Nature Communications - 10 July 2013

Weekly Content Alert 10 July 2013  Featured image: Lyu et al. show that rice varieties containing a mutation in a gene involved in abscisic acid synthesis have denser lateral roots. Latest content: Articles Corrigendum Erratum Journal homepage Recommend to library Web feed   Advertisement Nature Medicine and the Volkswagen Foundation present: Herrenhausen Symposium on Stem Cells and Regenerative Medicine October 8-10, 2013 Hanover, Germany  Click here for more information or to register for this conference today!       Latest Articles View all Articles     Evaluating cell lines as tumour models by comparison of genomic profiles OPEN Silvia Domcke, Rileen Sinha, Douglas A. Levine, Chris Sander and Nikolaus Schultz Cell lines are widely used in cancer research to study tumour biology. Here Domcke et al. compare genomic data from ovarian cancer cell lines with those from clinical ovarian tumour samples and identify cell lines that most closely resemble the genomic features of high-grade serous ovarian cancer. 09 July 2013 | doi: 10.1038/ncomms3126 Biological Sciences  Bioinformatics  Cancer  Genetics  Experimental realization of an optical second with strontium lattice clocks R. Le Targat, L. Lorini, Y. Le Coq, M. Zawada, J. Guéna, M. Abgrall, M. Gurov, P. Rosenbusch, D. G. Rovera, B. Nagórny, R. Gartman, P. G. Westergaard, M. E. Tobar, M. Lours, G. Santarelli, A. Clairon, S. Bize, P. Laurent, P. Lemonde and J. Lodewyck The SI second is based on caesium microwave fountains, but optical lattice clocks show increasingly greater performances. This work presents two strontium optical lattice clocks agreeing better than their comparison to three fountains, suggesting that such clocks may realize a better definition of the second. 09 July 2013 | doi: 10.1038/ncomms3109 Physical Sciences  Atomic and molecular physics  Optical physics  Temporal niche promotes biodiversity during adaptive radiation Jiaqi Tan, Colleen K. Kelly and Lin Jiang Environmental fluctuation is known to promote biodiversity on ecological timescales, but its consequences for the evolution of biodiversity are unknown. Here, the authors report that alternations in environmental conditions help maintain evolved biodiversity in rapidly diversifying bacterial populations. 09 July 2013 | doi: 10.1038/ncomms3102 Biological Sciences  Ecology  Evolution  The ARNT–STAT3 axis regulates the differentiation of intestinal intraepithelial TCRαβ+CD8αα+ cells Kohei Nakajima, Yoichi Maekawa, Keiko Kataoka, Chieko Ishifune, Jun Nishida, Hideki Arimochi, Akiko Kitamura, Takayuki Yoshimoto, Shuhei Tomita, Shinji Nagahiro and Koji Yasutomo Intraepithelial lymphocytes (IELs) defend against pathogens in the gut, and their differentiation depends on both diet and microbiota-derived factors. Nakajima et al. show that signalling through the aryl hydrocarbon receptor nuclear translocator and STAT3 is required for the development of a subset of IELs. 09 July 2013 | doi: 10.1038/ncomms3112 Biological Sciences  Immunology  The endoskeletal origin of the turtle carapace OPEN Tatsuya Hirasawa, Hiroshi Nagashima and Shigeru Kuratani The evolutionary origins of the costal and neural bony plates of the turtle shell have long remained elusive. Here the authors show, through comparative morphological and embryological analyses, that the most of the carapace is derived from endoskeletal ribs. 09 July 2013 | doi: 10.1038/ncomms3107 Biological Sciences  Developmental biology  Evolution  A new sauropod dinosaur from the Early Cretaceous of Tunisia with extreme avian-like pneumatization Federico Fanti, Andrea Cau, Mohsen Hassine and Michela Contessi The presence of an advance bird-like pulmonary system in sauropods has long remained a controversy. Here, the authors report a new sauropod species, Tataouinea hannibalis, which shows pervasive skeletal pneumatization, supporting an advanced bird-like pulmonary system. 09 July 2013 | doi: 10.1038/ncomms3080 Biological Sciences  Evolution  Palaeontology  Disparity between microRNA levels and promoter strength is associated with initiation rate and Pol II pausing Nadav Marbach-Bar, Amitai Ben-Noon, Shaked Ashkenazi, Ana Tamarkin-Ben Harush, Tali Avnit-Sagi, Michael D. Walker and Rivka Dikstein MicroRNAs are known to be transcribed by RNA polymerase II. The authors show that microRNA promoters driven by TATA-box or NF-κB have increased rates of transcription re-initiation, which leads to local crowding of RNA polymerase II and lower efficiency of microRNA synthesis. 