Nature Communications - 3 February 2016

Advertisement Nature Insight Frontiers in Biology  This year's Frontiers in Biology Insight features Reviews on the processes that underlie metastasis, the positive influence of inflammation on tissue repair, the role of endothelial cells in organ development, growth and regeneration, the endoplasmic reticulum stress response and its contribution to disease, and antibiotic resistance.        Weekly Content Alert Nature Communications is now fully open access. Read more. 03 February 2016  Featured image: Biesheuvel et al. report high-precision verification of quantum electrodynamics by measuring the vibrational transitions of trapped HD+ ions via laser spectroscopy. Latest content: Articles Corrigenda Erratum Journal homepage Recommend to library Web feed   Advertisement New! Nature Microbiology - First issue now published. The first issue of Nature Microbiology is now published and free to access online! This new journal covers all aspects of microorganisms, be it their evolution, physiology and cell biology; their interactions with each other, with a host or with an environment; or their societal significance. Ensure you stay up to date with future content by registering to receive the monthly e-alert.   Advertisement All content now free to access including archives! Nature Communications is an open access journal that publishes high-quality research from all areas of the natural sciences. Papers published by the journal represent important advances of significance to specialists within each subject area including chemistry. Visit the website to explore ALL the content available within your field.        Nature Communications - now fully open access All new submissions, if accepted, will be published open access and an article processing charge (APC) will apply. For more information visit the website. Visit our open access funding page or contact openaccess@nature.com to learn more about APC funding.       Latest Articles View all Articles     Ravens attribute visual access to unseen competitors OPEN Thomas Bugnyar, Stephan A. Reber and Cameron Buckner Theory of Mind experiments in animals have not previously discounted the possibility that individuals follow their competitors′ behavioural cues. Here, Bugnyar et al. show that ravens consider the possibility that they are being watched when caching food, even when they cannot see a conspecific competitor. 02 February 2016 | doi: 10.1038/ncomms10506 Biological Sciences  Zoology  GWAS of 89,283 individuals identifies genetic variants associated with self-reporting of being a morning person OPEN Youna Hu, Alena Shmygelska, David Tran, Nicholas Eriksson, Joyce Y. Tung and David A. Hinds Circadian rhythms and related behaviours vary across individuals. Here, a large genome-wide association study reveals common single nucleotide variants influencing whether an individual reports as being a ‘morning person’ by identifying 15 significant loci, including 7 near known circadian genes. 02 February 2016 | doi: 10.1038/ncomms10448 Biological Sciences  Genetics  Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis OPEN Krista Dubin, Margaret K. Callahan, Boyu Ren, Raya Khanin, Agnes Viale, Lilan Ling, Daniel No, Asia Gobourne, Eric Littmann, Curtis Huttenhower, Eric G. Pamer and Jedd D. Wolchok A subset of cancer patients treated with immune checkpoint blockade develops colitis. Here the authors show that lower abundance of Bacteroidetes and vitamin B biosynthetic modules in fecal samples of melanoma patients can predict their susceptibility to colitis following anti-CTLA-4 treatment. 02 February 2016 | doi: 10.1038/ncomms10391 Biological Sciences  Cancer  Immunology  Medical research  Unique features of a global human ectoparasite identified through sequencing of the bed bug genome OPEN Joshua B. Benoit, Zach N. Adelman, Klaus Reinhardt, Amanda Dolan, Monica Poelchau, Emily C. Jennings, Elise M. Szuter, Richard W. Hagan, Hemant Gujar, Jayendra Nath Shukla, Fang Zhu, M. Mohan, David R. Nelson, Andrew J. Rosendale, Christian Derst, Valentina Resnik, Sebastian Wernig, Pamela Menegazzi, Christian Wegener, Nicolai Peschel et al. The bed bug, Cimex lectularius, is a ubiquitous human ectoparasite with global distribution. Here, the authors sequence the genome of the bed bug and identify reductions in chemosensory genes, expansion of genes associated with blood digestion and genes linked to pesticide resistance. 02 February 2016 | doi: 10.1038/ncomms10165 Biological Sciences  Genetics  Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius OPEN Jeffrey A. Rosenfeld, Darryl Reeves, Mercer R. Brugler, Apurva Narechania, Sabrina Simon, Russell Durrett, Jonathan Foox, Kevin Shianna, Michael C. Schatz, Jorge Gandara, Ebrahim Afshinnekoo, Ernest T. Lam, Alex R. Hastie, Saki Chan, Han Cao, Michael Saghbini, Alex Kentsis, Paul J. Planet, Vladyslav Kholodovych, Michael Tessler et al. The common bedbug is a pest for humans, yet its molecular biology is poorly understood. Here, the authors sequence the common bedbug genome and profile gene expression across all life stages to show major changes in gene expression after feeding on human blood. 02 February 2016 | doi: 10.1038/ncomms10164 Biological Sciences  Genetics  Joint mouse–human phenome-wide association to test gene function and disease risk OPEN Xusheng Wang, Ashutosh K. Pandey, Megan K. Mulligan, Evan G. Williams, Khyobeni Mozhui, Zhengsheng Li, Virginija Jovaisaite, L. Darryl Quarles, Zhousheng Xiao, Jinsong Huang, John A. Capra, Zugen Chen, William L. Taylor, Lisa Bastarache, Xinnan Niu, Katherine S. Pollard, Daniel C. Ciobanu, Alexander O. Reznik, Artem V. Tishkov, Igor B. Zhulin et al. Phenome-wide association is a novel method that links sequence variants to a spectrum of phenotypes and diseases. Here the authors generate detailed mouse genetic and phenome data which links their phenome-wide association study (PheWAS) of mouse to corresponding PheWAS in human. 02 February 2016 | doi: 10.1038/ncomms10464 Biological Sciences  Genetics  Therapeutically engineered induced neural stem cells are tumour-homing and inhibit progression of glioblastoma OPEN Juli R. Bagó, Adolfo Alfonso-Pecchio, Onyi Okolie, Raluca Dumitru, Amanda Rinkenbaugh, Albert S. Baldwin, C. Ryan Miller, Scott T. Magness and Shawn D. Hingtgen Neural stem cells have a tropism for glioblastoma. Here the authors employ fibroblasts directly reprogrammed into induced neural stem cells and loaded with cytotoxic molecules to migrate to xenotransplanted brain tumours in mice, achieving tumour shrinkage and prolonged survival. 02 February 2016 | doi: 10.1038/ncomms10593 Biological Sciences  Cancer  Supercurrent in van der Waals Josephson junction OPEN Naoto Yabuki, Rai Moriya, Miho Arai, Yohta Sata, Sei Morikawa, Satoru Masubuchi and Tomoki Machida Van der Waals heterostructures, made of stacked two-dimensional materials, hold promise for modern electronics. Here, the authors build van der Waals junction between superconducting two-dimensional materials and reveal that the junction works as Josephson junction. 02 February 2016 | doi: 10.1038/ncomms10616 Physical Sciences  Condensed matter  Materials science  Nanotechnology  Exceptional damage-tolerance of a medium-entropy alloy CrCoNi at cryogenic temperatures OPEN Bernd Gludovatz, Anton Hohenwarter, Keli V. S. Thurston, Hongbin Bei, Zhenggang Wu, Easo P. George and Robert O. Ritchie High-entropy alloys derive their properties from being multi-element systems that can crystallize as a single phase. Here, the authors examine a medium-entropy alloy, CrCoNi, which displays strength-toughness properties exceeding those of high-entropy alloys and resulting from steady strain hardening. 02 February 2016 | doi: 10.1038/ncomms10602 Physical Sciences  Materials science  Nanotechnology  A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function OPEN Anton Kuzyk, Yangyang Yang, Xiaoyang Duan, Simon Stoll, Alexander O. Govorov, Hiroshi Sugiyama, Masayuki Endo and Na Liu Controlled operation of individual molecular machines on a larger scale, 10-100 nm, remains challenging. Here, Kuzyk et al. demonstrate a light-driven plasmonic nanosystem that can amplify the molecular motion of azobenzene through a host nanostructure and translates it into reversible chiroptical response. 