Monday, December 23, 2013

Nature Communications - 23 December 2013

 
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23 December 2013 
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Wang et al. develop a 'sugar blowing' technique to synthesize three-dimensional graphene networks for energy storage applications.
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Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs OPEN
Carolina Villarroya-Beltri, Cristina Gutiérrez-Vázquez, Fátima Sánchez-Cabo, Daniel Pérez-Hernández, Jesús Vázquez, Noa Martin-Cofreces, Dannys Jorge Martinez-Herrera, Alberto Pascual-Montano, María Mittelbrunn and Francisco Sánchez-Madrid
Cells secrete micro-RNAs by packaging them into exosomes; however, the mechanisms by which this packaging occurs are unclear. Here, the authors identify a sequence motif that confers exosomal targeting to micro-RNAs and identify a ribonucleoprotein complex that plays a role in this process.
20 December 2013 | doi: 10.1038/ncomms3980
Biological Sciences  Cell biology  Molecular biology 

Gap junction signalling is a stress-regulated component of adrenal neuroendocrine stimulus-secretion coupling in vivo
Michel G. Desarménien, Carole Jourdan, Bertrand Toutain, Emilie Vessières, Sheriar G. Hormuzdi and Nathalie C. Guérineau
Findings from ex vivo studies suggest that gap junctional coupling contributes to hormone release in neuroendocrine/endocrine tissues. Here, the authors provide in vivo evidence that direct communication between adrenal chromaffin cells via gap junctions contributes to catecholamine secretion.
20 December 2013 | doi: 10.1038/ncomms3938
Biological Sciences  Neuroscience 

Development of an ultra-thin film comprised of a graphene membrane and carbon nanotube vein support
Xiaoyang Lin, Peng Liu, Yang Wei, Qunqing Li, Jiaping Wang, Yang Wu, Chen Feng, Lina Zhang, Shoushan Fan and Kaili Jiang
Graphene has great potential in various electronic devices, but obtaining large-area suspended graphene is problematic. Here, the authors use carbon nanotubes as supports for graphene, enabling large areas of strong and 90% electron transparent suspended graphene to be realized.
20 December 2013 | doi: 10.1038/ncomms3920
Physical Sciences  Materials science  Nanotechnology 

Transcription factor IRF4 drives dendritic cells to promote Th2 differentiation
Jesse W. Williams, Melissa Y. Tjota, Bryan S. Clay, Bryan Vander Lugt, Hozefa S. Bandukwala, Cara L. Hrusch, Donna C. Decker, Kelly M. Blaine, Bethany R. Fixsen, Harinder Singh, Roger Sciammas and Anne I. Sperling
Asthma is often characterized by Th2-mediated inflammatory responses, which are initiated by lung dendritic cells. Here, Williams et al. demonstrate that dendritic cell expression of transcription factor IRF4 drives Th2 differentiation through IL-33 and IL-10 activation.
20 December 2013 | doi: 10.1038/ncomms3990
Biological Sciences  Immunology 

Poly(ADP-ribose) binding to Chk1 at stalled replication forks is required for S-phase checkpoint activation
WooKee Min, Christopher Bruhn, Paulius Grigaravicius, Zhong-Wei Zhou, Fu Li, Anja Krüger, Bénazir Siddeek, Karl-Otto Greulich, Oliver Popp, Chris Meisezahl, Cornelis F. Calkhoven, Alexander Bürkle, Xingzhi Xu and Zhao-Qi Wang
DNA damage at stalled replication forks activates Chk1 kinase and poly(ADP-ribose) (PAR) polymerase 1. Min et al. find that retention of Chk1 to stalled replication forks depends on its direct interaction with PAR, and show that PAR chain length fine-tunes Chk1 and S-phase checkpoint activation.
20 December 2013 | doi: 10.1038/ncomms3993
Biological Sciences  Cell biology 