08 July 2013 | doi: 10.1038/ncomms3118 Biological Sciences  Molecular biology  Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion OPEN Johannes Hohlbein, Louise Aigrain, Timothy D. Craggs, Oya Bermek, Olga Potapova, Pouya Shoolizadeh, Nigel D. F. Grindley, Catherine M. Joyce and Achillefs N. Kapanidis The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides. Here, by using an intramolecular single-molecule FRET assay, the authors establish and characterize the partially closed conformation as a crucial fidelity checkpoint. 08 July 2013 | doi: 10.1038/ncomms3131 Biological Sciences  Biochemistry  Molecular biology  Tumour PDGF-BB expression levels determine dual effects of anti-PDGF drugs on vascular remodelling and metastasis Kayoko Hosaka, Yunlong Yang, Takahiro Seki, Masaki Nakamura, Patrik Andersson, Pegah Rouhi, Xiaojuan Yang, Lasse Jensen, Sharon Lim, Ninghan Feng, Yuan Xue, Xuri Li, Ola Larsson, Toshio Ohhashi and Yihai Cao Anti-cancer drugs inhibiting platelet-derived growth factor (PDGF) can either promote or inhibit tumour growth and metastasis. Here, Hosaka et al. ascribe this dual effect of anti-PDGF drugs to the production of the angiogenic ligand PDGF-BB by tumours, which is shown to regulate PDGFR-β signalling in pericytes. 08 July 2013 | doi: 10.1038/ncomms3129 Biological Sciences  Cancer  Medical research  Spin injection and detection in lanthanum- and niobium-doped SrTiO3 using the Hanle technique Wei Han, Xin Jiang, Adam Kajdos, See-Hun Yang, Susanne Stemmer and Stuart S. P. Parkin A crucial prerequisite for semiconductor-based spintronic devices is that the spins of the charge carriers can be efficiently injected and detected. Here, the authors achieve such functionality in niobium-doped strontium titanate by the Hanle technique, and at the same time demonstrate the limitations of this approach. 08 July 2013 | doi: 10.1038/ncomms3134 Physical Sciences  Condensed matter  Materials science  R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli OPEN Hallie Wimberly, Chandan Shee, P. C. Thornton, Priya Sivaramakrishnan, Susan M. Rosenberg and P. J. Hastings DNA double-strand breaks commonly occur in all replicating cells. Wimberly and colleagues show that in non-replicating cells, aborted transcription/translation forms RNA/DNA hybrid R-loops that prime origin-independent replication, leading to DNA breakage, point mutations and chromosomal rearrangements. 05 July 2013 | doi: 10.1038/ncomms3115 Biological Sciences  Molecular biology  Choroid plexus transcytosis and exosome shuttling deliver folate into brain parenchyma Marcel Grapp, Arne Wrede, Michaela Schweizer, Sabine Hüwel, Hans-Joachim Galla, Nicolas Snaidero, Mikael Simons, Johanna Bückers, Philip S. Low, Henning Urlaub, Jutta Gärtner and Robert Steinfeld Impairments in cerebral folate transport are implicated in childhood-onset neurodegeneration. Grapp et al. show that folate receptors in the choroid plexus mediate folate transport by delivering folate receptor-containing exosomes into the brain parenchyma. 05 July 2013 | doi: 10.1038/ncomms3123 Biological Sciences  Cell biology  Medical research  Neuroscience  Tetrasaccharide iteration synthesis of a heparin-like dodecasaccharide and radiolabelling for in vivo tissue distribution studies OPEN Steen U. Hansen, Gavin J. Miller, Claire Cole, Graham Rushton, Egle Avizienyte, Gordon C. Jayson and John M. Gardiner Heparin-like oligosaccharides are implicated in various diseases. Hansen et al. report an efficient two-cycle [4+4+4] tetrasaccharide-iteration-based approach to synthesize a structurally defined heparin dodecasaccharide with a latent aldehyde tag for labelling and conjugation. 05 July 2013 | doi: 10.1038/ncomms3016 Chemical Sciences  Medicinal chemistry  Organic chemistry  Vibrationally induced inversion of photoelectron forward-backward asymmetry in chiral molecule photoionization by circularly polarized light OPEN Gustavo A. Garcia, Laurent Nahon, Steven Daly and Ivan Powis The Franck–Condon principle—frozen nuclear positions during electronic motion—is used to explain many physical phenomena. Garcia et al. show how this breaks down in a photoionized chiral molecule via the vibrational dependence of the photoelectron angular asymmetry in the laboratory frame. 