Nature Communications - 24 July 2013

Advertisement "Thank you for the rapid publication of our paper, it was the first report on the knockout of the gene Btg1; other competitors are working on it, so it was essential to proceed rapidly with the online publication." Frontiers Author Find out more about the Frontiers publishing model here     Weekly Content Alert 24 July 2013  Featured image: Carbonell et al. use a microfluidic stylus to perform a range of discrete femtolitre-scale reactions and crystallizations on a surface. Latest content: Articles Journal homepage Recommend to library Web feed   Advertisement CNIO, Nature, Nature Cell Biology and Nature Reviews Cancer present: CNIO Cancer Symposium: Frontiers in Tumor Heterogeneity and Plasticity October 27-30, 2013 Madrid, Spain  Click here for more information or to register for this conference today!       Latest Articles View all Articles     hESC-derived Olig2+ progenitors generate a subtype of astroglia with protective effects against ischaemic brain injury OPEN Peng Jiang, Chen Chen, Ruimin Wang, Olga V. Chechneva, Seung-Hyuk Chung, Mahendra S. Rao, David E. Pleasure, Ying Liu, Quanguang Zhang and Wenbin Deng Astroglia are heterogeneous in phenotype and not all astrocytes are equivalent in their ability to repair injured brain. Here, the authors show that two defined subtypes of astroglia generated from hESC-derived Olig2-positive versus Olig2-negative neural progenitors, exhibit distinct properties and neuroprotective effects. 23 July 2013 | doi: 10.1038/ncomms3196 Biological Sciences  Developmental biology  Neuroscience  Impact tolerance in mussel thread networks by heterogeneous material distribution Zhao Qin and Markus J. Buehler The ability of mussels to remain attached to rocks and the hulls of ships in the presence of impacting waves is surprising. Qin et al. show that a heterogeneous distribution of specific load-bearing materials in the attaching threads allows for this firm adhesion. 23 July 2013 | doi: 10.1038/ncomms3187 Physical Sciences  Materials science  Mean-field theory of random close packings of axisymmetric particles Adrian Baule, Romain Mari, Lin Bo, Louis Portal and Hernán A. Makse Finding the densest random packing of particles with a non-spherical shape is a long standing mathematical problem. Here, the authors develop a method based on a mean-field estimation of the Voronoi volume which can predict densest random packings in good agreement with empirical results. 23 July 2013 | doi: 10.1038/ncomms3194 Physical Sciences  Materials science  Theoretical physics  Identification of ROCK1 kinase as a critical regulator of Beclin1-mediated autophagy during metabolic stress Aditi U. Gurkar, Kiki Chu, Lakshmi Raj, Richard Bouley, Seung-Hwan Lee, Young-Bum Kim, Sandra E. Dunn, Anna Mandinova and Sam W. Lee The kinase ROCK1 has been implicated in apoptosis and other cellular functions. Here Gurkar et al. show that ROCK1 phosphorylates the autophagy regulator Beclin1, which activates autophagy by disrupting the association between Beclin-1 and Bcl-2. 23 July 2013 | doi: 10.1038/ncomms3189 Biological Sciences  Cell biology  DNA unmethylome profiling by covalent capture of CpG sites Edita Kriukienė, Viviane Labrie, Tarang Khare, Giedrė Urbanavičiūtė, Audronė Lapinaitė, Karolis Koncevičius, Daofeng Li, Ting Wang, Shraddha Pai, Carolyn Ptak, Juozas Gordevičius, Sun-Chong Wang, Artūras Petronis and Saulius Klimašauskas Chemical modifications of CpG dinucleotides form part of the epigenetic code and various methods for the detection of modified CpG sites exist. Here Kriukiene and colleagues report a complementary method that allows the profiling of unmodified CpG sites within the genome, which they call the 'unmethylome'. 23 July 2013 | doi: 10.1038/ncomms3190 Biological Sciences  Genetics  Molecular biology  In-situ ultra-sensitive infrared absorption spectroscopy of biomolecule interactions in real time with plasmonic nanoantennas OPEN Ronen Adato and Hatice Altug Infrared absorption spectroscopy provides important information about molecules, but is hampered by the absorption of water. Adato and Altug exploit the plasmonic enhancement from nanoantennas to overcome this, enabling chip-based monitoring of biological samples in aqueous environments. 