02 February 2016 | doi: 10.1038/ncomms10591 Physical Sciences  Biotechnology  Materials science  Nanotechnology  Evidence that ubiquitylated H2B corrals hDot1L on the nucleosomal surface to induce H3K79 methylation OPEN Linjiao Zhou, Matthew T. Holt, Nami Ohashi, Aishan Zhao, Manuel M. Müller, Boyuan Wang and Tom W. Muir The ubiquitylation of histone H2B on lysine 120 is an important modification with roles in a diverse range of nuclear processes. Here, the authors use 'designer' chromatin to show that H2B-ub orients hDot1L into the correct position for activation. 02 February 2016 | doi: 10.1038/ncomms10589 Biological Sciences  Biochemistry  Molecular biology  Topological nodal-line fermions in spin-orbit metal PbTaSe2 OPEN Guang Bian, Tay-Rong Chang, Raman Sankar, Su-Yang Xu, Hao Zheng, Titus Neupert, Ching-Kai Chiu, Shin-Ming Huang, Guoqing Chang, Ilya Belopolski, Daniel S. Sanchez, Madhab Neupane, Nasser Alidoust, Chang Liu, BaoKai Wang, Chi-Cheng Lee, Horng-Tay Jeng, Chenglong Zhang, Zhujun Yuan, Shuang Jia et al. Nodal-line shaped bands appearing near the Fermi level host unique properties in topological matter, which has yet to be confirmed in real materials. Here, the authors report the existence of topological nodal-line states in the non-centrosymmetric single-crystalline spin-orbit semimetal PbTaSe2. 02 February 2016 | doi: 10.1038/ncomms10556 Physical Sciences  Condensed matter  Materials science  Genetic variants near MLST8 and DHX57 affect the epigenetic age of the cerebellum OPEN Ake T. Lu, Eilis Hannon, Morgan E. Levine, Ke Hao, Eileen M. Crimmins, Katie Lunnon, Alexey Kozlenkov, Jonathan Mill, Stella Dracheva and Steve Horvath This genome-wide association study identifies five significant SNPs in two loci which are associated with the epigenetic age of post-mortem cerebellar tissue according to a DNA methylation based biomarker of human aging. 02 February 2016 | doi: 10.1038/ncomms10561 Biological Sciences  Fluids and plasma physics  Neuroscience  Mito-priming as a method to engineer Bcl-2 addiction OPEN Jonathan Lopez, Margaux Bessou, Joel S. Riley, Evangelos Giampazolias, Franziska Todt, Tony Rochegüe, Andrew Oberst, Douglas R. Green, Frank Edlich, Gabriel Ichim and Stephen W. G. Tait Apoptosis often requires mitochondrial outer membrane permeabilization, a process targeted by Bcl-2-binding BH3 mimetics. Here the authors describe and apply 'mito-priming', a method that allows triggering mitochondrial apoptosis in a synchronous manner, facilitating the investigation of mitochondrial apoptosis and its regulation by Bcl-2 proteins. 02 February 2016 | doi: 10.1038/ncomms10538 Biological Sciences  Cell biology  RAG2 and XLF/Cernunnos interplay reveals a novel role for the RAG complex in DNA repair OPEN Chloé Lescale, Vincent Abramowski, Marie Bedora-Faure, Valentine Murigneux, Gabriella Vera, David B. Roth, Patrick Revy, Jean-Pierre de Villartay and Ludovic Deriano Antigen receptor diversity relies on careful DNA cleavage and repair. Here the authors identify a functional interplay between RAG2 and XLF during V(D)J recombination, revealing an important role for the RAG complex in repairing induced DNA double-strand breaks and maintaining genome integrity. 02 February 2016 | doi: 10.1038/ncomms10529 Biological Sciences  Immunology  Molecular biology  Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression OPEN Michal Brunwasser-Meirom, Yaroslav Pollak, Sarah Goldberg, Lior Levy, Orna Atar and Roee Amit Some repressors down-regulate gene expression when they bind to a site up to 100 base pairs away from the nearest activator. Here, the authors show that this quenching-like repression can be achieved by the excluded volume effect when a DNA-bound protein alters the propensity of DNA to form a loop. 02 February 2016 | doi: 10.1038/ncomms10407 Biological Sciences  Biophysics  Molecular biology  Stabilization of p21 by mTORC1/4E-BP1 predicts clinical outcome of head and neck cancers OPEN Susana Llanos, Juana M. García-Pedrero, Lucia Morgado-Palacin, Juan P. Rodrigo and Manuel Serrano The molecular pathways involving p21 and mTORC1 are frequently deregulated in head and neck squamous cell carcinomas (HNSCC). Here, Llanos et al. report a mechanism that regulates p21 stability through the mTORC1/4E-BP1 pathway independently of p53, and show that the mechanism is prevalent in HNSCC. 02 February 2016 | doi: 10.1038/ncomms10438 Biological Sciences  Cancer  Medical research  Affinity and competition for TBP are molecular determinants of gene expression noise OPEN Charles N. J. Ravarani, Guilhem Chalancon, Michal Breker, Natalia Sanchez de Groot and M. Madan Babu TATA boxes in gene promoters are associated with high level of cell-to-cell variation in gene expression. Through integration of multiple data sets, the authors now provide insights into how the interactions of TBP with DNA and other proteins can lead to noisy expression. 02 February 2016 | doi: 10.1038/ncomms10417 Biological Sciences  Bioinformatics  Systems biology  Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions OPEN Lovorka Stojic, Malwina Niemczyk, Arturo Orjalo, Yoko Ito, Anna Elisabeth Maria Ruijter, Santiago Uribe-Lewis, Nimesh Joseph, Stephen Weston, Suraj Menon, Duncan T. Odom, John Rinn, Fanni Gergely and Adele Murrell LncRNAs regulate gene expression via their RNA product and through transcriptional interference. Here, Stojic et al. uncouple these functions by using multiple siRNAs against GNG12-AS1 to show that this lncRNA has a product related role in MET signaling while its transcription modulates DIRAS3 expression. 02 February 2016 | doi: 10.1038/ncomms10406 Biological Sciences  Cell biology  Molecular biology  Sequential domain assembly of ribosomal protein S3 drives 40S subunit maturation OPEN Valentin Mitterer, Guillaume Murat, Stéphane Réty, Magali Blaud, Lila Delbos, Tamsyn Stanborough, Helmut Bergler, Nicolas Leulliot, Dieter Kressler and Brigitte Pertschy Ribosome biogenesis involves the hierarchical assembly of several proteins and RNA components. Here the authors describe a mechanism for ribosomal protein S3 incorporation into 40S ribosomal subunits that involves S3 dimerization and stepwise incorporation of two distinct S3 interaction domains coupled to release of ribosomal maturation factors. 02 February 2016 | doi: 10.1038/ncomms10336 Biological Sciences  Biochemistry  Molecular biology  Endomucin prevents leukocyte–endothelial cell adhesion and has a critical role under resting and inflammatory conditions OPEN Alisar Zahr, Pilar Alcaide, Jinling Yang, Alexander Jones, Meredith Gregory, Nathaniel G. dela Paz, Sunita Patel-Hett, Tania Nevers, Adarsha Koirala, Francis W. Luscinskas, Magali Saint-Geniez, Bruce Ksander, Patricia A. D’Amore and Pablo Argüeso Endomucin is expressed by endothelial cells that line postcapillary venules—the site of leukocyte recruitment during inflammation. Zahr et al. show that endomucin is an anti-adhesive molecule that is downregulated by the cytokine TNF-a and thereby helps in the transition from a quiescent to a pro-adhesive inflamed endothelium. 02 February 2016 | doi: 10.1038/ncomms10363 Biological Sciences  Cell biology  Immunology  Genome-wide screening identifies a KCNIP1 copy number variant as a genetic predictor for atrial fibrillation OPEN Chia-Ti Tsai, Chia-Shan Hsieh, Sheng-Nan Chang, Eric Y. Chuang, Kwo-Chang Ueng, Chin-Feng Tsai, Tsung-Hsien Lin, Cho-Kai Wu, Jen-Kuang Lee, Lian-Yu Lin, Yi-Chih Wang, Chih-Chieh Yu, Ling-Ping Lai, Chuen-Den Tseng, Juey-Jen Hwang, Fu-Tien Chiang and Jiunn-Lee Lin Tsai et al. here utilize a multi-stage genome-wide association study in Taiwanese population to show a copy number variation in the intron of potassium interacting channel 1 gene (KCNIP1) to be strongly associated with atrial fibrillation. The study also examines the functionality of KCNIP1 in heart electrophysiological function using cultured myocytes and zebrafish. 02 February 2016 | doi: 10.1038/ncomms10190 Biological Sciences  Genetics  Molecular sled is an eleven-amino acid vehicle facilitating biochemical interactions via sliding components along DNA OPEN Walter F. Mangel, William J. McGrath, Kan Xiong, Vito Graziano and Paul C. Blainey Extremely compact environments can inhibit protein interactions by preventing 3-dimensional diffusion. Here the authors show that an 11-amino acid long peptide can function as a ‘molecular sled’, able to transport cargo linearly along DNA to enable interactions. 02 February 2016 | doi: 10.1038/ncomms10202 Biological Sciences  Molecular biology  C1q acts in the tumour microenvironment as a cancer-promoting factor independently of complement activation OPEN Roberta Bulla, Claudio Tripodo, Damiano Rami, Guang Sheng Ling, Chiara Agostinis, Carla Guarnotta, Sonia Zorzet, Paolo Durigutto, Marina Botto and Francesco Tedesco C1q is known to initiate the activation of the complement classical pathway. Here, the authors show the C1q is expressed in the tumour microenvironment and can promote cancer cell migration and adhesion in a complement activation-independent manner. 