Nature Communications - 16 October 2013

Weekly Content Alert 16 October 2013  Featured image: Cao et al. sequence the scorpion genome and highlight genes that are likely involved in the adaptation and evolution of arthropods. Latest content: Articles Corrigendum Journal homepage Recommend to library Web feed   Advertisement Nature Insight Tumour Heterogeneity Tumour heterogeneity has important clinical implications, as it can explain therapeutic resistance, but also point to novel strategies to effectively treat cancers in a more personalised manner.  Access the Insight free online for three months      Latest Articles View all Articles     The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods OPEN Zhijian Cao, Yao Yu, Yingliang Wu, Pei Hao, Zhiyong Di, Yawen He, Zongyun Chen, Weishan Yang, Zhiyong Shen, Xiaohua He, Jia Sheng, Xiaobo Xu, Bohu Pan, Jing Feng, Xiaojuan Yang, Wei Hong, Wenjuan Zhao, Zhongjie Li, Kai Huang, Tian Li et al. Scorpions have maintained the primary anatomical features of their Paleozoic arthropod ancestors. Here, the authors report the genome sequence of Mesobuthus martensii and highlight evidence of genetic and morphological evolution that represents a unique adaptation model of arthropods. 15 October 2013 | doi: 10.1038/ncomms3602 Biological Sciences  Evolution  Genetics  Palaeontology  Numerical processing in the human parietal cortex during experimental and natural conditions OPEN Mohammad Dastjerdi, Muge Ozker, Brett L. Foster, Vinitha Rangarajan and Josef Parvizi Human neuronal activity during cognitive processing is usually studied under experimental conditions but activity under natural conditions is poorly understood. Here, the authors develop a method to accurately characterize the activity of the same neuronal population under both conditions. 15 October 2013 | doi: 10.1038/ncomms3528 Biological Sciences  Neuroscience  Earthworms facilitate carbon sequestration through unequal amplification of carbon stabilization compared with mineralization Weixin Zhang, Paul F. Hendrix, Lauren E. Dame, Roger A. Burke, Jianping Wu, Deborah A. Neher, Jianxiong Li, Yuanhu Shao and Shenglei Fu The presence of earthworms in soil may significantly increase CO2 emissions, but the impacts of earthworms on net carbon sequestration are poorly understood. Zhang et al. introduce a new concept by which the effects of earthworms on the balance of carbon mineralization and stabilization can be quantified. 15 October 2013 | doi: 10.1038/ncomms3576 Earth Sciences  Biogeochemistry  Climate science  Real-time in vivo imaging of invasive- and biomaterial-associated bacterial infections using fluorescently labelled vancomycin Marleen van Oosten, Tina Schäfer, Joost A. C. Gazendam, Knut Ohlsen, Eleni Tsompanidou, Marcus C. de Goffau, Hermie J. M. Harmsen, Lucia M. A. Crane, Ed Lim, Kevin P. Francis, Lael Cheung, Michael Olive, Vasilis Ntziachristos, Jan Maarten van Dijl and Gooitzen M. van Dam Invasive and biomaterial-associated infections in humans are often difficult to diagnose and treat. Here, the authors demonstrate that real-time in vivo detection and imaging of these bacterial infections can be successfully performed with fluorescently labelled vancomycin. 15 October 2013 | doi: 10.1038/ncomms3584 Biological Sciences  Medical research  Microbiology  Mechanical adaptability of the Bouligand-type structure in natural dermal armour Elizabeth A. Zimmermann, Bernd Gludovatz, Eric Schaible, Neil K. N. Dave, Wen Yang, Marc A. Meyers and Robert O. Ritchie The scales of Arapaima gigas, a fresh water fish found in the Amazon Basin, act as effective armour against predators. Here, Zimmermann et al. elucidate the deformation mechanisms that allow for this resistance, concluding that lamellae in the scales reorient under an applied load, preventing fracture. 