23 July 2013 | doi: 10.1038/ncomms3154 Physical Sciences  Applied physics  Nanotechnology  Optical physics  Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica OPEN Michael Kube, Tatyana N. Chernikova, Yamal Al-Ramahi, Ana Beloqui, Nieves Lopez-Cortez, María-Eugenia Guazzaroni, Hermann J. Heipieper, Sven Klages, Oleg R. Kotsyurbenko, Ines Langer, Taras Y. Nechitaylo, Heinrich Lünsdorf, Marisol Fernández, Silvia Juárez, Sergio Ciordia, Alexander Singer, Olga Kagan, Olga Egorova, Pierre Alain Petit, Peter Stogios et al. Oleispira antarctica is an oil-degrading enzyme found in the cold and deep sea. Here Kube et al. report the genome sequence of O. antarctica and provide a comprehensive functional genetic and protein structural analysis, revealing insights into how this organism has adapted to its cold environment. 23 July 2013 | doi: 10.1038/ncomms3156 Biological Sciences  Genetics  Microbiology  Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota Yongfei Hu, Xi Yang, Junjie Qin, Na Lu, Gong Cheng, Na Wu, Yuanlong Pan, Jing Li, Liying Zhu, Xin Wang, Zhiqi Meng, Fangqing Zhao, Di Liu, Juncai Ma, Nan Qin, Chunsheng Xiang, Yonghong Xiao, Lanjuan Li, Huanming Yang, Jian Wang et al. The appearance of antibiotic resistance has been attributed to the misuse of antibiotics. By analysing the diversity of antibiotic resistance genes present in 162 human gut microbiota samples, the authors find that Chinese individuals harbour a larger pool of resistance genes than Spanish or Danish counterparts. 23 July 2013 | doi: 10.1038/ncomms3151 Biological Sciences  Genetics  Medical research  Microbiology  One hundred fold increase in current carrying capacity in a carbon nanotube–copper composite OPEN Chandramouli Subramaniam, Takeo Yamada, Kazufumi Kobashi, Atsuko Sekiguchi, Don N. Futaba, Motoo Yumura and Kenji Hata High electrical conductivity and ampacity are usually mutually exclusive properties. Here, in a carbon nanotube–copper composite, Subramaniam et al. achieve a similar conductivity to copper, but with a hundred fold increase in current carrying capacity. 23 July 2013 | doi: 10.1038/ncomms3202 Physical Sciences  Materials science  Nanotechnology  Rare-earth-doped biological composites as in vivo shortwave infrared reporters D. J. Naczynski, M. C. Tan, M. Zevon, B. Wall, J. Kohl, A. Kulesa, S. Chen, C. M. Roth, R. E. Riman and P. V. Moghe The short-wavelength infrared spectral region is of interest for bio-imaging applications as biological tissue is transparent to such light. Here Naczynski et al. fabricate rare-earth-based nanomaterials and demonstrate multispectral, real-time short-wavelength infrared in-vivo imaging. 22 July 2013 | doi: 10.1038/ncomms3199 Chemical Sciences  Chemical biology  Nanotechnology  Small molecules enable neurogenin 2 to efficiently convert human fibroblasts into cholinergic neurons Meng-Lu Liu, Tong Zang, Yuhua Zou, Joshua C. Chang, Jay R. Gibson, Kimberly M. Huber and Chun-Li Zhang Human non-neuronal somatic cells can be converted into neurons; however, this is a low-efficiency process and the resulting neuronal subtypes are of low purity. Here the authors show that two small molecules enable NGN2 to efficiently convert human fibroblasts into pure cholinergic neurons. 22 July 2013 | doi: 10.1038/ncomms3183 Biological Sciences  Developmental biology  Neuroscience  The p53–PUMA axis suppresses iPSC generation Yanxin Li, Haizhong Feng, Haihui Gu, Dale W. Lewis, Youzhong Yuan, Lei Zhang, Hui Yu, Peng Zhang, Haizi Cheng, Weimin Miao, Weiping Yuan, Shi-Yuan Cheng, Susanne M. Gollin and Tao Cheng Inhibition of the p53–p21 axis increases reprogramming efficiency of somatic cells into induced pluripotent stem cells (iPSCs). Here the authors show that depletion of the pro-apoptotic factor PUMA, acting downstream of p53, increases reprogramming efficiency, providing new insights into the roles of p53 in reprogramming. 22 July 2013 | doi: 10.1038/ncomms3174 Biological Sciences  Developmental biology  Molecular biology  SNAP-25 regulates spine formation through postsynaptic binding to p140Cap Romana Tomasoni, Daniele Repetto, Raffaella Morini, Chiara Elia, Fabrizio Gardoni, Monica Di Luca, Emilia Turco, Paola Defilippi and Michela Matteoli The SNARE protein family member, SNAP-25, is implicated in modulating synaptic plasticity. Tomasoni et al. show that SNAP-25 recruits the protein p140Cap in order to regulate the density, morphology and functionality of dendritic spines. 