Nature Communications - 13 January 2016

Advertisement A*STAR Research - Highlighting the best of research at the Agency for Science, Technology and Research (A*STAR), Singapore's premier research organization   Recent Highlights Cell biology: A cell surface-to-nucleus super highway | Immunology: Understanding infants' itchy skin | Genetics: Regulatory regions revealed in one shot  Download the A*STAR Research app now!       Weekly Content Alert Nature Communications is now fully open access. Read more. 13 January 2016  Featured image: Currivan-Incorvia et al. develop nanowire logic devices which can cascade to form circuits and are compatible with existing transistor technology. Latest content: Articles Corrigenda Erratum Advertisement Nature Index 2015 China The 2015 Nature Index supplement dedicated to China reveals the country's output of high quality science continues to grow - a trend that shows no signs of slowing.  Access now for free. Journal homepage Recommend to library Web feed   Advertisement Online-only and open access, Cell Death Discovery will publish scientifically sound research at the intersection of cell death and medicine. Increasing the reproducibility of research, the journal will foster a dynamic dialogue with a focus on cancer, neurobiology and inflammation research. Submit your manuscript     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     Global marine protected areas do not secure the evolutionary history of tropical corals and fishes OPEN D. Mouillot, V. Parravicini, D. R. Bellwood, F. Leprieur, D. Huang, P. F. Cowman, C. Albouy, T. P. Hughes, W. Thuiller and F. Guilhaumon Marine protected areas (MPAs) are established to conserve species, but the extent to which they also conserve evolutionary history is not clear. Here, Mouillot et al. show that for tropical corals and fish, the current global MPA network secures only 1.7 and 17.6% of phylogenetic diversity, respectively. 12 January 2016 | doi: 10.1038/ncomms10359 Biological Sciences  Ecology  Evolution  Oceanography  Periprostatic adipocytes act as a driving force for prostate cancer progression in obesity OPEN Victor Laurent, Adrien Guérard, Catherine Mazerolles, Sophie Le Gonidec, Aurélie Toulet, Laurence Nieto, Falek Zaidi, Bilal Majed, David Garandeau, Youri Socrier, Muriel Golzio, Thomas Cadoudal, Karima Chaoui, Cedric Dray, Bernard Monsarrat, Odile Schiltz, Yuan Yuan Wang, Bettina Couderc, Philippe Valet, Bernard Malavaud et al. Obesity is associated with an elevated risk of prostate cancer. Here, the authors show that periprostatic adipose tissue promotes the migration and local invasion of prostate cancer cells by secreting the chemokine, CCL7, and that this process is enhanced in the context of obesity. 12 January 2016 | doi: 10.1038/ncomms10230 Biological Sciences  Cancer  Medical research  Clouds enhance Greenland ice sheet meltwater runoff OPEN K. Van Tricht, S. Lhermitte, J. T. M. Lenaerts, I. V. Gorodetskaya, T. S. L’Ecuyer, B. Noël, M. R. van den Broeke, D. D. Turner and N. P. M. van Lipzig Clouds play a pivotal role in the energy and mass balance of the Greenland ice sheet, thereby affecting its contribution to global sea-level rise. Here, using a combination of observations and model simulations, the authors show that clouds enhance Greenland ice sheet meltwater runoff by more than 30%. 12 January 2016 | doi: 10.1038/ncomms10266 Earth Sciences  Atmospheric science  Climate science  An electrostatic mechanism for Ca2+-mediated regulation of gap junction channels OPEN Brad C. Bennett, Michael D. Purdy, Kent A. Baker, Chayan Acharya, William E. McIntire, Raymond C. Stevens, Qinghai Zhang, Andrew L. Harris, Ruben Abagyan and Mark Yeager Intercellular signalling can be mediated by gap junction channels, and calcium blocks this signally during tissue injury. Here, the authors use X-ray crystallography and molecular dynamics to show that the calcium forms an electrostatic barrier to prevent transport of cations. 12 January 2016 | doi: 10.1038/ncomms9770 Biological Sciences  Biochemistry  A draft map of the mouse pluripotent stem cell spatial proteome OPEN Andy Christoforou, Claire M. Mulvey, Lisa M. Breckels, Aikaterini Geladaki, Tracey Hurrell, Penelope C. Hayward, Thomas Naake, Laurent Gatto, Rosa Viner, Alfonso Martinez Arias and Kathryn S. Lilley The spatial location of proteins within a cell is a key element of protein function. Here the authors describe hyperLOPIT—a proteomics workflow that allows the simultaneous assignment of thousands of proteins to subcellular niches with high resolution—and apply it to mouse pluripotent stem cells. 