01 February 2016 | doi: 10.1038/ncomms10346 Biological Sciences  Cancer  Immunology  Network-based in silico drug efficacy screening OPEN Emre Guney, Jörg Menche, Marc Vidal and Albert-László Barábasi Attempts to predict novel use for existing drugs rarely consider information on the impact on the genes perturbed in a given disease. Here, the authors present a novel network-based drug-disease proximity measure that provides insight on gene specific therapeutic effect of drugs and may facilitate drug repurposing. 01 February 2016 | doi: 10.1038/ncomms10331 Biological Sciences  Bioinformatics  Medical research  Systems biology  New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk OPEN Yingchang Lu, Felix R. Day, Stefan Gustafsson, Martin L. Buchkovich, Jianbo Na, Veronique Bataille, Diana L. Cousminer, Zari Dastani, Alexander W. Drong, Tõnu Esko, David M. Evans, Mario Falchi, Mary F. Feitosa, Teresa Ferreira, Åsa K. Hedman, Robin Haring, Pirro G. Hysi, Mark M. Iles, Anne E. Justice, Stavroula Kanoni et al. A genome-wide association meta-analysis study here shows novel genetic loci to be associated to body fat percentage, and describes cross-phenotype association that further demonstrate a close relationship between adiposity and cardiovascular disease risk. 01 February 2016 | doi: 10.1038/ncomms10495 Biological Sciences  Genetics  Complex Greenland outlet glacier flow captured OPEN Andy Aschwanden, Mark A. Fahnestock and Martin Truffer Quantifying Greenland's future contribution to sea level requires accurate portrayal of its outlet glaciers in ice sheet simulations. Here, the authors show that outlet glacier flow can be captured if ice thickness is well constrained and vertical shearing as well as membrane stresses are included in the model. 01 February 2016 | doi: 10.1038/ncomms10524 Earth Sciences  Geology and geophysics  The puzzling Venusian polar atmospheric structure reproduced by a general circulation model OPEN Hiroki Ando, Norihiko Sugimoto, Masahiro Takagi, Hiroki Kashimura, Takeshi Imamura and Yoshihisa Matsuda Unlike some planets, the Venusian polar vortex is warmer than the mid-latitudes at cloud-top level, but the mechanism behind this is unknown. Here, the authors use a general circulation model and suggest the cold collar and warm polar regions are due to residual mean meridional circulation intensified by thermal tides. 01 February 2016 | doi: 10.1038/ncomms10398 Earth Sciences  Atmospheric science  Planetary sciences  4Pi-RESOLFT nanoscopy OPEN Ulrike Böhm, Stefan W. Hell and Roman Schmidt The ability to discriminate objects along the optic axis is a benchmark for three-dimensional imaging techniques. Here, the authors combine metastable-state switching and opposing objective lenses to suppress out-of-focus background and record three-dimensional nanoscale images of living cells. 01 February 2016 | doi: 10.1038/ncomms10504 Physical Sciences  Biophysics  Nanotechnology  Optical physics  Strain effects on the work function of an organic semiconductor OPEN Yanfei Wu, Annabel R. Chew, Geoffrey A. Rojas, Gjergji Sini, Greg Haugstad, Alex Belianinov, Sergei V. Kalinin, Hong Li, Chad Risko, Jean-Luc Brédas, Alberto Salleo and C. Daniel Frisbie The understanding of strain effect on electronic properties of organic semiconductors is crucial for the designs of flexible electronics. Here, Wu et al. characterize the tensile and compressive strain effects on the work function of rubrene single crystals as a benchmark system. 01 February 2016 | doi: 10.1038/ncomms10270 Physical Sciences  Condensed matter  Materials science  MDM2 E3 ligase-mediated ubiquitination and degradation of HDAC1 in vascular calcification OPEN Duk-Hwa Kwon, Gwang Hyeon Eom, Jeong Hyeon Ko, Sera Shin, Hosouk Joung, Nakwon Choe, Yoon Seok Nam, Hyun-Ki Min, Taewon Kook, Somy Yoon, Wanseok Kang, Yong Sook Kim, Hyung Seok Kim, Hyuck Choi, Jeong-Tae Koh, Nacksung Kim, Youngkeun Ahn, Hyun-Jai Cho, In-Kyu Lee, Dong Ho Park et al. Vascular calcification (VC) increases morbidity and mortality in cardiovascular and metabolic diseases. Here, Kwon et al. show that calcification stimuli induce MDM2- mediated ubiquitination and proteasomal degradation of HDAC1, suggesting a possible therapeutic strategy for treatment of VC patients. 01 February 2016 | doi: 10.1038/ncomms10492 Biological Sciences  Medical research  Engineering of frustration in colloidal artificial ices realized on microfeatured grooved lattices OPEN Antonio Ortiz-Ambriz and Pietro Tierno Visualizing the dynamics of electron spins in frustrated systems is a challenging task, which may require an alternative way at the microscale. Here, the authors realize an artificial system composed of interacting colloidal particles to mimick frustrated spins, which is potentially helpful in information storage. 01 February 2016 | doi: 10.1038/ncomms10575 Physical Sciences  Applied physics  Condensed matter  Export of malaria proteins requires co-translational processing of the PEXEL motif independent of phosphatidylinositol-3-phosphate binding OPEN Justin A. Boddey, Matthew T. O’Neill, Sash Lopaticki, Teresa G. Carvalho, Anthony N. Hodder, Thomas Nebl, Stephan Wawra, Pieter van West, Zeinab Ebrahimzadeh, Dave Richard, Sven Flemming, Tobias Spielmann, Jude Przyborski, Jeff J. Babon and Alan F. Cowman Export of Plasmodium falciparum proteins into infected erythrocytes relies upon the PEXEL motif in target proteins. Here Boddey et al. challenge the hypothesis that the PEXEL motif mediates export by binding PI(3)P and instead suggest it acts via cleavage by plasmepsin V. 01 February 2016 | doi: 10.1038/ncomms10470 Biological Sciences  Biochemistry  Microbiology  Three-dimensional porous carbon composites containing high sulfur nanoparticle content for high-performance lithium–sulfur batteries OPEN Guoxing Li, Jinhua Sun, Wenpeng Hou, Shidong Jiang, Yong Huang and Jianxin Geng Lithium–sulfur batteries have high theoretical capacities but their performance is limited by poor conductivity and low stability. Here, the authors fabricate three-dimensional porous graphitic carbon composites containing sulfur nanoparticles and probe the effect of sulfur content on battery performance. 01 February 2016 | doi: 10.1038/ncomms10601 Chemical Sciences  Materials science  Nanotechnology  Physical chemistry  Stem cells of the suture mesenchyme in craniofacial bone development, repair and regeneration OPEN Takamitsu Maruyama, Jaeim Jeong, Tzong-Jen Sheu and Wei Hsu The suture mesenchyme has been postulated to act as the niche for stem cells for calvarial bones but the identity of the stem cells is unknown. Here, Maruyama et al. suggest that Axin2 expressing cells act as stem cells not only in craniofacial bone development and homeostasis but in injury-induced repair. 01 February 2016 | doi: 10.1038/ncomms10526 Biological Sciences  Cell biology  Developmental biology  Ultra-high gain diffusion-driven organic transistor OPEN Fabrizio Torricelli, Luigi Colalongo, Daniele Raiteri, Zsolt Miklós Kovács-Vajna and Eugenio Cantatore Organic field-effect transistors offer limited gain due to the large contact resistance and the channel length modulation. Here, Torricelli et al. show a new transistor architecture where the charge injection and extraction are driven by the charge diffusion and a gain larger than 700 is achieved. 01 February 2016 | doi: 10.1038/ncomms10550 Physical Sciences  Applied physics  Materials science  Nanotechnology  Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels OPEN Tuomas O. Kilpeläinen, Jayne F. Martin Carli, Alicja A. Skowronski, Qi Sun, Jennifer Kriebel, Mary F Feitosa, Åsa K. Hedman, Alexander W. Drong, James E. Hayes, Jinghua Zhao, Tune H. Pers, Ursula Schick, Niels Grarup, Zoltán Kutalik, Stella Trompet, Massimo Mangino, Kati Kristiansson, Marian Beekman, Leo-Pekka Lyytikäinen, Joel Eriksson et al. This meta-analysis of genome-wide association studies identifies four genetic loci associated with circulating leptin levels independent of adiposity. Examination in mouse adipose tissue explants provides functional support for the leptin-associated loci. 01 February 2016 | doi: 10.1038/ncomms10494 Biological Sciences  Genetics  Observing mesoscale eddy effects on mode-water subduction and transport in the North Pacific OPEN Lixiao Xu, Peiliang Li, Shang-Ping Xie, Qinyu Liu, Cong Liu and Wendian Gao Physical processes by which mesoscale eddies affect subduction remain unclear. Here, through a specially designed eddy-resolving field experiment, the authors capture the eddy enhancement of mode water subduction and transport, and confirm the dominance of eddy lateral advection over the eddy trapping effect. 