19 July 2013 | doi: 10.1038/ncomms3136 Biological Sciences  Cell biology  Neuroscience  Distinct iron isotopic signatures and supply from marine sediment dissolution OPEN William B. Homoky, Seth G. John, Tim M. Conway and Rachel A. Mills The dissolution of iron from sediments along ocean margins may stimulate photosynthesis and moderate global climate. This study shows how margin sediments supply iron in varying amounts between regions, and by distinct mechanisms, which may be due to geological characteristics and hydrological controls on land. 19 July 2013 | doi: 10.1038/ncomms3143 Earth Sciences  Biogeochemistry  Oceanography  A green lead hydrometallurgical process based on a hydrogen-lead oxide fuel cell Junqing Pan, Yanzhi Sun, Wei Li, James Knight and Arumugam Manthiram Lead-acid batteries are used worldwide, but their recycling remains challenging because of lead pollution and high energy consumption. Pan et al. solve these problems in a high-yield, hydrometallurgical process based on hydrogen-lead oxide fuel cell reactions, which produce water as the by-product. 19 July 2013 | doi: 10.1038/ncomms3178 Chemical Sciences  Inorganic chemistry  Physical chemistry  Understanding the role of phase in chemical bond breaking with coincidence angular streaking J. Wu, M. Magrakvelidze, L.P.H. Schmidt, M. Kunitski, T. Pfeifer, M. Schöffler, M. Pitzer, M. Richter, S. Voss, H. Sann, H. Kim, J. Lower, T. Jahnke, A. Czasch, U. Thumm and R. Dörner Ultrafast laser pulses are useful to study electron dynamics in chemical bonds, but their influence on bond breaking is not fully understood. Wu et al. study H2 bond breaking with coincidence techniques, and find a phase-dependent anisotropy of the H+ fragmentation even for isotropic multicycle laser pulses. 19 July 2013 | doi: 10.1038/ncomms3177 Physical Sciences  Atomic and molecular physics  Optical physics  Physical chemistry  Desktop nanofabrication with massively multiplexed beam pen lithography Xing Liao, Keith A. Brown, Abrin L. Schmucker, Guoliang Liu, Shu He, Wooyoung Shim and Chad A. Mirkin The development of a desktop nanofabrication tool allowing high-resolution patterning and high-throughput synthesis is a long-standing goal in many nanoscience fields. Here, the authors report a system that can write arbitrary patterns composed of diffraction-unlimited features over square centimetre areas. 19 July 2013 | doi: 10.1038/ncomms3103 Chemical Sciences  Materials science  Nanotechnology  Bio-responsive polymer hydrogels homeostatically regulate blood coagulation OPEN Manfred F. Maitz, Uwe Freudenberg, Mikhail V. Tsurkan, Marion Fischer, Theresa Beyrich and Carsten Werner Implementing biomolecular recognition mechanisms in synthetic materials may enable a wealth of biomedical and related applications. Here Maitz et al. present a bio-responsive hydrogel that releases the anticoagulant heparin in amounts proportional to the environmental levels of the procoagulatory protein thrombin. 19 July 2013 | doi: 10.1038/ncomms3168 Chemical Sciences  Materials science  Medical research  Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites Douglas J. Bakkum, Urs Frey, Milos Radivojevic, Thomas L. Russell, Jan Müller, Michele Fiscella, Hirokazu Takahashi and Andreas Hierlemann Optical techniques that are used to study neuronal action potential propagation are limited by phototoxicity and photobleaching. Here the authors describe a microelectrode system that allows simultaneous stimulation and recordings of action potential propagation across hundreds of sites in cultured neurons. 19 July 2013 | doi: 10.1038/ncomms3181 Biological Sciences  Neuroscience  Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer OPEN Henrik J. Johansson, Betzabe C. Sanchez, Filip Mundt, Jenny Forshed, Aniko Kovacs, Elena Panizza, Lina Hultin-Rosenberg, Bo Lundgren, Ulf Martens, Gyöngyvér Máthé, Zohar Yakhini, Khalil Helou, Kamilla Krawiec, Lena Kanter, Anders Hjerpe, Olle Stål, Barbro K. Linderholm and Janne Lehtiö Many patients with breast cancer develop resistance to the drug tamoxifen and relapse. Here Johansson et al. identify the nuclear receptor retinoic acid receptor alpha (RARA) as a marker of tamoxifen resistance and show that RARA expression correlates negatively with relapse-free survival of patients. 