Spliced MDM2 isoforms promote mutant p53 accumulation and gain-of-function in tumorigenesis
Tongsen Zheng, Jiabei Wang, Yuhan Zhao, Cen Zhang, Meihua Lin, Xiaowen Wang, Haiyang Yu, Lianxin Liu, Zhaohui Feng and Wenwei Hu
Mdm2 controls the levels of the tumour suppressor p53 in cells and p53 is often mutated in cancer. Here, Zheng et al. show that a particular Mdm2 isoform that is altered in cancer leads to elevated levels of mutant p53 protein and enhanced gain-of-function of the protein.
20 December 2013 | doi: 10.1038/ncomms3996
Biological Sciences  Cancer 

Mapping the evolution of hierarchical microstructures in a Ni-based superalloy
Florian Vogel, Nelia Wanderka, Zoltan Balogh, Mohammed Ibrahim, Patrick Stender, Guido Schmitz and John Banhart
Phase separation in nickel-based superalloys is known to be complex and to determine the resulting microstructure and mechanical properties. Here, the authors use atom probe tomography to study phase development, finding that nickel concentration is critical in driving the formation of the γ phase from γ'.
20 December 2013 | doi: 10.1038/ncomms3955
Physical Sciences  Materials science 

Inactivation of the Hippo tumour suppressor pathway by integrin-linked kinase OPEN
Isabel Serrano, Paul C. McDonald, Frances Lock, William J. Muller and Shoukat Dedhar
The Hippo tumour suppressor pathway is inactivated in many cancer types, but how this occurs is unclear. Here, the authors show that integrin-linked kinase (ILK) has a role in inhibiting the Hippo pathway and pharmacological inhibition of ILK reduces the size of tumours in mice.
20 December 2013 | doi: 10.1038/ncomms3976
Biological Sciences  Cancer  Cell biology 

Transcription factors FOXG1 and Groucho/TLE promote glioblastoma growth
Federica Verginelli, Alessandro Perin, Rola Dali, Karen H. Fung, Rita Lo, Pierluigi Longatti, Marie-Christine Guiot, Rolando F. Del Maestro, Sabrina Rossi, Umberto di Porzio, Owen Stechishin, Samuel Weiss and Stefano Stifani
Glioblastoma cancers contain brain tumour-initiating cells and targeting these specific cells is an attractive opportunity for therapy. In this study, the authors show that FOXG1 and Groucho/TLE transcription factors are important for glioblastoma growth and might be useful therapeutic targets.
20 December 2013 | doi: 10.1038/ncomms3956
Biological Sciences  Cancer  Cell biology 

Ultrashort single-walled carbon nanotubes in a lipid bilayer as a new nanopore sensor OPEN
Lei Liu, Chun Yang, Kai Zhao, Jingyuan Li and Hai-Chen Wu
Nanopore sensors are a promising tool for the controlled detection of a range of possible substrates. Here the authors describe a nanopore sensor based on short single-walled carbon nanotubes inserted into a lipid bilayer, with modified sensing properties compared to longer nanotubes.
19 December 2013 | doi: 10.1038/ncomms3989
Physical Sciences  Biotechnology  Materials science 

Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography OPEN
Linda C. Johansson, David Arnlund, Gergely Katona, Thomas A. White, Anton Barty, Daniel P. DePonte, Robert L. Shoeman, Cecilia Wickstrand, Amit Sharma, Garth J. Williams, Andrew Aquila, Michael J. Bogan, Carl Caleman, Jan Davidsson, R Bruce Doak, Matthias Frank, Raimund Fromme, Lorenzo Galli, Ingo Grotjohann, Mark S. Hunter et al.
Serial femtosecond crystallography is an X-ray free-electron-laser-based method that uses X-ray bursts to determine protein structures. Here the authors present the structure of a photosynthetic reaction centre, an integral membrane protein, achieved with no sign of X-ray-induced radiation damage.
19 December 2013 | doi: 10.1038/ncomms3911
Physical Sciences  Biochemistry  Biophysics 