01 February 2016 | doi: 10.1038/ncomms10505 Earth Sciences  Oceanography  The limits of precision monomer placement in chain growth polymerization OPEN Guillaume Gody, Per B. Zetterlund, Sébastien Perrier and Simon Harrisson Chemists increasingly seek to control monomer sequencing in aperiodic copolymers. Here, the authors show that the statistical nature of chain growth strongly limits the achievable control, and establish parameters for polymer design that balance precise control with simplicity of synthesis. 01 February 2016 | doi: 10.1038/ncomms10514 Chemical Sciences  Materials science  Organic chemistry  Two distinct types of remapping in primate cortical area V4 OPEN Sujaya Neupane, Daniel Guitton and Christopher C. Pack Visual receptive fields are known to change positions around the time of a saccade, but the nature of this remapping is unclear. Here Neupane and colleagues show that neurons in area V4 of the visual cortex exhibit two types of remapping, one consistent with a role in maintaining perceptual stability, and a second that seems to reflect shifts of attention. 01 February 2016 | doi: 10.1038/ncomms10402 Biological Sciences  Neuroscience  Phylogenomic and biogeographic reconstruction of the Trichinella complex OPEN Pasi K. Korhonen, Edoardo Pozio, Giuseppe La Rosa, Bill C. H. Chang, Anson V. Koehler, Eric P. Hoberg, Peter R. Boag, Patrick Tan, Aaron R. Jex, Andreas Hofmann, Paul W. Sternberg, Neil D. Young and Robin B. Gasser Trichinellosis is a globally important food-borne disease caused by roundworms of the Trichinella complex. Here the authors present genomic sequences representing all 12 recognized Trichinella species and genotypes, and reconstruct their phylogeny and biogeography. 01 February 2016 | doi: 10.1038/ncomms10513 Biological Sciences  Evolution  Genetics  Arrhythmogenesis in Timothy Syndrome is associated with defects in Ca2+-dependent inactivation OPEN Ivy E. Dick, Rosy Joshi-Mukherjee, Wanjun Yang and David T. Yue Timothy Syndrome (TS) is a multisystem disorder caused by two mutations leading to dysfunction of the CaV1.2 channel. Here, Dick et al. uncover a major and mechanistically divergent effect of both mutations on Ca2+/calmodulin-dependent inactivation of CaV1.2 channels, suggesting genetic variant-tailored therapy for TS treatment. 29 January 2016 | doi: 10.1038/ncomms10370 Biological Sciences  Medical research  A Phytophthora infestans RXLR effector targets plant PP1c isoforms that promote late blight disease OPEN Petra C. Boevink, Xiaodan Wang, Hazel McLellan, Qin He, Shaista Naqvi, Miles R. Armstrong, Wei Zhang, Ingo Hein, Eleanor M. Gilroy, Zhendong Tian and Paul R. J. Birch Phytophtora infestans is the causative agent of late blight disease in plants. Here Boevink et al. provide evidence that host protein phosphatases are targeted by a P. infestans effector protein and are required for disease development. 29 January 2016 | doi: 10.1038/ncomms10311 Biological Sciences  Microbiology  Plant sciences  Non-random walk diffusion enhances the sink strength of semicoherent interfaces OPEN A. Vattré, T. Jourdan, H. Ding, M.-C. Marinica and M. J. Demkowicz Materials resistant to radiation damage could improve the safety, efficiency and sustainability of nuclear energy. Here, the authors suggest that some materials and interfaces may be effective sinks for defects caused by this damage and propose that elastic interactions enhance sink strength. 29 January 2016 | doi: 10.1038/ncomms10424 Physical Sciences  Condensed matter  Materials science  Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy OPEN Douglas B. Johnson, Monica V. Estrada, Roberto Salgado, Violeta Sanchez, Deon B. Doxie, Susan R. Opalenik, Anna E. Vilgelm, Emily Feld, Adam S. Johnson, Allison R. Greenplate, Melinda E. Sanders, Christine M. Lovly, Dennie T. Frederick, Mark C. Kelley, Ann Richmond, Jonathan M. Irish, Yu Shyr, Ryan J. Sullivan, Igor Puzanov, Jeffrey A. Sosman et al. Immunotherapy is used to treat melanoma, however patient responses vary widely highlighting the need for factors that can predict therapeutic success. Here, the authors show that MHC-II molecules expressed by tumour cells are positively correlated with a good response to therapy and overall patient survival. 29 January 2016 | doi: 10.1038/ncomms10582 Biological Sciences  Cancer  Immunology  Medical research  Theory of antiskyrmions in magnets OPEN Wataru Koshibae and Naoto Nagaosa Skyrmions are swirling topological magnetic textures that behave as if they were particles. Here, the authors present numerical simulations that describe the creation and destruction of these spin vortices in both chiral and dipolar magnets, and show what happens when skyrmions and antiskyrmions collide. 29 January 2016 | doi: 10.1038/ncomms10542 Physical Sciences  Condensed matter  Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells OPEN Lee M. Butcher, Mitsuteru Ito, Minodora Brimpari, Tiffany J. Morris, Filipa A. C. Soares, Lars Ährlund-Richter, Nessa Carey, Ludovic Vallier, Anne C. Ferguson-Smith and Stephan Beck The methylation of non-CpG residues is a poorly understood marker of pluripotent cells, gradually lost as cells differentiate. Here the authors show non-CG methylation can be used as a marker of differentiation potential. 29 January 2016 | doi: 10.1038/ncomms10458 Biological Sciences  Developmental biology  Molecular biology  Nucleophilic arylation with tetraarylphosphonium salts OPEN Zuyong Deng, Jin-Hong Lin and Ji-Chang Xiao Carbon based nucleophiles often are synthetically limited by the high basicity/reactivity of the starting materials. Here, the authors show that tetraarylphosphonium salts can be induced to act as C-aryl nucleophiles for the addition to carbonyls and imines. 29 January 2016 | doi: 10.1038/ncomms10337 Chemical Sciences  Organic chemistry  Emergence of core–peripheries in networks OPEN T. Verma, F. Russmann, N.A.M. Araújo, J. Nagler and H.J. Herrmann Many transport networks exhibit a core–periphery structure, where few nodes are highly interconnected and the rest form a tree-shaped structure. Here, the authors demonstrate how to generate such a structure through a pruning process based on removal of underutilized links and redistribution of loads. 29 January 2016 | doi: 10.1038/ncomms10441 Physical Sciences  Theoretical physics  The Hippo signalling pathway maintains quiescence in Drosophila neural stem cells OPEN Rouven Ding, Kevin Weynans, Torsten Bossing, Claudia S. Barros and Christian Berger Drosophila neural stem cells (NSCs) are quiescent at early larval stages but how this is regulated is unclear. Here, Ding et al. show that quiescence of NSCs is mediated by cell-contact inhibition via the Hippo pathway transmembrane proteins Crumbs and Echinoid, which in turn are regulated by nutrient levels. 29 January 2016 | doi: 10.1038/ncomms10510 Biological Sciences  Cell biology  Developmental biology  Live-cell protein labelling with nanometre precision by cell squeezing OPEN Alina Kollmannsperger, Armon Sharei, Anika Raulf, Mike Heilemann, Robert Langer, Klavs F. Jensen, Ralph Wieneke and Robert Tampé The direct observation of intracellular processes through microscopy can provide key insight into biological pathways. Here the authors demonstrate the combination of microfluidic cell squeezing and fluorescent label delivery to native proteins for high throughput live cell super-resolution imaging. 29 January 2016 | doi: 10.1038/ncomms10372 Biological Sciences  Biotechnology  Cell biology  Human predation contributed to the extinction of the Australian megafaunal bird Genyornis newtoni ∼47 ka OPEN Gifford Miller, John Magee, Mike Smith, Nigel Spooner, Alexander Baynes, Scott Lehman, Marilyn Fogel, Harvey Johnston, Doug Williams, Peter Clark, Christopher Florian, Richard Holst and Stephen DeVogel The impact of humans on megafaunal extinction is Australia is unclear. Here, the authors show burn patterns on eggshells of the extinct megafaunal bird, Genyornis newtoni, created by humans across Australia, suggesting that human predation contributed to the extinction of this bird around 47 thousand years ago. 29 January 2016 | doi: 10.1038/ncomms10496 Biological Sciences  Evolution  Palaeontology  Inactivation of nuclear GSK3β by Ser389 phosphorylation promotes lymphocyte fitness during DNA double-strand break response OPEN Tina M. Thornton, Pilar Delgado, Liang Chen, Beatriz Salas, Dimitry Krementsov, Miriam Fernandez, Santiago Vernia, Roger J. Davis, Ruth Heimann, Cory Teuscher, Michael S. Krangel, Almudena R. Ramiro and Mercedes Rincón Double stranded DNA breaks are generated during rearrangements of lymphocyte antigen receptors. Here the authors show that the DNA breaks induce phosphorylation of nuclear GSK3β at Ser389/Thr390, protecting the activated lymphocytes from necroptosis-mediated cell death. 