12 January 2016 | doi: 10.1038/ncomms9992 Biological Sciences  Biochemistry  Cell biology  Manipulation of charge transfer and transport in plasmonic-ferroelectric hybrids for photoelectrochemical applications OPEN Zhijie Wang, Dawei Cao, Liaoyong Wen, Rui Xu, Manuel Obergfell, Yan Mi, Zhibing Zhan, Nasori Nasori, Jure Demsar and Yong Lei Photoelectrochemical systems based on plasmonics require control of band bending at the interface as well as transport of hot carriers. Here, Wang et al. employ a ferroelectric material, Pb(Zr,Ti)O3, with gold on ITO to capture hot electrons from the metal and manipulate the photoexcited charges for energy conversion. 12 January 2016 | doi: 10.1038/ncomms10348 Physical Sciences  Materials science  Optical physics  The Atg1–kinase complex tethers Atg9-vesicles to initiate autophagy OPEN Yijian Rao, Marco G. Perna, Benjamin Hofmann, Viola Beier and Thomas Wollert Autophagosome biogenesis is initiated by recruitment of Atg9-vesicles to the phagophore assembly site. Here Rao et al. use a reconstituted in vitro system to describe the mechanism by which activation of the Atg1-kinase complex from its constituent parts recruits and tethers Atg9-vesicles. 12 January 2016 | doi: 10.1038/ncomms10338 Biological Sciences  Biochemistry  Biophysics  Cell biology  Two-dimensional honeycomb network through sequence-controlled self-assembly of oligopeptides OPEN Sabine Abb, Ludger Harnau, Rico Gutzler, Stephan Rauschenbach and Klaus Kern Peptide nanostructures are currently arousing interest thanks to their potential applications in medicine, electronics and coatings. Here, through experiment and theory, the authors demonstrate exquisite control over surface peptide assembly behaviour through manipulation of amino acid sequence. 12 January 2016 | doi: 10.1038/ncomms10335 Biological Sciences  Bioengineering  Materials science  Nanotechnology  Impairment of PARK14-dependent Ca2+ signalling is a novel determinant of Parkinson’s disease OPEN Qingde Zhou, Allen Yen, Grzegorz Rymarczyk, Hirohide Asai, Chelsea Trengrove, Nadine Aziz, Michael T. Kirber, Gustavo Mostoslavsky, Tsuneya Ikezu, Benjamin Wolozin and Victoria M. Bolotina PLA2g6 regulates store-operated Ca2+ entry and is linked to Parkinson’s disease. Here, Zhou et al find faulty PLA2g6-dependent Ca2+ signaling in idiopathic PD patients, and show that its impairment triggers autophagic dysfunction and loss of dopaminergic neurons in a new PLA2g6 ex2KO mouse model. 12 January 2016 | doi: 10.1038/ncomms10332 Biological Sciences  Cell biology  Neuroscience  Yap is required for ependymal integrity and is suppressed in LPA-induced hydrocephalus OPEN Raehee Park, Uk Yeol Moon, Jun Young Park, Lucinda J. Hughes, Randy L. Johnson, Seo-Hee Cho and Seonhee Kim Failure of the ependymal cell layer that lines the ventricular surfaces of the brain can result in fetal hydrocephalus. Park et al. reveal a role for the Hippo pathway gene Yap in the generation of ependymal cells, and show that suppression of Yap is observed in a model of hydrocephalus. 12 January 2016 | doi: 10.1038/ncomms10329 Biological Sciences  Developmental biology  Neuroscience  Identification of p62/SQSTM1 as a component of non-canonical Wnt VANGL2–JNK signalling in breast cancer OPEN Tania M. Puvirajesinghe, François Bertucci, Ashish Jain, Pierluigi Scerbo, Edwige Belotti, Stéphane Audebert, Michael Sebbagh, Marc Lopez, Andreas Brech, Pascal Finetti, Emmanuelle Charafe-Jauffret, Max Chaffanet, Rémy Castellano, Audrey Restouin, Sylvie Marchetto, Yves Collette, Anthony Gonçalvès, Ian Macara, Daniel Birnbaum, Laurent Kodjabachian et al. Defects in non-canonical Wnt/planar cell polarity signalling have recently been linked to breast cancer aggressiveness. Puvirajesinghe et al. identify VANGL2, p62/SQSTM1 and JNK as important players in this pathway which may be amenable to therapeutic intervention in breast cancer. 12 January 2016 | doi: 10.1038/ncomms10318 Biological Sciences  Cancer  Cell biology  Interrogating cellular fate decisions with high-throughput arrays of multiplexed cellular communities OPEN Sisi Chen, Andrew W. Bremer, Olivia J. Scheideler, Yun Suk Na, Michael E. Todhunter, Sonny Hsiao, Prithvi R. Bomdica, Michel M. Maharbiz, Zev J. Gartner and David V. Schaffer In vitro assays involving multiple cell types cannot control the stoichiometry or contact times of cell-cell interactions. Here, the authors present a patterned co-culture platform based on printed oligonucleotides capable of controlling cell-cell interactions of up to four different cell types at the single-cell level. 