15 October 2013 | doi: 10.1038/ncomms3634 Physical Sciences  Materials science  A search for varying fundamental constants using hertz-level frequency measurements of cold CH molecules OPEN S. Truppe, R.J. Hendricks, S.K. Tokunaga, H.J. Lewandowski, M.G. Kozlov, Christian Henkel, E.A. Hinds and M.R. Tarbutt Some theories predict that fundamental constants may depend on time, position or the local density of matter. Truppe et al. compare new precise frequency measurements of microwave transitions in cold CH with Milky Way data, placing a new limit on variation in the fine structure constant. 15 October 2013 | doi: 10.1038/ncomms3600 Physical Sciences  Astronomy  Atomic and molecular physics  Optical physics  Structural basis of allosteric interactions among Ca2+-binding sites in a K+ channel RCK domain Frank J. Smith, Victor P.T. Pau, Gino Cingolani and Brad S. Rothberg Regulator of K+ conductance (RCK) domains control the gating of potassium channels in response to ligands such as calcium. Smith et al. solve structures of the MthK RCK domain with varying numbers of calcium ions bound, and reveal the structural basis of allosteric coupling between calcium binding sites. 15 October 2013 | doi: 10.1038/ncomms3621 Biological Sciences  Biochemistry  Biophysics  Source time function properties indicate a strain drop independent of earthquake depth and magnitude Martin Vallée Earthquakes occur on a broad range of depths and magnitudes, making their origins and impacts difficult to assess. Here, the analysis of 1,700 earthquakes reveals that strain drop is globally invariant, providing constraints on the rupture process and simplifying the task of earthquake damage predictions. 15 October 2013 | doi: 10.1038/ncomms3606 Earth Sciences  Geology and geophysics  Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation Grégory F. Schneider, Qiang Xu, Susanne Hage, Stephanie Luik, Johannes N. H. Spoor, Sairam Malladi, Henny Zandbergen and Cees Dekker Graphene nanopores hold great potential for single-molecule DNA screening; however, pore clogging due to hydrophobic interactions is a severe problem. Schneider et al. show that this can be prevented by non-covalently coating graphene with an ultrathin hydrophilic self-assembled monolayer. 15 October 2013 | doi: 10.1038/ncomms3619 Physical Sciences  Biophysics  Biotechnology  Smurf2 suppresses B-cell proliferation and lymphomagenesis by mediating ubiquitination and degradation of YY1 Charusheila Ramkumar, Hang Cui, Yahui Kong, Stephen N. Jones, Rachel M. Gerstein and Hong Zhang Mice deficient in the E3 ubiquitin ligase Smurf2 spontaneously develop B-cell lymphomas. Here, Ramkumar et al. show that Smurf2 regulates B-cell proliferation by ubiquitinating the transcription factor YY1, and that Smurf2 expression correlates negatively with survival of patients with diffuse large B-cell lymphoma. 14 October 2013 | doi: 10.1038/ncomms3598 Biological Sciences  Cancer  Cell biology  Evidence for distinct human auditory cortex regions for sound location versus identity processing Jyrki Ahveninen, Samantha Huang, Aapo Nummenmaa, John W. Belliveau, An-Yi Hung, Iiro P. Jääskeläinen, Josef P. Rauschecker, Stephanie Rossi, Hannu Tiitinen and Tommi Raij Observational imaging studies in humans have suggested that sound identification and localization occur in the same region of the auditory cortex. Ahveninen et al. now show that sound identity and location are processed in anterior and posterior regions, respectively, of the auditory cortex. 14 October 2013 | doi: 10.1038/ncomms3585 Biological Sciences  Neuroscience  Zinc-finger nickase-mediated insertion of the lysostaphin gene into the beta-casein locus in cloned cows OPEN Xu Liu, Yongsheng Wang, Wenjiang Guo, Bohao Chang, Jun Liu, Zekun Guo, Fusheng Quan and Yong Zhang Zinc-finger nickases are programmable nucleases that can be used to generate site-specific single-strand breaks in DNA. Liu et al. use this technology to insert an antimicrobial gene into the endogenous beta-casein locus in cloned cows, with the aim of providing protection against mastitis. 