29 January 2016 | doi: 10.1038/ncomms10553 Biological Sciences  Immunology  Molecular biology  Genome-wide association study and targeted metabolomics identifies sex-specific association of CPS1 with coronary artery disease OPEN Jaana A. Hartiala, W. H. Wilson Tang, Zeneng Wang, Amanda L. Crow, Alexandre F. R. Stewart, Robert Roberts, Ruth McPherson, Jeanette Erdmann, Christina Willenborg, Stanley L. Hazen and Hooman Allayee Dietary choline metabolites, such as trimethylamine N-oxide and betaine, have been associated with coronary artery disease (CAD). Here, Hartiala et al. identify two genetic loci for betaine levels on chromosomes 2q34 and 5q14.1 and find that the 2q34 locus was also associated with other pathway intermediates, and decreased risk of CAD in women. 29 January 2016 | doi: 10.1038/ncomms10558 Biological Sciences  Genetics  Climate change not to blame for late Quaternary megafauna extinctions in Australia OPEN Frédérik Saltré, Marta Rodríguez-Rey, Barry W. Brook, Christopher N Johnson, Chris S. M. Turney, John Alroy, Alan Cooper, Nicholas Beeton, Michael I. Bird, Damien A. Fordham, Richard Gillespie, Salvador Herrando-Pérez, Zenobia Jacobs, Gifford H. Miller, David Nogués-Bravo, Gavin J. Prideaux, Richard G. Roberts and Corey J. A. Bradshaw Global megafaunal extinctions took place in the late Quaternary, yet the relative impact of climate and humans in the faunal collapse is unclear. Here, the authors show that megafaunal extinctions in Australia were independent of climate variability and took place approximately 13,500 years after human arrival. 29 January 2016 | doi: 10.1038/ncomms10511 Biological Sciences  Evolution  Palaeontology  E2F function in muscle growth is necessary and sufficient for viability in Drosophila OPEN Maria Paula Zappia and Maxim V. Frolov The transcriptional regulators E2F/Dp play a critical role in cell-cycle regulation, but it is unclear why E2F-deficient flies die. Here, the authors show this is linked to the function of E2F in adult Drosophila skeletal muscle, with the contribution of E2f1 being most important in post-fusion muscle. 29 January 2016 | doi: 10.1038/ncomms10509 Biological Sciences  Cell biology  Developmental biology  Defective DNA single-strand break repair is responsible for senescence and neoplastic escape of epithelial cells OPEN Joe Nassour, Sébastien Martien, Nathalie Martin, Emeric Deruy, Elisa Tomellini, Nicolas Malaquin, Fatima Bouali, Laure Sabatier, Nicolas Wernert, Sébastien Pinte, Eric Gilson, Albin Pourtier, Olivier Pluquet and Corinne Abbadie It is recognized that cellular senescence is triggered by DNA damage as a protective mechanism against tumorigenesis. Here the authors show that DNA single-strand breaks of oxidative origin can induce a transient senescent state followed by the emergence of clonal transformed cells. 29 January 2016 | doi: 10.1038/ncomms10399 Biological Sciences  Molecular biology  Pure-quartic solitons OPEN Andrea Blanco-Redondo, de Sterke C. Martijn, J.E. Sipe, Thomas F. Krauss, Benjamin J. Eggleton and Chad Husko Optical solitons are pulses that propagate undistorted. Here, the authors demonstrate a class of soliton arising from the interaction of self-phase modulation with quartic dispersion, rather than with quadratic dispersion as occurs in conventional solitons. 29 January 2016 | doi: 10.1038/ncomms10427 Physical Sciences  Optical physics  Scrutinizing the double superconducting gaps and strong coupling pairing in (Li1−xFex)OHFeSe OPEN Zengyi Du, Xiong Yang, Hai Lin, Delong Fang, Guan Du, Jie Xing, Huan Yang, Xiyu Zhu and Hai-Hu Wen Whilst superconductivity is understood to emerge when electronic pairing allows for conduction without resistance, the mechanism at work in Fe-based superconductors is unclear. Here, the authors address the details of Fermi surfaces and associated gaps as well as the pairing mechanism of (Li1−x Fe x )OHFeSe via scanning tunnelling methods. 29 January 2016 | doi: 10.1038/ncomms10565 Physical Sciences  Condensed matter  Reduction of aberrant NF-κB signalling ameliorates Rett syndrome phenotypes in Mecp2-null mice OPEN Noriyuki Kishi, Jessica L. MacDonald, Julia Ye, Bradley J. Molyneaux, Eiman Azim and Jeffrey D. Macklis Rett syndrome is a neurodevelopmental disorder caused by mutations in Mecp2. Here the authors show that Mecp2 loss-of-function leads to upregulation of the NF-κB pathway, and that reducing NF-κB signalling ameliorates phenotypes of Mecp2-null mice, thus offering a potential therapeutic strategy. 29 January 2016 | doi: 10.1038/ncomms10520 Biological Sciences  Neuroscience  DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer OPEN Andrew E Teschendorff, Yang Gao, Allison Jones, Matthias Ruebner, Matthias W. Beckmann, David L. Wachter, Peter A. Fasching and Martin Widschwendter Altered epigenetics is a feature of cancer but whether these changes occur early in tumour development is unclear. Here, the authors analyse methylation events in breast cancer and adjacent normal pairs, and show that methylation changes in the normal tissue are also found in the tumour, suggesting that some of these events occur early in cancer. 29 January 2016 | doi: 10.1038/ncomms10478 Biological Sciences  Cancer  Genetics  Molecular biology  Structure sensitivity in the nonscalable regime explored via catalysed ethylene hydrogenation on supported platinum nanoclusters OPEN Andrew S. Crampton, Marian D. Rötzer, Claron J. Ridge, Florian F. Schweinberger, Ueli Heiz, Bokwon Yoon and Uzi Landman Ethylene hydrogenation often serves as an example of a structure insensitive reaction. Here, the authors study the reaction, catalyzed by a range of size-selected platinum nanocatalysts, and demonstrate that in the sub-nanometer regime particle size can be used to tune hydrogenation activity and selectivity. 28 January 2016 | doi: 10.1038/ncomms10389 Chemical Sciences  Catalysis  Materials science  Physical chemistry  RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency OPEN Jun Song, Dongshan Yang, Jie Xu, Tianqing Zhu, Y. Eugene Chen and Jifeng Zhang CRISPR/Cas9 and transcription activator-like effector nuclease (TALEN) are becoming major tools for genome editing. Here, Song et al. show that RS-1, a small-molecule enhancer for homology directed repair, increases the CRISPR/Cas9 and TALEN mediated knock-in efficiency both in vitro and in vivo with rabbit. 28 January 2016 | doi: 10.1038/ncomms10548 Biological Sciences  Biotechnology  Molecular biology  MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation OPEN Sophie Nolivos, Amy L. Upton, Anjana Badrinarayanan, Julius Müller, Katarzyna Zawadzka, Jakub Wiktor, Amber Gill, Lidia Arciszewska, Emilien Nicolas and David Sherratt MukBEF, the bacterial structural maintenance of chromosomes complex, is known to associate with origins of replication and topoisomerase IV. Here the authors show an association of MukBEF with MatP and replication termination regions, important for proper sister chromatid decatenation and segregation. 28 January 2016 | doi: 10.1038/ncomms10466 Biological Sciences  Molecular biology  A mouse model for a partially inactive obesity-associated human MC3R variant OPEN Bonggi Lee, Jashin Koo, Joo Yun Jun, Oksana Gavrilova, Yongjun Lee, Arnold Y. Seo, Dezmond C. Taylor-Douglas, Diane C. Adler-Wailes, Faye Chen, Ryan Gardner, Dimitri Koutzoumis, Roya Sherafat Kazemzadeh, Robin B. Roberson and Jack A. Yanovski The melanocortin receptor, MC3R, regulates organismal energy homeostasis. Here, Lee et al. create knock-in mice with the a mutated version of the human MC3R receptor found in obese children, and show these mice have more fat and smaller bone, yet are by and large metabolically healthy. 