05 July 2013 | doi: 10.1038/ncomms3132 Physical Sciences  Atomic and molecular physics  Analysis of elite variety tag SNPs reveals an important allele in upland rice OPEN Jun Lyu, Shilai Zhang, Yang Dong, Weiming He, Jing Zhang, Xianneng Deng, Yesheng Zhang, Xin Li, Baoye Li, Wangqi Huang, Wenting Wan, Yang Yu, Qiong Li, Jun Li, Xin Liu, Bo Wang, Dayun Tao, Gengyun Zhang, Jun Wang, Xun Xu et al. Quantitative trait loci mapping has traditionally been used to discover desirable alleles in plants. In this study, Lyu et al. use a comparative genome approach to identify an allele that is prevalent in upland rice varieties and alters the function of a protein involved in abscisic acid biosynthesis. 05 July 2013 | doi: 10.1038/ncomms3138 Biological Sciences  Genetics  Plant sciences  The importance of stress percolation patterns in rocks and other polycrystalline materials OPEN P.C. Burnley All rocks contain patterns, but how they form is not clear. Here, finite element models are used to show that grain-to-grain variations in elastic moduli cause stress to percolate in polycrystalline materials, causing shear localization and providing a template for foliation development in rocks. 04 July 2013 | doi: 10.1038/ncomms3117 Earth Sciences  Geology and geophysics  Materials science  Rudimentary substrates for vocal learning in a suboscine Wan-chun Liu, Kazuhiro Wada, Erich Jarvis and Fernando Nottebohm Vocal learning is a feature that is specific to some species of mammals and birds, including oscine songbirds. Liu et al study the vocal, non-learning, eastern phoebe suboscine, and find that it uses the forebrain to control the vocal-motor system, similar to vocal learning oscines. 04 July 2013 | doi: 10.1038/ncomms3082 Biological Sciences  Neuroscience  Zoology  Morphology and mixing state of individual freshly emitted wildfire carbonaceous particles OPEN Swarup China, Claudio Mazzoleni, Kyle Gorkowski, Allison C. Aiken and Manvendra K. Dubey Biomass burning is a major source of carbonaceous particles, including tar balls and soot, that affect earth's climate. Studying a wildfire plume, this work identifies two types of tar balls and classifies soot according to its mixing state with implications for the calculation of aerosol radiative forcing. 04 July 2013 | doi: 10.1038/ncomms3122 Earth Sciences  Atmospheric science  Climate science  Bacterial colonization dampens influenza-mediated acute lung injury via induction of M2 alveolar macrophages OPEN Jian Wang, Fengqi Li, Rui Sun, Xiang Gao, Haiming Wei, Lan-Juan Li and Zhigang Tian Bacterial infections can influence disease outcome in influenza infection; however, the mechanisms mediating these complex interactions remain unclear. Wang et al. reveal how infection with a component of the airway microbiota enhances survival during influenza infection via induction of anti-inflammatory macrophages. 03 July 2013 | doi: 10.1038/ncomms3106 Biological Sciences  Immunology  Microbiology  Virology  Engineering p-wave interactions in ultracold atoms using nanoplasmonic traps B. Juliá-Díaz, T. Graß, O. Dutta, D.E. Chang and M. Lewenstein Controlling p-wave interactions between fermions would enable studies of interesting quantum phenomena. Towards this end, Juliá-Díaz et al. propose a combination of strongly confined nanoplasmonic traps and laser-induced gauge fields that could produce the necessary coupling of atomic states. 03 July 2013 | doi: 10.1038/ncomms3046 Physical Sciences  Atomic and molecular physics  Optical physics  Realistic loophole-free Bell test with atom–photon entanglement C. Teo, M. Araújo, M. T. Quintino, J. Minář, D. Cavalcanti, V. Scarani, M. Terra Cunha and M. França Santos A violation of Bell's inequality would prove that a classical deterministic view of the universe is incorrect; however, despite long-standing efforts, irrefutable experimental proof of such a violation has yet to be produced. Teo et al. propose a realistic scenario that may finally overcome this challenge. 03 July 2013 | doi: 10.1038/ncomms3104 Physical Sciences  Theoretical physics  Emergence of charge order from the vortex state of a high-temperature superconductor Tao Wu, Hadrien Mayaffre, Steffen Krämer, Mladen Horvatić, Claude Berthier, Philip L. Kuhns, Arneil P. Reyes, Ruixing Liang, W. N. Hardy, D. A. Bonn and Marc-Henri Julien The recent discovery of charge order in YBa2Cu3Oy was unexpected. A systematic study of the evolution of this phenomenon as a function of magnetic field conducted by Wu et al. reveals how the competition between charge order and superconductivity may actually be universal to the underdoped cuprates. 