14 October 2013 | doi: 10.1038/ncomms3565 Biological Sciences  Biotechnology  Molecular biology  Analysis of mitochondrial genome diversity identifies new and ancient maternal lineages in Cambodian aborigines Xiaoming Zhang, Xuebin Qi, Zhaohui Yang, Bun Serey, Tuot Sovannary, Long Bunnath, Hong Seang Aun, Ham Samnom, Hui Zhang, Qiang Lin, Mannis van Oven, Hong Shi and Bing Su Population genetics studies provide valuable insight into human evolution and migration. Here, the authors have sequenced mitochondrial DNA (mtDNA) from 1,054 Cambodians across 14 populations, reporting eight ancient mtDNA lineages and providing evidence for human migration to Southeast Asia via India. 14 October 2013 | doi: 10.1038/ncomms3599 Biological Sciences  Evolution  Genetics  Septins promote dendrite and axon development by negatively regulating microtubule stability via HDAC6-mediated deacetylation OPEN Natsumi Ageta-Ishihara, Takaki Miyata, Chika Ohshima, Masahiko Watanabe, Yoshikatsu Sato, Yuki Hamamura, Tetsuya Higashiyama, Ralph Mazitschek, Haruhiko Bito and Makoto Kinoshita Septins are a family of heteropolymerizing GTP/GDP-binding proteins and are implicated in neuritogenesis in nematodes. Ageta-Ishihara et al. show that septins also facilitate this process in the developing mouse brain as scaffolds that coordinate HDAC6-mediated deacetylation of microtubules. 11 October 2013 | doi: 10.1038/ncomms3532 Biological Sciences  Cell biology  Developmental biology  Neuroscience  Inferring tumour purity and stromal and immune cell admixture from expression data OPEN Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Treviño, Hui Shen, Peter W. Laird, Douglas A. Levine, Scott L. Carter, Gad Getz, Katherine Stemke-Hale, Gordon B. Mills and Roel G.W. Verhaak Tumour biopsies contain contaminating normal cells and these can influence the analysis of tumour samples. In this study, Yoshihara et al. develop an algorithm based on gene expression profiles from The Cancer Genome Atlas to estimate the number of contaminating normal cells in tumour samples. 11 October 2013 | doi: 10.1038/ncomms3612 Biological Sciences  Bioinformatics  Cancer  Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss Maxim Y. Sheinin, Ming Li, Mohammad Soltani, Karolin Luger and Michelle D. Wang Histone H2A-H2B heterodimers are lost from nucleosomes during transcription by RNA polymerase II. Here, Sheinin et al. investigate the behaviour of single nucleosomes subjected to DNA supercoiling and observe a loss of these heterodimers under positive supercoiling, which might have implications for histone turnover during transcription in vivo. 11 October 2013 | doi: 10.1038/ncomms3579 Biological Sciences  Molecular biology  Deranged fatty acid composition causes pulmonary fibrosis in Elovl6-deficient mice Hiroaki Sunaga, Hiroki Matsui, Manabu Ueno, Toshitaka Maeno, Tatsuya Iso, Mas Rizky A. A. Syamsunarno, Saki Anjo, Takashi Matsuzaka, Hitoshi Shimano, Tomoyuki Yokoyama and Masahiko Kurabayashi The enzyme Elovl6 catalyses a rate-limiting step in the elongation of fatty acids. Here, Sunaga et al. show that Elovl6 knockout mice are more susceptible to pulmonary fibrosis, suggesting that the dysregulation of lipid components impairs alveolar epithelial cell function and pulmonary homeostasis. 11 October 2013 | doi: 10.1038/ncomms3563 Biological Sciences  Medical research  Pellino3 targets RIP1 and regulates the pro-apoptotic effects of TNF-α Shuo Yang, Bingwei Wang, Lisa S. Tang, Jakub Siednienko, John J. Callanan and Paul N. Moynagh Pellino family proteins are ubiquitin ligases known to regulate immune signalling. Here, Yang et al. show that Pellino3 regulates apoptotic TNF signalling by modulating the composition of the death-induced signalling complex, and that absence of Pellino3 sensitizes mice to TNF. 11 October 2013 | doi: 10.1038/ncomms3583 Biological Sciences  Cell biology  Evolutionary history predicts the stability of cooperation in microbial communities Alexandre Jousset, Nico Eisenhauer, Eva Materne and Stefan Scheu Persistence of cooperation requires limited spread of defectors, but it is unclear how evolutionary history affects the spread of these individuals. Here, Jousset et al. show that microbial cooperators can only inhibit defectors that are closely related to them, suggesting that evolutionary history can predict the stability of cooperation. 