Virginie Prod’Homme, Nina Fenouille, Damien Ambrosetti, Aude Mallavialle, Michael Cerezo, Mickaël Ohanna, Stéphane Audebert, Stéphane Rocchi, Damien Giacchero, Fériel Boukari, Maryline Allegra, Jean-Claude Chambard, Jean-Philippe Lacour, Jean-François Michiels, Jean-Paul Borg, Marcel Deckert and Sophie Tartare-Deckert Metastatic cells are thought to influence vascular permeability through secreted factors but the mechanisms are unclear. Here, the authors identify melanoma-secreted SPARC as a major regulator of cancer cell extravasation that modulates endothelial intercellular junctions. 30 April 2015 | doi: 10.1038/ncomms7993 Biological Sciences  Cancer  Cell biology  The molecular landscape of colorectal cancer cell lines unveils clinically actionable kinase targets Enzo Medico, Mariangela Russo, Gabriele Picco, Carlotta Cancelliere, Emanuele Valtorta, Giorgio Corti, Michela Buscarino, Claudio Isella, Simona Lamba, Barbara Martinoglio, Silvio Veronese, Salvatore Siena, Andrea Sartore-Bianchi, Marco Beccuti, Marcella Mottolese, Michael Linnebacher, Francesca Cordero, Federica Di Nicolantonio and Alberto Bardelli Precision oncology relies on model systems that reflect the genomic heterogeneity of human cancers. Here the authors characterize a panel of 151 colorectal cancer cell lines with respect to genetic mutations, expression profiles and drug sensitivity to identify new therapeutic targets. 30 April 2015 | doi: 10.1038/ncomms8002 Biological Sciences  Cancer  Molecular biology  Acetylation of MAT IIα represses tumour cell growth and is decreased in human hepatocellular cancer OPEN Hong-Bin Yang, Ying-Ying Xu, Xiang-Ning Zhao, Shao-Wu Zou, Ye Zhang, Min Zhang, Jin-Tao Li, Feng Ren, Li-Ying Wang and Qun-Ying Lei Folate plays an essential role in dividing cells and is regulated by methionine adenosyltransferase (MAT), where a switch from MAT Iα to MAT IIα expression seems to promote liver cancer progression. Here the authors demonstrate that MAT IIα stability is regulated by acetylation and this regulation is important for tumour growth. 30 April 2015 | doi: 10.1038/ncomms7973 Biological Sciences  Cancer  Molecular biology  A mechanistic model of tau amyloid aggregation based on direct observation of oligomers OPEN Sarah L. Shammas, Gonzalo A. Garcia, Satish Kumar, Magnus Kjaergaard, Mathew H. Horrocks, Nadia Shivji, Eva Mandelkow, Tuomas P.J. Knowles, Eckhard Mandelkow and David Klenerman Alzheimer’s disease is characterized by the aggregation of the Abeta peptide and the tau protein. Here the authors track the formation of wild-type or mutant tau oligomers through to large aggregates and gain insights into the molecular basis of how tau mutations cause disease by altering the aggregation pathway. 30 April 2015 | doi: 10.1038/ncomms8025 Biological Sciences  Biophysics  Correction of human phospholamban R14del mutation associated with cardiomyopathy using targeted nucleases and combination therapy OPEN Ioannis Karakikes, Francesca Stillitano, Mathieu Nonnenmacher, Christos Tzimas, Despina Sanoudou, Vittavat Termglinchan, Chi-Wing Kong, Stephanie Rushing, Jens Hansen, Delaine Ceholski, Fotis Kolokathis, Dimitrios Kremastinos, Alexandros Katoulis, Lihuan Ren, Ninette Cohen, Johannes M.I.H. Gho, Dimitrios Tsiapras, Aryan Vink, Joseph C. Wu, Folkert W. Asselbergs et al. Phospholamban (PLN) is a regulator of heart contractility. Here the authors show that cardiomyocytes derived from induced pluripotent stem cells of a cardiomyopathy patient with mutant PLN exhibit functional defects consistent with the disease, and that this mutation can be functionally corrected by genome editing and gene therapy. 