28 January 2016 | doi: 10.1038/ncomms10522 Biological Sciences  Medical research  Volta phase plate cryo-EM of the small protein complex Prx3 OPEN Maryam Khoshouei, Mazdak Radjainia, Amy J. Phillips, Juliet A. Gerrard, Alok K. Mitra, Jürgen M. Plitzko, Wolfgang Baumeister and Radostin Danev Although the resolution achievable with cryo-EM can now rival crystallography, its application to small protein assemblies remains challenging. Here the authors demonstrate the use of the Volta phase plate for single particle analysis and its potential for the study of small specimens. 28 January 2016 | doi: 10.1038/ncomms10534 Biological Sciences  Biochemistry  Biophysics  Serotonin neurons in the dorsal raphe nucleus encode reward signals OPEN Yi Li, Weixin Zhong, Daqing Wang, Qiru Feng, Zhixiang Liu, Jingfeng Zhou, Chunying Jia, Fei Hu, Jiawei Zeng, Qingchun Guo, Ling Fu and Minmin Luo How neurons in the dorsal raphe nucleus (DRN) respond to reward related behaviours is not known. Here, Li and colleagues report that DRN serotoninergic neurons are phasically activated by rewards such as sex, food and sucrose, and tonically activated during reward anticipation, while GABAergic neurons respond to punishment. 28 January 2016 | doi: 10.1038/ncomms10503 Biological Sciences  Neuroscience  Microbial diversity drives multifunctionality in terrestrial ecosystems OPEN Manuel Delgado-Baquerizo, Fernando T. Maestre, Peter B. Reich, Thomas C. Jeffries, Juan J. Gaitan, Daniel Encinar, Miguel Berdugo, Colin D. Campbell and Brajesh K. Singh The role of microbial diversity in ecosystems is less well understood than, for example, that of plant diversity. Analysing two independent data sets at a global and regional scale, Delgado-Baquerizo et al. show positive effects of soil diversity on multiple terrestrial ecosystem functions. 28 January 2016 | doi: 10.1038/ncomms10541 Biological Sciences  Ecology  Microbiology  Cytotoxicity of crystals involves RIPK3-MLKL-mediated necroptosis OPEN Shrikant R. Mulay, Jyaysi Desai, Santhosh V. Kumar, Jonathan N. Eberhard, Dana Thomasova, Simone Romoli, Melissa Grigorescu, Onkar P. Kulkarni, Bastian Popper, Volker Vielhauer, Gabriele Zuchtriegel, Christoph Reichel, Jan Hinrich Bräsen, Paola Romagnani, Rostyslav Bilyy, Luis E. Munoz, Martin Herrmann, Helen Liapis, Stefan Krautwald, Andreas Linkermann et al. Kidney stone disease is caused by accumulation of oxalate crystals, which trigger tissue injury, inflammation and cell death. Mulay et al. show that crystals induce cell death in the kidney through necroptosis, and propose that this pathway may be a target for the treatment of crystal-induced disease. 28 January 2016 | doi: 10.1038/ncomms10274 Biological Sciences  Cell biology  Immunology  Medical research  Toughness and strength of nanocrystalline graphene OPEN Ashivni Shekhawat and Robert O. Ritchie Graphene is known to be a remarkably strong material, but it can often contain defects. Here, the authors use large-scale simulations and continuum modelling to show that the statistical variation in toughness and strength of polycrystalline graphene can be understood with 'weakest-link' statistics. 28 January 2016 | doi: 10.1038/ncomms10546 Physical Sciences  Materials science  SCFCyclin F-dependent degradation of CDC6 suppresses DNA re-replication OPEN David Walter, Saskia Hoffmann, Eirini-Stavroula Komseli, Juri Rappsilber, Vassilis Gorgoulis and Claus Storgaard Sørensen To ensure genome stability, cells need to restrict DNA replication to once per cell cycle. Here the authors show that Cyclin F interacts with and targets the licensing factor CDC6 for degradation, preventing re-firing of replication origins. 28 January 2016 | doi: 10.1038/ncomms10530 Biological Sciences  Molecular biology  Amplification and generation of ultra-intense twisted laser pulses via stimulated Raman scattering OPEN J. Vieira, R. M. G. M. Trines, E. P. Alves, R. A. Fonseca, J. T. Mendonça, R. Bingham, P. Norreys and L. O. Silva High intensity light with a non-zero orbital angular momentum could aid the development of laser-wakefield particle accelerators. Here, the authors theoretically show that stimulated Raman backscattering in plasmas can generate and amplify orbital angular momentum lasers to petawatt intensities. 28 January 2016 | doi: 10.1038/ncomms10371 Physical Sciences  Fluids and plasma physics  Optical physics  Evidence and implications of direct charge excitation as the dominant mechanism in plasmon-mediated photocatalysis OPEN Calvin Boerigter, Robert Campana, Matthew Morabito and Suljo Linic The excitation of metal nanoparticles with light can lead to localized surface plasmon resonances, capable of driving chemical reactions in bound species. Here, the authors elucidate this mechanism and suggest that future plasmonic catalysts may be able to selectively activate specific chemical bonds. 28 January 2016 | doi: 10.1038/ncomms10545 Chemical Sciences  Catalysis  Physical chemistry  Genome-wide association studies in the Japanese population identify seven novel loci for type 2 diabetes OPEN Minako Imamura, Atsushi Takahashi, Toshimasa Yamauchi, Kazuo Hara, Kazuki Yasuda, Niels Grarup, Wei Zhao, Xu Wang, Alicia Huerta-Chagoya, Cheng Hu, Sanghoon Moon, Jirong Long, Soo Heon Kwak, Asif Rasheed, Richa Saxena, Ronald C. W. Ma, Yukinori Okada, Minoru Iwata, Jun Hosoe, Nobuhiro Shojima et al. Here, Imamura et al. conduct meta-analysis of genome-wide association studies to identify novel susceptibility loci for type 2 diabetes (T2D) in the Japanese population. By doing so, this study shows that both ethnicity-specific and ethnically-shared genetic loci can contribute to T2D risk. 28 January 2016 | doi: 10.1038/ncomms10531 Biological Sciences  Genetics  Follicular regulatory T cells can be specific for the immunizing antigen and derive from naive T cells OPEN Meryem Aloulou, Edward J. Carr, Mylène Gador, Alexandre Bignon, Roland S. Liblau, Nicolas Fazilleau and Michelle A. Linterman T follicular regulatory cells control the magnitude of the germinal centre response. Here the authors show that these cells display specificity to self as well as foreign antigens, and can arise from Foxp3-negative precursors at early stages of immunization in a PD-L1 dependent manner. 28 January 2016 | doi: 10.1038/ncomms10579 Biological Sciences  Immunology  Spontaneous liquid crystal and ferromagnetic ordering of colloidal magnetic nanoplates OPEN M. Shuai, A. Klittnick, Y. Shen, G. P. Smith, M. R. Tuchband, C. Zhu, R. G. Petschek, A. Mertelj, D. Lisjak, M. Čopič, J. E. Maclennan, M. A. Glaser and N. A. Clark Ferromagnetism has been known as a material property of solids since the time of the ancient Greeks. Here, Shuai et al. report that magnetic nanoplates suspended in a simple solvent can spontaneously align to form a ferromagnetic liquid, capable of both producing and sensing magnetic fields. 28 January 2016 | doi: 10.1038/ncomms10394 Physical Sciences  Condensed matter  Fluids and plasma physics  Materials science  Excitation of coherent propagating spin waves by pure spin currents OPEN Vladislav E. Demidov, Sergei Urazhdin, Ronghua Liu, Boris Divinskiy, Andrey Telegin and Sergej O. Demokritov Dynamical effects driven by pure spin currents in magnetic nanostructures have so far been limited to spatially confined excitations, limiting potential magnonic applications. Here, the authors demonstrate the generation of coherent propagating spin waves in NiFe films induced by pure spin currents. 28 January 2016 | doi: 10.1038/ncomms10446 Physical Sciences  Applied physics  Nanotechnology  The occurrence of intracranial rhabdoid tumours in mice depends on temporal control of Smarcb1 inactivation OPEN Zhi-Yan Han, Wilfrid Richer, Paul Fréneaux, Céline Chauvin, Carlo Lucchesi, Delphine Guillemot, Camille Grison, Delphine Lequin, Gaelle Pierron, Julien Masliah-Planchon, André Nicolas, Dominique Ranchère-Vince, Pascale Varlet, Stéphanie Puget, Isabelle Janoueix-Lerosey, Olivier Ayrault, Didier Surdez, Olivier Delattre and Franck Bourdeaut SMARCB1 inactivation is prevalent in human atypical teratoid/rhabdoid tumours but a mouse model that accurately phenocopies the human disease is lacking. Here, the authors show that inactivation of SMARCB1 between E6 and E10 in mice results in tumours that better recapitulate the human phenotype, compared to previously reported models. 28 January 2016 | doi: 10.1038/ncomms10421 Biological Sciences  Cancer  Developmental biology  Neuroscience  Magnetic ground state of an individual Fe2+ ion in strained semiconductor nanostructure OPEN T. Smoleński, T. Kazimierczuk, J. Kobak, M. Goryca, A. Golnik, P. Kossacki and W. Pacuski Iron Fe2+ ions embedded in semiconductor matrix usually have zero magnetic moment in the ground state. Here, the authors show theoretically and experimentally that a nearly doubly degenerate magnetic ground state is produced when iron ions are subjected to strain in epitaxial quantum dots, suggesting they could be used in spintronics and solotronics. 