11 October 2013 | doi: 10.1038/ncomms3573 Biological Sciences  Evolution  Structural and functional characterization of two alpha-synuclein strains OPEN Luc Bousset, Laura Pieri, Gemma Ruiz-Arlandis, Julia Gath, Poul Henning Jensen, Birgit Habenstein, Karine Madiona, Vincent Olieric, Anja Böckmann, Beat H. Meier and Ronald Melki α-synuclein is implicated in neurodegenerative diseases. Bousset et al. generate two α-synuclein polymorphs and find differences in aggregation, function and toxicity, suggesting that these altered properties may be the cause for differences in disease progression. 10 October 2013 | doi: 10.1038/ncomms3575 Biological Sciences  Biophysics  Neuroscience  Multiplexed biomimetic lipid membranes on graphene by dip-pen nanolithography OPEN Michael Hirtz, Antonios Oikonomou, Thanasis Georgiou, Harald Fuchs and Aravind Vijayaraghavan The sensitivity and selectivity of graphene-based biosensors depends on attaching various functional groups to graphene. Hirtz et al. use dip-pen nanolithography to directly write phospholipid membranes on graphene, which enables multiplexed and heterogeneous non-covalent functionalization. 10 October 2013 | doi: 10.1038/ncomms3591 Physical Sciences  Applied physics  Nanotechnology  Circuit reactivation dynamically regulates synaptic plasticity in neocortex Peter B. Kruskal, Lucy Li and Jason N MacLean Slow-wave neural activity, which comprises up and down states, regulates long-term potentiation. Kruskal et al. show that endogenous neural circuit activity corresponding to up states acts as a potent and dynamic promoter of long-term potentiation. 10 October 2013 | doi: 10.1038/ncomms3574 Biological Sciences  Neuroscience  Photochemical reflectance index as an indirect estimator of foliar isoprenoid emissions at the ecosystem level Josep Peñuelas, Giovanni Marino, Joan LLusia, Catherine Morfopoulos, Gerard Farré-Armengol and Iolanda Filella Isoprene and monoterpenes, emitted by terrestrial plants, have an important role in both plant biology and environment, but they are poorly quantified at the ecosystem level. Peñuelas et al. show that the photochemical reflectance index can be used to indirectly estimate foliar isoprenoid emissions remotely. 10 October 2013 | doi: 10.1038/ncomms3604 Earth Sciences  Atmospheric science  Biogeochemistry  Blurry topography for precise target-distance computations in the auditory cortex of echolocating bats Julio C. Hechavarría, Silvio Macías, Marianne Vater, Cornelia Voss, Emanuel C. Mora and Manfred Kössl Topographic cortical representation of echo delay is instrumental for general orientation in bats. Hechavarría et al. show that topographic maps in the bat auditory cortex that are associated with minimal and optimal echo delays are less organized than maps associated with maximum echo delays. 10 October 2013 | doi: 10.1038/ncomms3587 Biological Sciences  Neuroscience  Integrated spatial multiplexing of heralded single-photon sources OPEN M.J. Collins, C. Xiong, I.H. Rey, T.D. Vo, J. He, S. Shahnia, C. Reardon, T.F. Krauss, M.J. Steel, A.S. Clark and B.J. Eggleton Photonic quantum technologies will require efficient single-photon sources and spatial multiplexing has been explored as a route to achieve this. Here, the authors present a scheme to integrate several single-photon sources using spatial multiplexing for on-chip applications at telecommunications wavelengths. 10 October 2013 | doi: 10.1038/ncomms3582 Physical Sciences  Applied physics  Optical physics  DNA-based highly tunable particle focuser Kyowon Kang, Sung Sik Lee, Kyu Hyun, Seong Jae Lee and Ju Min Kim Particle focusing in microfluidic channels can be done in viscoelastic mediums such as synthetic polymer solutions. Kang et al. report that dilute DNA solutions are more efficient elasticity enhancers for this purpose and the same degree of focusing can be achieved at much lower concentrations. 