29 April 2015 | doi: 10.1038/ncomms7955 Biological Sciences  Cell biology  Medical research  Nanoscale surface chemistry directs the tunable assembly of silver octahedra into three two-dimensional plasmonic superlattices OPEN Yih Hong Lee, Wenxiong Shi, Hiang Kwee Lee, Ruibin Jiang, In Yee Phang, Yan Cui, Lucio Isa, Yijie Yang, Jianfang Wang, Shuzhou Li and Xing Yi Ling The self-assembly of anisotropic nanoparticles into large-area superlattices remains challenging. Here the authors exploit surface chemistry to tune the wettability of silver nano-octahedra, and direct a continuous superlattice structural evolution, from close-packed to progressively open structures. 29 April 2015 | doi: 10.1038/ncomms7990 Chemical Sciences  Materials science  Nanotechnology  Demonstration of a quantum error detection code using a square lattice of four superconducting qubits OPEN A.D. Córcoles, Easwar Magesan, Srikanth J. Srinivasan, Andrew W. Cross, M. Steffen, Jay M. Gambetta and Jerry M. Chow The physical realization of a quantum computer requires built-in error-correcting codes that compensate the disruption of quantum information arising from noise. Here, the authors demonstrate a quantum error detection scheme for arbitrary single-qubit errors on a four superconducting qubit lattice. 29 April 2015 | doi: 10.1038/ncomms7979 Physical Sciences  Applied physics  Crystalline silica-induced leukotriene B4-dependent inflammation promotes lung tumour growth Shuchismita R. Satpathy, Venkatakrishna R. Jala, Sobha R. Bodduluri, Elangovan Krishnan, Bindu Hegde, Gary W. Hoyle, Mostafa Fraig, Andrew D. Luster and Bodduluri Haribabu Chronic exposure to silica crystals can cause lung inflammation and cancer. Here, the authors show that mast cells and macrophages respond to silica crystals by producing leukotriene B4, which recruits neutrophils leading to inflammation, and that blocking this pathway attenuates cancer progression. 29 April 2015 | doi: 10.1038/ncomms8064 Biological Sciences  Cancer  Immunology  Id1 suppresses anti-tumour immune responses and promotes tumour progression by impairing myeloid cell maturation OPEN Marianna Papaspyridonos, Irina Matei, Yujie Huang, Maria do Rosario Andre, Helene Brazier-Mitouart, Janelle C. Waite, April S. Chan, Julie Kalter, Ilyssa Ramos, Qi Wu, Caitlin Williams, Jedd D. Wolchok, Paul B. Chapman, Hector Peinado, Niroshana Anandasabapathy, Allyson J. Ocean, Rosandra N. Kaplan, Jeffrey P. Greenfield, Jacqueline Bromberg, Dimitris Skokos et al. Tumour progression is promoted by the generation of an immunosuppressive macroenvironment. Here, the authors demonstrate that the Inhibitor of Differentiation 1 promotes the switch from dendritic cell differentiation towards myeloid-derived suppressor cell expansion during tumour progression. 29 April 2015 | doi: 10.1038/ncomms7840 Biological Sciences  Immunology  The NOXA–MCL1–BIM axis defines lifespan on extended mitotic arrest OPEN Manuel D. Haschka, Claudia Soratroi, Susanne Kirschnek, Georg Häcker, Richard Hilbe, Stephan Geley, Andreas Villunger and Luca L. Fava Cells experiencing extended mitotic arrest often undergo cell death as a result of steadily declining levels of the apoptotic inhibitor MCL1, but the mechanism controlling this process is poorly understood. Here, Haschka et al. show that the BH3-only protein NOXA promotes the degradation of MCL1, enabling BIM-dependent cell death. 29 April 2015 | doi: 10.1038/ncomms7891 Biological Sciences  Cell biology  Detecting bit-flip errors in a logical qubit using stabilizer measurements OPEN D. Ristè, S. Poletto, M.-Z. Huang, A. Bruno, V. Vesterinen, O.-P. Saira and L. DiCarlo Future quantum computers will employ error correction to protect quantum data from decoherence and faulty hardware. Here, using a quantum processor with five superconducting qubits, the authors demonstrate how to protect one logical qubit from bitflip errors using multi-qubit, stabilizer measurements. 