19 July 2013 | doi: 10.1038/ncomms3175 Biological Sciences  Cancer  Medical research  Semiclassical Monte-Carlo approach for modelling non-adiabatic dynamics in extended molecules OPEN Vyacheslav N. Gorshkov, Sergei Tretiak and Dmitry Mozyrsky Many interesting chemical problems like photosynthesis and photovoltaics involve non-adiabatic dynamical phenomena, which are difficult to predict theoretically. Here, the authors develop a new numerical method capable of recovering quantum interferences that are neglected by conventional methods. 18 July 2013 | doi: 10.1038/ncomms3144 Physical Sciences  Physical chemistry  Theoretical physics  Fast GCaMPs for improved tracking of neuronal activity Xiaonan R. Sun, Aleksandra Badura, Diego A. Pacheco, Laura A. Lynch, Eve R. Schneider, Matthew P. Taylor, Ian B. Hogue, Lynn W. Enquist, Mala Murthy and Samuel S. -H. Wang Genetically encoded calcium indicators are commonly used to study cellular activity, but their usefulness is limited by their response kinetics. Here the authors generate indicators with faster responses to calcium events in both Drosophila melanogaster and mammalian neurons. 18 July 2013 | doi: 10.1038/ncomms3170 Biological Sciences  Neuroscience  Pirt functions as an endogenous regulator of TRPM8 Zongxiang Tang, Andrew Kim, Thorsten Masuch, Kyoungsook Park, HaoJui Weng, Christian Wetzel and Xinzhong Dong The gene Pirt encodes a transmembrane domain protein that is expressed in sensory neurons. Tang and colleagues use calcium imaging and electrophysiology to show that Pirt positively regulates the transient receptor potential channel TRPM8, and that deletion of this protein results in impaired cold sensitivity. 18 July 2013 | doi: 10.1038/ncomms3179 Biological Sciences  Neuroscience  Meta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2 OPEN Paul Guilhamon, Malihe Eskandarpour, Dina Halai, Gareth A. Wilson, Andrew Feber, Andrew E. Teschendorff, Valenti Gomez, Alexander Hergovich, Roberto Tirabosco, M. Fernanda Amary, Daniel Baumhoer, Gernot Jundt, Mark T. Ross, Adrienne M. Flanagan and Stephan Beck Cancer-associated mutations in isocitrate dehydrogenase are proposed to impair TET2-dependent DNA demethylation. By comparing the methylomes of IDH-mutant cancers, the authors identify the transcription factor EBF1 as a partner of TET2, suggesting a possible means for targeting TET2 to specific DNA sequences. 18 July 2013 | doi: 10.1038/ncomms3166 Biological Sciences  Cancer  Molecular biology  Reconstructing genome evolution in historic samples of the Irish potato famine pathogen OPEN Michael D. Martin, Enrico Cappellini, Jose A. Samaniego, M. Lisandra Zepeda, Paula F. Campos, Andaine Seguin-Orlando, Nathan Wales, Ludovic Orlando, Simon Y. W. Ho, Fred S. Dietrich, Piotr A. Mieczkowski, Joseph Heitman, Eske Willerslev, Anders Krogh, Jean B. Ristaino and M. Thomas P. Gilbert Phytophthora infestans caused the potato famine in the nineteenth century. Martin et al. sequence the nuclear genomes of five archival samples of the pathogen and compare these to extant specimens allowing the reconstruction of the evolutionary history of P. infestans. 18 July 2013 | doi: 10.1038/ncomms3172 Biological Sciences  Bioinformatics  Evolution  Genetics  Microbiology  Interfacial liquid-state surface-enhanced Raman spectroscopy Kihoon Kim, Hye Soo Han, Inhee Choi, Chiwon Lee, SoonGweon Hong, Sang-Hee Suh, Luke P. Lee and Taewook Kang Assembly of functional colloidal nanoparticles has many technological applications, but its three-dimensional realization remains challenging. Kim et al. report a spontaneous self-orientation of gold nanorods at an oil/water interface and use it to amplify signal in surface-enhanced Raman spectroscopy. 18 July 2013 | doi: 10.1038/ncomms3182 Physical Sciences  Nanotechnology  Optical physics  Physical chemistry  Two FLX family members are non-redundantly required to establish the vernalization requirement in Arabidopsis Joohyun Lee and Richard M. Amasino FLC and FRI are two genes required for vernalization in Arabidopsis. In this study, the authors identified a new gene—FLL4—that is required for the upregulation of FLC, and found that fll4 mutants flower more rapidly. 