10 October 2013 | doi: 10.1038/ncomms3567 Physical Sciences  Biophysics  Fluids and plasma physics  Apical membrane antigen 1 mediates apicomplexan parasite attachment but is dispensable for host cell invasion OPEN Daniel Y. Bargieri, Nicole Andenmatten, Vanessa Lagal, Sabine Thiberge, Jamie A. Whitelaw, Isabelle Tardieux, Markus Meissner and Robert Ménard Plasmodium and Toxoplasma apical membrane antigen 1 (AMA1) is believed to be actively involved in host cell invasion by these parasites. Bargieri et al. now demonstrate that although AMA1 facilitates adhesion, invasion can proceed in the absence of the protein. 10 October 2013 | doi: 10.1038/ncomms3552 Biological Sciences  Hydrodefluorination of carbon–fluorine bonds by the synergistic action of a ruthenium–palladium catalyst Sara Sabater, Jose A. Mata and Eduardo Peris Selective hydrodefluoridization is important as an industrial reaction and in the disposal of chlorofluorocarbons. Here, the authors prepare a heterodimetallic ruthenium–palladium complex, which is active in the hydrodefluorination of aromatic and aliphatic molecules under mild reaction conditions. 09 October 2013 | doi: 10.1038/ncomms3553 Chemical Sciences  Catalysis  Inorganic chemistry  Organic chemistry  Substrate ectodomain is critical for substrate preference and inhibition of γ-secretase OPEN Satoru Funamoto, Toru Sasaki, Seiko Ishihara, Mika Nobuhara, Masaki Nakano, Miho Watanabe-Takahashi, Takashi Saito, Nobuto Kakuda, Tomohiro Miyasaka, Kiyotaka Nishikawa, Takaomi C. Saido and Yasuo Ihara γ-Secretase inhibitors are studied for their potential to treat Alzheimer's disease, but their use is limited by side effects. Funamoto et al. show that γ-secretase preferentially cleaves substrates with short ectodomains and that inhibitors based on these ectodomains reduce disease-like pathology in mice. 09 October 2013 | doi: 10.1038/ncomms3529 Biological Sciences  Neuroscience  Hyperbolic spin vortices and textures in exciton–polariton condensates F. Manni, Y. Léger, Y.G. Rubo, R. André and B. Deveaud Topologically stable excitations in quantum systems are important to the understanding of phase transitions in many systems, from cosmology to condensed matter physics. Here, Manni et al. observe such topological objects, spin vortices in exciton–polariton condensates, allowing for a more detailed understanding of such quantum fluids. 09 October 2013 | doi: 10.1038/ncomms3590 Physical Sciences  Condensed matter  Optical physics    Nature Communications JOBS of the week Research Associate The University of Warwick Post Doctoral Research Fellow Otto-Von-Guericke University Magdeburg Research Associate King's College London Postdoctoral Fellow Oklahoma University Health Science Center Postdoctoral Associate University of Iowa Carver College of Medicine PhD student (f / m) Universitätsklinikum Carl Gustav Carus Research Associate University of Glasgow Associate Research Scientist Columbia University Postdoctoral Scientist University of Oxford PhD student Institute of Physical Chemistry, Polish Academy of Sciences More Science jobs from Nature Communications EVENT NanoBio-Europe Congress 2014 02.06.14 Münster, Germany More science events from       Latest Corrigendum     Corrigendum: High frequency of telomerase reverse-transcriptase promoter somatic mutations in hepatocellular carcinoma and preneoplastic lesions Jean Charles Nault, Maxime Mallet, Camilla Pilati, Julien Calderaro, Paulette Bioulac-Sage, Christophe Laurent, Alexis Laurent, Daniel Cherqui, Charles Balabaud and Jessica Zucman-Rossi 10 October 2013 | doi: 10.1038/ncomms3577 Biological Sciences  Cancer  Genetics      Advertisement UCSD Clinical and Translational Research Institute and Nature Medicine present: Bench to Bedside 2013: Cancer Therapeutics November 4-6, 2013 Estancia La Jolla Hotel La Jolla, CA, USA  Click here for more information or to register for this conference today!     Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. 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