03 July 2013 | doi: 10.1038/ncomms3113 Physical Sciences  Condensed matter  Connection between Bell nonlocality and Bayesian game theory Nicolas Brunner and Noah Linden A Bayesian game is one in which each player has incomplete information about all other players in the game. Nicolas Brunner and Noah Linden establish a direct connection between Bayesian games and the abstract theory of Bell nonlocality, which has a prominent role in quantum physics. 03 July 2013 | doi: 10.1038/ncomms3057 Physical Sciences  Theoretical physics  Demonstration of the spin solar cell and spin photodiode effect OPEN B. Endres, M. Ciorga, M. Schmid, M. Utz, D. Bougeard, D. Weiss, G. Bayreuther and C.H. Back Finding ways to accumulate electronic spins of a given polarization in a given location is important to the development of spintronics. Endres et al. demonstrate a device that uses light to drive the accumulation of spin using a similar principle that a solar cell uses to drive the accumulation of charge. 03 July 2013 | doi: 10.1038/ncomms3068 Physical Sciences  Condensed matter  Optical physics  Perceptual judgements and chronic imaging of altered odour maps indicate comprehensive stimulus template matching in olfaction OPEN Edward F. Bracey, Bruno Pichler, Andreas T. Schaefer, Damian J. Wallace and Troy W. Margrie Disruption of glomerular activity maps in the olfactory bulb is believed to have little effect on odour-quality perception. Bracey et al. test this by disrupting olfactory bulb inputs and find that odour recognition relies on matching input patterns to templates from previously encountered odours. 03 July 2013 | doi: 10.1038/ncomms3100 Biological Sciences  Neuroscience  A DNA tweezer-actuated enzyme nanoreactor Minghui Liu, Jinglin Fu, Christian Hejesen, Yuhe Yang, Neal W. Woodbury, Kurt Gothelf, Yan Liu and Hao Yan The control of regulatory enzymes is essential for the modulation of biochemical cellular pathways. Here, the authors fabricate a tweezer-like DNA nanodevice to actuate the activity of an enzyme/cofactor pair, and are able to control enzyme inhibition and activation over multiple cycles. 03 July 2013 | doi: 10.1038/ncomms3127 Chemical Sciences  Nanotechnology  Rapid changes in the electrical state of the 1999 Izmit earthquake rupture zone OPEN Yoshimori Honkura, Naoto Oshiman, Masaki Matsushima, Şerif Barış, Mustafa Kemal Tunçer, Sabri Bülent Tank, Cengiz Çelik and Elif Tolak Çiftçi Low-resistivity crustal fluids occur near fault zones, but their relation to earthquake generation is unclear. Here, electromagnetic data from the Izmit earthquake reflect the pressure-induced transition between isolated and interconnected fluids that is linked to foreshocks before large earthquakes. 03 July 2013 | doi: 10.1038/ncomms3116 Earth Sciences  Geology and geophysics    Nature Communications JOBS of the week Postdoctoral Research Associate University of Southern California Graduate student University of Alberta Research Associate University of Glasgow Six Research Fellows Uppsala University PhD student CEITEC - Central European Institute of Technology Scientific Officer Cancer Research UK / London Research Institute Research Technician Imperial College London Postdocoral Position Cellular and Molecular Immunology at the Free University of Brussels Laboratory Technician UCL Postdoctoral Scientist Medical Research Council, Toxicology Unit More Science jobs from Nature Communications EVENT Cancer Therapeutics 2013: From Bench to Bedside 04.11.13 La Jolla, USA More science events from       Latest Corrigendum     Corrigendum: A low-temperature method to produce highly reduced graphene oxide Hongbin Feng, Rui Cheng, Xin Zhao, Xiangfeng Duan and Jinghong Li 08 July 2013 | doi: 10.1038/ncomms2848 Chemical Sciences  Materials science  Nanotechnology        Latest Erratum     Erratum: GaAs nanopillar-array solar cells employing in situ surface passivation Giacomo Mariani, Adam C. Scofield, Chung-Hong Hung and Diana L. Huffaker 04 July 2013 | doi: 10.1038/ncomms3026 Physical Sciences  Applied physics  Nanotechnology        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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