18 July 2013 | doi: 10.1038/ncomms3186 Biological Sciences  Plant sciences  Genome-scale proteome quantification by DEEP SEQ mass spectrometry Feng Zhou, Yu Lu, Scott B. Ficarro, Guillaume Adelmant, Wenyu Jiang, C. John Luckey and Jarrod A. Marto The complexity and dynamic range of mammalian proteomes has stymied comprehensive protein quantification for the past twenty years. Zhou et al. develop DEEP SEQ mass spectrometry and use it to quantify a murine stem cell proteome to a depth equivalent to RNA-seq-based ribosome profiling. 18 July 2013 | doi: 10.1038/ncomms3171 Biological Sciences  Biochemistry  Systems biology  Spatial entanglement of bosons in optical lattices M. Cramer, A. Bernard, N. Fabbri, L. Fallani, C. Fort, S. Rosi, F. Caruso, M. Inguscio and M.B. Plenio Estimating the entanglement in a system is vital for quantum information processing, particularly in many-body systems. To this end, Cramer et al. experimentally quantify multi-partite entanglement in an optical lattice across the superfluid-Mott insulator phase transition and at different temperatures. 18 July 2013 | doi: 10.1038/ncomms3161 Physical Sciences  Atomic and molecular physics  Theoretical physics  NMR spectroscopic detection of chirality and enantiopurity in referenced systems without formation of diastereomers OPEN Jan Labuta, Shinsuke Ishihara, Tomáš Šikorský, Zdeněk Futera, Atsuomi Shundo, Lenka Hanyková, Jaroslav V. Burda, Katsuhiko Ariga and Jonathan P. Hill The enantiopurity of chiral compounds is key in determining their activity or therapeutic action. Here, the authors present a versatile NMR method of enantiomeric excess determination using a symmetrical achiral molecule as resolving agent, based on complexation with analyte, without formation of diastereomers. 17 July 2013 | doi: 10.1038/ncomms3188 Chemical Sciences  Analytical chemistry  Organic chemistry  Physical chemistry  Hace1 controls ROS generation of vertebrate Rac1-dependent NADPH oxidase complexes OPEN Mads Daugaard, Roberto Nitsch, Babak Razaghi, Lindsay McDonald, Ameer Jarrar, Stéphanie Torrino, Sonia Castillo-Lluva, Barak Rotblat, Liheng Li, Angeliki Malliri, Emmanuel Lemichez, Amel Mettouchi, Jason N. Berman, Josef M. Penninger and Poul H. Sorensen HACE1 is an E3 ligase that promotes degradation of the GTPase Rac1. Here Daugaard et al. show that HACE1 inhibits the activity of Rac1-dependent NADPH oxidase complexes, which reduces the production of cellular reactive oxygen species and cell cycle progression. 17 July 2013 | doi: 10.1038/ncomms3180 Biological Sciences  Cell biology  Femtolitre chemistry assisted by microfluidic pen lithography OPEN Carlos Carbonell, Kyriakos C. Stylianou, Jordi Hernando, Emi Evangelio, Sarah A. Barnett, Saju Nettikadan, Inhar Imaz and Daniel Maspoch Chemical reactions on femtolitre scales are necessary to study confined biological processes. Here, the authors use a microfluidic pen lithography technique to perform a series of discrete femtoscale acid-base and synthetic reactions, and crystallizations on a surface with high registration accuracy. 17 July 2013 | doi: 10.1038/ncomms3173 Chemical Sciences  Materials science  Nanotechnology  Designing tensile ductility in metallic glasses OPEN Baran Sarac and Jan Schroers Metallic glasses are normally stronger than their crystalline counterparts, but not good at deforming under tensile stress. Sarac and Schroers test the ductility of metallic glasses in a precisely engineered microsystem and identify an ideal heterostructure with maximized strength and toughness. 17 July 2013 | doi: 10.1038/ncomms3158 Physical Sciences  Materials science  Nanotechnology    Nature Communications JOBS of the week Postdoctoral Position German Cancer Research Center (DKFZ) Post-doctoral Positions The Paterson Institute for Cancer Research Postdoctoral Fellow SUNY Upstate Medical University Research Scientists Texas Heart Institute Research Fellow Duke-NUS Graduate Medical School (Duke-NUS) Research technician King's College London PhD student position in Biostatistics Chalmers University of Technology Research Assistant Icahn School of Medicine at Mount Sinai Research Technical Assistant University College Dublin PhD Student Poznan University of Medical Sciences More Science jobs from Nature Communications EVENT Cell Based Assays 18.11.13 London, UK More science events from       Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. 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