29 April 2015 | doi: 10.1038/ncomms7983 Physical Sciences  Applied physics  Granulocyte macrophage colony-stimulating factor is required for aortic dissection/intramural haematoma Bo-Kyung Son, Daigo Sawaki, Shota Tomida, Daishi Fujita, Kenichi Aizawa, Hiroki Aoki, Masahiro Akishita, Ichiro Manabe, Issei Komuro, Scott L. Friedman, Ryozo Nagai and Toru Suzuki Aortic dissection and intramural haematoma are caused by separation of the aortic wall via an unknown mechanism. Here the authors show that the inflammatory cytokine, granulocyte macrophage colony-stimulating factor, is a central regulatory molecule causative of these conditions in mice and humans. 29 April 2015 | doi: 10.1038/ncomms7994 Biological Sciences  Medical research  A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation OPEN Saori Tomita, Mohamed Osama Ali Abdalla, Saori Fujiwara, Haruka Matsumori, Kazumitsu Maehara, Yasuyuki Ohkawa, Hirotaka Iwase, Noriko Saitoh and Mitsuyoshi Nakao Estrogen-receptor-positive breast cancer cells undergo hormone-independent proliferation after long-term oestrogen deprivation and become resistant to endocrine therapies. Here, the authors report a cluster of noncoding RNAs important for this adaptation process. 29 April 2015 | doi: 10.1038/ncomms7966 Biological Sciences  Cancer  Molecular biology  Ablation of the p16INK4a tumour suppressor reverses ageing phenotypes of klotho mice OPEN Seidai Sato, Yuka Kawamata, Akiko Takahashi, Yoshinori Imai, Aki Hanyu, Atsushi Okuma, Masaki Takasugi, Kimi Yamakoshi, Hiroyuki Sorimachi, Hiroaki Kanda, Yuichi Ishikawa, Saburo Sone, Yasuhiko Nishioka, Naoko Ohtani and Eiji Hara The protein p16INK4a promotes senescence in tissue stem cells and thereby contributes to organismal ageing. Here the authors reveal that p16INK4a also downregulates expression of a-klotho, thereby revealing an additional ageing-promoting function of 16INK4a that is independent from its role in senescence. 29 April 2015 | doi: 10.1038/ncomms8035 Biological Sciences  Medical research  Cochlear supporting cell transdifferentiation and integration into hair cell layers by inhibition of ephrin-B2 signalling Jean Defourny, Susana Mateo Sánchez, Lies Schoonaert, Wim Robberecht, Alice Davy, Laurent Nguyen and Brigitte Malgrange Cochlear sensory hair cells produced during development are not replaced after loss so converting the surrounding supporting cells into hair cells could be a potential regenerative strategy. Here the authors show that hair cells can be directly generated from adjacent supporting cells in developing mouse embryos by inhibition of ephrin-B2 signalling. 29 April 2015 | doi: 10.1038/ncomms8017 Biological Sciences  Developmental biology  Neuroscience    NatureCommunications JOBS of the week Post Doctoral Fellow Northwestern University- Feinberg School of Medicine Research Assistant / Associate University of Glasgow PhD fellowship Norwegian PSC research center Diabetes UK PhD Studentships Diabetes UK NASA Postdoctoral Fellowships NASA / Oak Ridge Associated Universities Postdoctoral researcher University of Edinburgh Research Associate Keele University Postdoctoral Fellow Iowa State University Postdoc in Neuroscience Institute of Experimental Medicine (IEM) of the Hungarian Academy of Sciences Post-Doctoral Research Assistant Queen Mary University of London More Science jobs from NatureCommunications EVENT EMBO Practical Course: Two-photon imaging of brain function: From spiny dendrites to circuits 05.09.15 Munich, Germany More science events from     Advertisement Nature Genetics, Central South University, and Anhui Medical University present: Genome Variation in Precision Medicine 2015 May 17-19, 2015 | Changsha, China  Register Now!    Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. 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