STIM1/Orai1 coiled-coil interplay in the regulation of store-operated calcium entry OPEN
Peter B. Stathopulos, Rainer Schindl, Marc Fahrner, Le Zheng, Geneviève M. Gasmi-Seabrook, Martin Muik, Christoph Romanin and Mitsuhiko Ikura
When endoplasmic reticulum calcium levels are low, STIM1 binds to and opens Orai1 channels in the plasma membrane to replenish calcium stores. Stathopulos et al. present solution structures of the STIM1 coiled-coil domain in the presence and absence of Orai1, revealing the structural basis for this interaction.
19 December 2013 | doi: 10.1038/ncomms3963
Biological Sciences  Biochemistry  Cell biology 

Forced protein unfolding leads to highly elastic and tough protein hydrogels
Jie Fang, Alexander Mehlich, Nobuyasu Koga, Jiqing Huang, Rie Koga, Xiaoye Gao, Chunguang Hu, Chi Jin, Matthias Rief, Juergen Kast, David Baker and Hongbin Li
Protein-based hydrogels are of great interest for many biomedical applications. Here, the authors demonstrate the use of mechanical labile proteins to initiate large-scale forced unfolding in order to engineer the mechanical properties of protein-based biomaterials.
19 December 2013 | doi: 10.1038/ncomms3974
Physical Sciences  Materials science 

Binding of PHF1 Tudor to H3K36me3 enhances nucleosome accessibility
Catherine A. Musselman, Matthew D. Gibson, Erik W. Hartwick, Justin A. North, Jovylyn Gatchalian, Michael G. Poirier and Tatiana G. Kutateladze
Binding of the Tudor domain of the PHD finger protein PHF1 to H3K36me3 inhibits Polycomb PRC2 complex methyltransferase activity. Here, Musselman et al. characterize this interaction in the context of the full nucleosome and show dual binding of the PHF1 Tudor domain to H3K36me3 and double-stranded DNA.
19 December 2013 | doi: 10.1038/ncomms3969
Biological Sciences  Molecular biology 

Functional anatomy of an allosteric protein
Prasad Purohit, Shaweta Gupta, Snehal Jadey and Anthony Auerbach
ϕ analysis provides a means to tease apart the dynamics of fast conformational changes in proteins by analysing the thermodynamic impact of point mutations. Purohit et al. apply this approach on a grand scale to map energy changes associated with the opening and closing of an acetylcholine receptor.
19 December 2013 | doi: 10.1038/ncomms3984
Biological Sciences  Biochemistry  Biophysics 

Spatial optimization of carbon-stocking projects across Africa integrating stocking potential with co-benefits and feasibility
Michelle Greve, Belinda Reyers, Anne Mette Lykke and Jens-Christian Svenning
Africa is one of the fastest growing regions for the voluntary carbon market. Here, Greve et al. quantify the potential for aboveground C stocking across tropical Africa and assess the optimal placement of carbon-stocking projects when also taking co-benefits and feasibility into account.
19 December 2013 | doi: 10.1038/ncomms3975
Earth Sciences  Biogeochemistry  Climate science 

Evolution of the average avalanche shape with the universality class OPEN
Lasse Laurson, Xavier Illa, Stéphane Santucci, Ken Tore Tallakstad, Knut Jørgen Måløy and Mikko J Alava
The processes of earthquakes and plastic deformation are examples of systems which respond to slow external forces by avalanche dynamics. Here, the authors show how a fundamental fingerprint of such dynamics - the average shape of the avalanches - evolves with its universality class.
19 December 2013 | doi: 10.1038/ncomms3927
Physical Sciences  Theoretical physics 

Adenosine is required for sustained inflammasome activation via the A2A receptor and the HIF-1α pathway
Xinshou Ouyang, Ayaz Ghani, Ahsan Malik, Tuere Wilder, Oscar Rene Colegio, Richard Anthony Flavell, Bruce Neil Cronstein and Wajahat Zafar Mehal
Inflammasome activation can lead to chronic inflammatory conditions; however, the mechanisms controlling the duration of this activation are not well understood. Here, Ouyang et al. report that adenosine sustains inflammasome activity, which brings insights into the pathology of chronic inflammatory diseases.
19 December 2013 | doi: 10.1038/ncomms3909
Biological Sciences  Cell biology  Immunology 