28 January 2016 | doi: 10.1038/ncomms10484 Physical Sciences  Condensed matter  Nanotechnology  F-actin-rich contractile endothelial pores prevent vascular leakage during leukocyte diapedesis through local RhoA signalling OPEN Niels Heemskerk, Lilian Schimmel, Chantal Oort, Jos van Rijssel, Taofei Yin, Bin Ma, Jakobus van Unen, Bettina Pitter, Stephan Huveneers, Joachim Goedhart, Yi Wu, Eloi Montanez, Abigail Woodfin and Jaap D. van Buul Endothelial cells can support leukocyte extravasation without causing vascular leakage, but the exact mechanism underlying this process has not been fully elucidated. Here the authors show that it is regulated through actomyosin-based endothelial pore confinement, which requires local endothelial RhoA activation. 27 January 2016 | doi: 10.1038/ncomms10493 Biological Sciences  Cell biology  Immunology  Electrochemical camera chip for simultaneous imaging of multiple metabolites in biofilms OPEN Daniel L. Bellin, Hassan Sakhtah, Yihan Zhang, Alexa Price-Whelan, Lars E. P. Dietrich and Kenneth L. Shepard Much remains to be understood about the biochemical basis of microbial community behaviour in biofilms. Here the authors describe a novel electrochemical camera chip that allows simultaneous spatial imaging of multiple metabolites that are crucial to community behaviour within whole microbial biofilms. 27 January 2016 | doi: 10.1038/ncomms10535 Biological Sciences  Bioengineering  Biotechnology  Microbiology  Rapid endothelial cytoskeletal reorganization enables early blood–brain barrier disruption and long-term ischaemic reperfusion brain injury OPEN Yejie Shi, Lili Zhang, Hongjian Pu, Leilei Mao, Xiaoming Hu, Xiaoyan Jiang, Na Xu, R. Anne Stetler, Feng Zhang, Xiangrong Liu, Rehana K. Leak, Richard F. Keep, Xunming Ji and Jun Chen Matrix metalloproteinases (MMPs) released from infiltrating immune cells are a major contributor to blood-brain barrier (BBB) breakdown following stroke. Here, the authors identify an early, MMP-independent BBB breakdown mechanism caused by rapid cytoskeletal rearrangements in endothelial cells, which could be inhibited by ADF. 27 January 2016 | doi: 10.1038/ncomms10523 Biological Sciences  Cell biology  Neuroscience  ADAR-mediated RNA editing suppresses sleep by acting as a brake on glutamatergic synaptic plasticity OPEN J. E. Robinson, J. Paluch, D. K. Dickman and W. J. Joiner Sleep is postulated to offset buildup in net synaptic strength that occurs during waking experience. Here, the authors identify a role for the RNA editing gene Adar in regulating glutamatergic synaptic plasticity and show that disruption in Adar expression impairs normal waking in flies. 27 January 2016 | doi: 10.1038/ncomms10512 Biological Sciences  Neuroscience  Direct growth of single-crystalline III–V semiconductors on amorphous substrates OPEN Kevin Chen, Rehan Kapadia, Audrey Harker, Sujay Desai, Jeong Seuk Kang, Steven Chuang, Mahmut Tosun, Carolin M. Sutter-Fella, Michael Tsang, Yuping Zeng, Daisuke Kiriya, Jubin Hazra, Surabhi Rao Madhvapathy, Mark Hettick, Yu-Ze Chen, James Mastandrea, Matin Amani, Stefano Cabrini, Yu-Lun Chueh, Joel W. Ager III et al. Growth of high-quality III–V semiconductors for electronics and optoelectronics usually requires an atomic-lattice matched substrate. Here, the authors use templated liquid-phase crystal growth to create single-crystalline III–V material up to ten micrometres across on an amorphous substrate. 27 January 2016 | doi: 10.1038/ncomms10502 Physical Sciences  Materials science  Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types OPEN Cheng Wang, Yayun Gu, Kai Zhang, Kaipeng Xie, Meng Zhu, Ningbin Dai, Yue Jiang, Xuejiang Guo, Mingxi Liu, Juncheng Dai, Linxiang Wu, Guangfu Jin, Hongxia Ma, Tao Jiang, Rong Yin, Yankai Xia, Li Liu, Shouyu Wang, Bin Shen, Ran Huo et al. Genes normally expressed in the testis but aberrantly expressed in cancer are termed cancer testis antigens. In this study, the authors catalogue the expression of these genes in 19 different cancer types and correlate expression with some somatically mutated oncogenes. 27 January 2016 | doi: 10.1038/ncomms10499 Biological Sciences  Cancer  Genetics  Towards do-it-yourself planar optical components using plasmon-assisted etching OPEN Hao Chen, Abdul M. Bhuiya, Qing Ding, Harley T. Johnson and Kimani C. Toussaint Jr Recently, there has been a growing interest in do-it-yourself components to accelerate development of inexpensive fabrication approaches. Here, Chen et al. present a plasmon-assisted etching technique to fabricate planar optical components using arrays of gold pillar-supported bowtie nanoantennas as a template. 27 January 2016 | doi: 10.1038/ncomms10468 Physical Sciences  Applied physics  Materials science  Nanotechnology  High-contrast and fast electrochromic switching enabled by plasmonics OPEN Ting Xu, Erich C. Walter, Amit Agrawal, Christopher Bohn, Jeyavel Velmurugan, Wenqi Zhu, Henri J. Lezec and A. Alec Talin Slow switching speeds in device configurations have severely limited the applications of electrochromic materials. Here, Xu et al. use plasmonic nanoslit arrays and demonstrate fast, high-contrast, monochromatic and full-colour electrochromic switching using two different electrochromic polymers. 27 January 2016 | doi: 10.1038/ncomms10479 Physical Sciences  Nanotechnology  Optical physics  Physical chemistry  Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs OPEN Emiley A. Eloe-Fadrosh, David Paez-Espino, Jessica Jarett, Peter F. Dunfield, Brian P. Hedlund, Anne E. Dekas, Stephen E. Grasby, Allyson L. Brady, Hailiang Dong, Brandon R. Briggs, Wen-Jun Li, Danielle Goudeau, Rex Malmstrom, Amrita Pati, Jennifer Pett-Ridge, Edward M. Rubin, Tanja Woyke, Nikos C. Kyrpides and Natalia N. Ivanova The analysis of existing metagenomic data can lead to discovery of new microorganisms. Here, Eloe-Fadrosh et al. perform a large-scale analysis of global metagenomic data, followed by genome reconstruction and single-cell genomics, to describe a new bacterial phylum that inhabits geothermal springs. 27 January 2016 | doi: 10.1038/ncomms10476 Biological Sciences  Ecology  Microbiology  Nanoelectronic primary thermometry below 4 mK OPEN D. I. Bradley, R. E. George, D. Gunnarsson, R. P. Haley, H. Heikkinen, Yu. A. Pashkin, J. Penttilä, J. R. Prance, M. Prunnila, L. Roschier and M. Sarsby When cooled to the millikelvin scale, nanoelectronic structures can become thermally detached from their environment, limiting nanoscale electronic thermometry. Here, the authors demonstrate the robust cooling of optimally-designed Coulomb blockade thermometer devices down to the millikelvin scale. 27 January 2016 | doi: 10.1038/ncomms10455 Physical Sciences  Condensed matter  Harnessing spin precession with dissipation OPEN A. D. Crisan, S. Datta, J. J. Viennot, M. R. Delbecq, A. Cottet and T. Kontos Control over the orientation of electronic spins forms the basis for spintronic devices in both classical and quantum systems. Here, the authors observe electrically-tunable dissipation-controlled spin precession in a carbon nanotube quantum dot bridging two non-collinearly magnetized electrodes. 27 January 2016 | doi: 10.1038/ncomms10451 Physical Sciences  Condensed matter  Pd(II)-catalysed meta-C–H functionalizations of benzoic acid derivatives OPEN Shangda Li, Lei Cai, Huafang Ji, Long Yang and Gang Li While directed ortho-metalation is a well-established protocol, meta-functionalisation of aromatic groups is more challenging. Here, the authors report a directed meta-C-H functionalisation of benzoic acid derivatives, using a nitrile-based sulfonamide directing group. 27 January 2016 | doi: 10.1038/ncomms10443 Chemical Sciences  Catalysis  Organic chemistry  Demonstration of a near-IR line-referenced electro-optical laser frequency comb for precision radial velocity measurements in astronomy OPEN X. Yi, K. Vahala, J. Li, S. Diddams, G. Ycas, P. Plavchan, S. Leifer, J. Sandhu, G. Vasisht, P. Chen, P. Gao, J. Gagne, E. Furlan, M. Bottom, E. C. Martin, M. P. Fitzgerald, G. Doppmann and C. Beichman Laser frequency combs emit a spectrum of equally spaced peaks that can provide precise frequency references useful for astronomy. Here, the authors demonstrate a frequency comb using electro-optical modulation, which has a line spacing that is resolvable using grating spectrographs unlike the mode-locking approach. 