Ultrafast viscous water flow through nanostrand-channelled graphene oxide membranes
Hubiao Huang, Zhigong Song, Ning Wei, Li Shi, Yiyin Mao, Yulong Ying, Luwei Sun, Zhiping Xu and Xinsheng Peng
Pressure-driven ultrafiltration membranes are important for industrial and environmental applications. Here, the authors describe nanochannelled graphene oxide membranes, fabricated via a copper hydroxide nanostrand templating approach and evaluate their performance in water purification processes.
19 December 2013 | doi: 10.1038/ncomms3979
Physical Sciences  Materials science 

TCTP directly regulates ATM activity to control genome stability and organ development in Drosophila melanogaster
Sung-Tae Hong and Kwang-Wook Choi
Human TCTP, a highly conserved protein linked to tumorigenesis, has been implicated in the cellular DNA damage response in an ATM kinase-dependent manner. Here, Hong et al. demonstrate in vivo that Drosophila dTCTP controls genome stability by enhancing dATM activity towards its substrate H2Av.
19 December 2013 | doi: 10.1038/ncomms3986
Biological Sciences  Cell biology  Molecular biology 

Continuous adsorption in highly ordered porous matrices made by nanolithography
Giampaolo Mistura, Alessandro Pozzato, Gianluca Grenci, Lorenzo Bruschi and Massimo Tormen
The idea that closed-end pores should not display an adsorption–desorption hysteresis loop has long been proposed but never experimentally confirmed. Here, through the preparation of highly uniform pores with smooth walls, the authors confirm the presence of a reversible isotherm in such systems.
19 December 2013 | doi: 10.1038/ncomms3966
Physical Sciences  Condensed matter  Materials science 

Nanotechnology 

Indoleamides are active against drug-resistant Mycobacterium tuberculosis
Shichun Lun, Haidan Guo, Oluseye K. Onajole, Marco Pieroni, Hendra Gunosewoyo, Gang Chen, Suresh K. Tipparaju, Nicole C. Ammerman, Alan P. Kozikowski and William R. Bishai
New classes of antitubercular drugs are in constant demand as drug-resistant strains of Mycobacterium tuberculosis become more prevalent. Here, the authors characterize a class of drugs that are active against various M. tuberculosis strains, including those resistant to currently used antituberculars.
19 December 2013 | doi: 10.1038/ncomms3907
Biological Sciences  Medical research  Microbiology 

Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons
Christoffer Lind, Johan Sund and Johan Åqvist
Unconventional stop codons in the mitochondrial genome were thought to be recognized by the mitochondrial release factors mtRF1 and mtRF1a. Here, Lind et al. employ homology modelling and simulations to show that neither reads the putative stop codons AGA/AGG; instead, termination is due to their paralogue ICT1.
19 December 2013 | doi: 10.1038/ncomms3940
Biological Sciences  Molecular biology 

Structural basis of AMPK regulation by small molecule activators OPEN
Bing Xiao, Matthew J. Sanders, David Carmena, Nicola J. Bright, Lesley F. Haire, Elizabeth Underwood, Bhakti R. Patel, Richard B. Heath, Philip A. Walker, Stefan Hallen, Fabrizio Giordanetto, Stephen R. Martin, David Carling and Steven J. Gamblin
Small molecule activators of the energy sensing kinase AMPK are promising candidates as therapies for metabolic disease. Xiao et al. present the crystal structure of AMPK in complex with a small molecule activator, and show that the drug stabilizes interaction between the catalytic and carbohydrate-binding domains.
19 December 2013 | doi: 10.1038/ncomms4017
Biological Sciences  Biochemistry  Cell biology 

Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell
Ignacio Asial, Yue Xiang Cheng, Henrik Engman, Maria Dollhopf, Binghuang Wu, Pär Nordlund and Tobias Cornvik
Methods to improve protein stability are important in the biopharmaceutical industry. Here, the authors describe a high-throughput screen to increase protein thermostability and identify thermostable variants from a broad range of proteins.
19 December 2013 | doi: 10.1038/ncomms3901
Biological Sciences  Biotechnology  Molecular biology 

Structural insights into the role of the Smoothened cysteine-rich domain in Hedgehog signalling
Rajashree Rana, Candace E. Carroll, Ho-Jin Lee, Ju Bao, Suresh Marada, Christy R.R. Grace, Cristina D. Guibao, Stacey K. Ogden and Jie J. Zheng
The Wnt receptor Frizzled binds its endogenous ligand via a cysteine-rich domain; however, the function of the equivalent domain in Smoothened, a mediator of Hedgehog signalling, is unknown. Rana et al. present the NMR solution structure of this domain, and characterize its interaction with the glucocorticoid budesonide.
19 December 2013 | doi: 10.1038/ncomms3965
Biological Sciences  Cell biology 

Topological structure dynamics revealing collective evolution in active nematics OPEN
Xia-qing Shi and Yu-qiang Ma
Topological defects are observed in a range of active systems, but their dynamical properties are largely unknown. Here, the authors use a simulation of self-propelled hard-rods to generate topological defects in active nematics, finding that their anomalous dynamics may lead to large-scale collective motions.
18 December 2013 | doi: 10.1038/ncomms4013
Physical Sciences  Condensed matter  Materials science 

Surface electronic structure of the topological Kondo-insulator candidate correlated electron system SmB6
M. Neupane, N. Alidoust, S-Y. Xu, T. Kondo, Y. Ishida, D. J. Kim, Chang Liu, I. Belopolski, Y. J. Jo, T-R. Chang, H-T. Jeng, T. Durakiewicz, L. Balicas, H. Lin, A. Bansil, S. Shin, Z. Fisk and M. Z. Hasan
Samarium hexaboride, a well-known Kondo insulator, shows transport anomalies at low temperatures, which recently have been proposed to be of topological origin. Using laser- and synchrotron-based photoemission techniques, Neupane et al. find evidence for a topological Fermi surface.
18 December 2013 | doi: 10.1038/ncomms3991
Physical Sciences  Condensed matter 

Postnatal muscle modification by myogenic factors modulates neuropathology and survival in an ALS mouse model
Kevin H. J. Park, Sonia Franciosi and Blair R. Leavitt
MyoD and myogenin are muscle regulatory factors that are involved in muscle development. Park et al. study a mouse model of amyotrophic lateral sclerosis and find that MyoD and myogenin have positive and negative effects, respectively, on motor neuron degeneration and muscle denervation.
18 December 2013 | doi: 10.1038/ncomms3906
Biological Sciences  Neuroscience 

Observation of possible topological in-gap surface states in the Kondo insulator SmB6 by photoemission OPEN
J. Jiang, S. Li, T. Zhang, Z. Sun, F. Chen, Z.R. Ye, M. Xu, Q.Q. Ge, S.Y. Tan, X.H. Niu, M. Xia, B.P. Xie, Y.F. Li, X.H. Chen, H.H. Wen and D.L. Feng
The Kondo insulator samarium hexaboride exhibits low-temperature transport anomalies, which might be due to topological surface states. Here Jiang et al. perform angle-resolved photoemission and its circular dichroism measurements, which suggest that the anomalies might be of topological origin.
18 December 2013 | doi: 10.1038/ncomms4010
Physical Sciences  Condensed matter 

A strategic approach to recharging lithium-sulphur batteries for long cycle life
Yu-Sheng Su, Yongzhu Fu, Thomas Cochell and Arumugam Manthiram
Capacity degradation over extended cycles is a major problem in lithium-sulphur batteries. Here, Su et al. report a charge operation control strategy to inhibit dissolution of polysulphides leading to enhanced capacity retention over multiple cycles.
18 December 2013 | doi: 10.1038/ncomms3985
Chemical Sciences  Inorganic chemistry  Materials science 