27 January 2016 | doi: 10.1038/ncomms10436 Physical Sciences  Astronomy  Optical physics  Graphene–ferroelectric metadevices for nonvolatile memory and reconfigurable logic-gate operations OPEN Woo Young Kim, Hyeon-Don Kim, Teun-Teun Kim, Hyun-Sung Park, Kanghee Lee, Hyun Joo Choi, Seung Hoon Lee, Jaehyeon Son, Namkyoo Park and Bumki Min Metamaterial memory devices often require a large stimulus to switch states or suffer from poor thermal stability. Here, the authors fabricate a terahertz metadevice driven by ferroelectric and graphene layers, and obtain multiple level memory devices stable at room temperature. 27 January 2016 | doi: 10.1038/ncomms10429 Physical Sciences  Materials science  Nanotechnology  Optical physics  Misorientation-angle-dependent electrical transport across molybdenum disulfide grain boundaries OPEN Thuc Hue Ly, David J. Perello, Jiong Zhao, Qingming Deng, Hyun Kim, Gang Hee Han, Sang Hoon Chae, Hye Yun Jeong and Young Hee Lee Grain boundaries can degrade the performance of electronic devices made from single atomic layers of transition metal dichalcogenides. Here, the authors combine transport measurements and transmission electron microscopy to find a correlation between field-effect mobility and grain misorientation angle. 27 January 2016 | doi: 10.1038/ncomms10426 Physical Sciences  Materials science  Nanotechnology  Gyre-driven decay of the Earth’s magnetic dipole OPEN Christopher C. Finlay, Julien Aubert and Nicolas Gillet The magnitude of the Earth’s magnetic dipole has decreased by 9% over the past 175 years. Here, the authors suggest that the rate of dipole decay is controlled by a huge gyre in the liquid metal outer core acting on a field asymmetry, and that decay is set to continue for the next few decades. 27 January 2016 | doi: 10.1038/ncomms10422 Earth Sciences  Geology and geophysics  Wavelength-tunable entangled photons from silicon-integrated III–V quantum dots OPEN Yan Chen, Jiaxiang Zhang, Michael Zopf, Kyubong Jung, Yang Zhang, Robert Keil, Fei Ding and Oliver G. Schmidt Deterministic sources of entangled photons are important for photonic quantum networks, but many applications are only possible when their wavelengths are tunable. Here, the authors use on-chip strain engineering to demonstrate such a source with silicon-integrated InAs/GaAs quantum dots. 27 January 2016 | doi: 10.1038/ncomms10387 Physical Sciences  Materials science  Nanotechnology  Optical physics  Polaronic metal state at the LaAlO3/SrTiO3 interface OPEN C. Cancellieri, A. S. Mishchenko, U. Aschauer, A. Filippetti, C. Faber, O. S. Barišić, V. A. Rogalev, T. Schmitt, N. Nagaosa and V. N. Strocov Polarons are quasiparticles formed when an electron strongly couples to the lattice vibrations, or phonons, in a crystalline material. Here, the authors use soft-X-ray angle-resolved photoelectron spectroscopy to identify signatures of metal polarons at the interface between two oxide materials. 27 January 2016 | doi: 10.1038/ncomms10386 Physical Sciences  Condensed matter  Materials science  Probing QED and fundamental constants through laser spectroscopy of vibrational transitions in HD+ OPEN J. Biesheuvel, J.-Ph. Karr, L. Hilico, K. S. E. Eikema, W. Ubachs and J. C. J. Koelemeij Molecular hydrogen ions, the simplest molecules in nature, constitute a benchmark system for tests of quantum electrodynamics in complex forms of matter. Here, the authors report on a laser spectroscopic frequency measurement of a transition in HD+ in agreement with theory within 0.6 (1.1) part-per-billion. 27 January 2016 | doi: 10.1038/ncomms10385 Physical Sciences  Atomic and molecular physics  Generation of coherent spin-wave modes in yttrium iron garnet microdiscs by spin–orbit torque OPEN M. Collet, X. de Milly, O. d’Allivy Kelly, V. V. Naletov, R. Bernard, P. Bortolotti, J. Ben Youssef, V. E. Demidov, S. O. Demokritov, J. L. Prieto, M. Muñoz, V. Cros, A. Anane, G. de Loubens and O. Klein Spin-orbit interactions allow for pure spin current to be injected into a ferromagnetic insulator from a current-carrying heavy metal, generating torque on the magnetization. Here, the authors evidence magnetic auto-oscillations driven by spin-orbit torque in thin film microdiscs of yttrium iron garnet. 27 January 2016 | doi: 10.1038/ncomms10377 Physical Sciences  Condensed matter  Wavelength-tunable sources of entangled photons interfaced with atomic vapours OPEN Rinaldo Trotta, Javier Martín-Sánchez, Johannes S. Wildmann, Giovanni Piredda, Marcus Reindl, Christian Schimpf, Eugenio Zallo, Sandra Stroj, Johannes Edlinger and Armando Rastelli Quantum dots can produce entangled photons, but careful control over photon wavelength is required for real-life applications. Here, the authors use three-directional strain engineering to overcome this problem and to interface entangled photons from quantum dots with a cloud of natural atoms. 27 January 2016 | doi: 10.1038/ncomms10375 Physical Sciences  Materials science  Nanotechnology  Optical physics  Restricting mutualistic partners to enforce trade reliance OPEN Gregory A. K. Wyatt, E. Toby Kiers, Andy Gardner and Stuart A. West Mutualistic interactions involve trading benefits between cooperative species. Here, the authors show that restricting the resource acquisition of a mutualistic partner can increase mutualism by promoting resource trade, which suggests that conflict may lead to increased cooperation. 27 January 2016 | doi: 10.1038/ncomms10322 Biological Sciences  Ecology  Evolution  Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells OPEN Charlotte L. Scott, Fang Zheng, Patrick De Baetselier, Liesbet Martens, Yvan Saeys, Sofie De Prijck, Saskia Lippens, Chloé Abels, Steve Schoonooghe, Geert Raes, Nick Devoogdt, Bart N. Lambrecht, Alain Beschin and Martin Guilliams Tissue-resident macrophages are mostly derived from embryonic progenitors. Scott et al. develop a mouse model to specifically deplete Kupffer cells (KC) in vivo and show that monocyte-derived cells can repopulate KC niche and behave similar to their embryonically-derived counterparts. 27 January 2016 | doi: 10.1038/ncomms10321 Biological Sciences  Immunology    Nature Communications JOBS of the week Postdoc Positions Max Planck Institute for the Physics of Complex Systems Postdoctoral Scholar University of Chicago Postdoctoral Associate Sanford Burnham Prebys Medical Discovery Institute Postdoctoral Research Associate University of Liverpool Bioinformatician (Fixed Term) University of Cambridge NMR Metabolomics Technician University of Birmingham Doctoral student in computational biochemistry Linnaeus University 12 Doctoral Positions Justus-Liebig-Universität Gießen Scientist I The Allen Institute for Brain Science More Science jobs from Nature Communications EVENT Techniques &Applications of Molecular Biology 11.07.16 Coventry, UK More science events from       Latest Corrigenda     Corrigendum: Optically initialized robust valley-polarized holes in monolayer WSe2 OPEN Wei-Ting Hsu, Yen-Lun Chen, Chang-Hsiao Chen, Pang-Shiuan Liu, Tuo-Hung Hou, Lain-Jong Li and Wen-Hao Chang 01 February 2016 | doi: 10.1038/ncomms10396 Physical Sciences  Condensed matter      Corrigendum: Photon number statistics uncover the fluctuations in non-equilibrium lattice dynamics OPEN Martina Esposito, Kelvin Titimbo, Klaus Zimmermann, Francesca Giusti, Francesco Randi, Davide Boschetto, Fulvio Parmigiani, Roberto Floreanini, Fabio Benatti and Daniele Fausti 01 February 2016 | doi: 10.1038/ncomms10651 Physical Sciences  Condensed matter  Optical physics  Theoretical physics      Corrigendum: High-performance n-type black phosphorus transistors with type control via thickness and contact-metal engineering OPEN David J. Perello, Sang Hoon Chae, Seunghyun Song and Young Hee Lee 28 January 2016 | doi: 10.1038/ncomms10428 Physical Sciences  Applied physics  Materials science        Latest Erratum     Erratum: The assembly dynamics of the cytolytic pore toxin ClyA OPEN Stephan Benke, Daniel Roderer, Bengt Wunderlich, Daniel Nettels, Rudi Glockshuber and Benjamin Schuler 01 February 2016 | doi: 10.1038/ncomms10650 Biological Sciences  Biochemistry  Biophysics      Advertisement NATURE CONFERENCE ON TISSUE ENGINEERING AND REGENERATIVE MEDICINE  Presented by: State Key Laboratory of Ophthalmology | Zhongshan Ophthalmic Center | Sun Yat-sen University Nature Materials | Nature Reviews Materials April 7—9, 2016 | Ocean Hotel, Guangzhou, China REGISTER NOW!   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. 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