Heterovalent cation substitutional doping for quantum dot homojunction solar cells OPEN
Alexandros Stavrinadis, Arup K. Rath, F. Pelayo García de Arquer, Silke L. Diedenhofen, César Magén, Luis Martinez, David So and Gerasimos Konstantatos
To use colloidal quantum dots in applications such as p-n junction solar cells, doping of the quantum dots is needed. Here, Stavrinadis et al. achieve lead sulphide quantum dot p-n homojunctions by heterovalent cation substitution of lead using bismuth.
18 December 2013 | doi: 10.1038/ncomms3981
Physical Sciences  Nanotechnology  Optical physics 

Unravelling the biodiversity of nanoscale signatures of spider silk fibres
Luciano P. Silva and Elibio L. Rech
Spider silk fibre is known to be composed of arrangements of structural domains. Here, the authors implement multiple atomic force microscopy modes to study the nanoscale morphology and mechanics of these fibres from nine spiders, and relate them to their molecular structures.
18 December 2013 | doi: 10.1038/ncomms4014
Physical Sciences  Materials science 

The atypical mechanosensitive microRNA-712 derived from pre-ribosomal RNA induces endothelial inflammation and atherosclerosis
Dong Ju Son, Sandeep Kumar, Wakako Takabe, Chan Woo Kim, Chih-Wen Ni, Noah Alberts-Grill, In-Hwan Jang, Sangok Kim, Wankyu Kim, Sang Won Kang, Andrew H. Baker, Jai Woong Seo, Katherine W. Ferrara and Hanjoong Jo
Gene expression in the vascular endothelium is sensitive to shear forces exerted by the circulation. Here the authors identify miR-712 as a mechanosensitive microRNA expressed in endothelial cells and show that miR-712 inhibits pro-atherogenic processes by downregulating tissue inhibitor of metalloproteinase 3.
18 December 2013 | doi: 10.1038/ncomms4000
Biological Sciences  Medical research 

Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides
Dor Salomon, Yirui Guo, Lisa N. Kinch, Nick V. Grishin, Kevin H. Gardner and Kim Orth
Many Gram-negative bacterial pathogens use the type III secretion system to translocate effectors into the host cell. Here, the authors characterize a bacterial phosphoinositide-binding domain, which is conserved in diverse type III effectors of both plant and animal pathogens and couples membrane localization with refolding.
18 December 2013 | doi: 10.1038/ncomms3973
Biological Sciences  Cell biology  Microbiology 

Direct observation of the oxygenated species during oxygen reduction on a platinum fuel cell cathode
Hernan Sanchez Casalongue, Sarp Kaya, Venkatasubramanian Viswanathan, Daniel J. Miller, Daniel Friebel, Heine A. Hansen, Jens K. Nørskov, Anders Nilsson and Hirohito Ogasawara
Understanding the oxygen reduction reaction at fuel cell cathodes requires information on adsorbed oxygenated species. Sanchez Casalongue et al. report in situ identification of oxygenated intermediates at cathodes and establish a correlation between the cathode potential and the surface speciation.
18 December 2013 | doi: 10.1038/ncomms3817
Chemical Sciences  Catalysis  Physical chemistry 
 
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  Latest Corrigendum  
 
Corrigendum: Two-dome structure in electron-doped iron arsenide superconductors
Soshi Iimura, Satoru Matsuishi, Hikaru Sato, Taku Hanna, Yoshinori Muraba, Sung Wng Kim, Jung Eun Kim, Masaki Takata and Hideo Hosono
20 December 2013 | doi: 10.1038/ncomms4058
Physical Sciences  Condensed matter  Materials science 
 
 
  Latest Erratum  
 
Erratum: 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
19 December 2013 | doi: 10.1038/ncomms3937
Biological Sciences  Medical research 
 
 
 
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