12 January 2016 | doi: 10.1038/ncomms10309 Biological Sciences  Biotechnology  Cell biology  The H-index of a network node and its relation to degree and coreness OPEN Linyuan Lü, Tao Zhou, Qian-Ming Zhang and H. Eugene Stanley Identifying influential nodes in networks is important for the understanding of their structure and function, but there are several so far unrelated measures to assess this. Here, the authors unfold relations among knows criteria and construct a family of indices that interpolate between degree and coreness. 12 January 2016 | doi: 10.1038/ncomms10168 Physical Sciences  Theoretical physics  Logic circuit prototypes for three-terminal magnetic tunnel junctions with mobile domain walls OPEN J. A. Currivan-Incorvia, S. Siddiqui, S. Dutta, E. R. Evarts, J. Zhang, D. Bono, C. A. Ross and M. A. Baldo Ferromagnetic nanowires act as conduits for magnetic domain walls which may in principle be used to encode and propagate information. Here, the authors present current-based nanowire domain wall logic prototypes with operational properties required for real devices. 12 January 2016 | doi: 10.1038/ncomms10275 Physical Sciences  Condensed matter  Spatio-temporal propagation of cascading overload failures in spatially embedded networks OPEN Jichang Zhao, Daqing Li, Hillel Sanhedrai, Reuven Cohen and Shlomo Havlin Overload failures propagate through hidden functional dependencies across networked systems. Here, the authors study the spatio-temporal propagation behaviour of cascading overload failures, and find that they spread radially from their origin with an approximately constant velocity. 12 January 2016 | doi: 10.1038/ncomms10094 Physical Sciences  Theoretical physics  Ancient origin and maternal inheritance of blue cuckoo eggs OPEN Frode Fossøy, Michael D Sorenson, Wei Liang, Torbjørn Ekrem, Arne Moksnes, Anders P Møller, Jarkko Rutila, Eivin Røskaft, Fugo Takasu, Canchao Yang and Bård G Stokke The common cuckoo lays its eggs in nests of a variety of species and their eggs mimic the ones of their hosts. Here, the authors show that blue egg colouration in the common cuckoo is maternally inherited, originated in Asia and then expanded to Europe. 12 January 2016 | doi: 10.1038/ncomms10272 Biological Sciences  Evolution  Zoology  Anaplastic large cell lymphoma arises in thymocytes and requires transient TCR expression for thymic egress OPEN Tim I. M. Malcolm, Patrick Villarese, Camilla J. Fairbairn, Laurence Lamant, Amélie Trinquand, C. Elizabeth Hook, G. A. Amos Burke, Laurence Brugières, Katherine Hughes, Dominique Payet, Olaf Merkel, Ana-Iris Schiefer, Ibraheem Ashankyty, Shahid Mian, Mariusz Wasik, Martin Turner, Lukas Kenner, Vahid Asnafi, Elizabeth Macintyre and Suzanne D. Turner et al. Anaplastic large cell lymphoma is characterized by an NPM–ALK fusion but the cell of origin for this cancer is unclear. Here, the authors show that, in an NPM–ALK mouse model, the tumours likely arise from early thmyocytes and require an initial burst of TCR signalling for initiation. 12 January 2016 | doi: 10.1038/ncomms10087 Biological Sciences  Cancer  Immunology  Novel role for anti-Müllerian hormone in the regulation of GnRH neuron excitability and hormone secretion OPEN Irene Cimino, Filippo Casoni, Xinhuai Liu, Andrea Messina, Jyoti Parkash, Soazik P. Jamin, Sophie Catteau-Jonard, Francis Collier, Marc Baroncini, Didier Dewailly, Pascal Pigny, Mel Prescott, Rebecca Campbell, Allan E. Herbison, Vincent Prevot and Paolo Giacobini Anti-Müllerian hormone (AMH) plays a role in sexual differentiation and gonadal function, but extra-gonadal effects of AMH are not known. Here Cimino et al. show that AMH activates a subset of gonadotrophin-releasing hormone (GnRH)-releasing neurons, contributing to luteinizing hormone secretion from the pituitary gland. 12 January 2016 | doi: 10.1038/ncomms10055 Biological Sciences  Cell biology  Neuroscience  A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization OPEN Jasper H. M. van der Velde, Jens Oelerich, Jingyi Huang, Jochem H. Smit, Atieh Aminian Jazi, Silvia Galiani, Kirill Kolmakov, Giorgos Guoridis, Christian Eggeling, Andreas Herrmann, Gerard Roelfes and Thorben Cordes Synthetic organic fluorophores are powerful tools for bioimaging, but frequently display shortened observation times and signal fluctuations. Here, the authors report a general method to covalently label a biomolecule with a fluorophore and photostabilizer, reducing unwanted photophysical effects by intramolecular quenching of reactive fluorophore states. 11 January 2016 | doi: 10.1038/ncomms10144 Chemical Sciences  Biophysics  Organic chemistry  Physical chemistry  Replication landscape of the human genome OPEN Nataliya Petryk, Malik Kahli, Yves d'Aubenton-Carafa, Yan Jaszczyszyn, Yimin Shen, Maud Silvain, Claude Thermes, Chun-Long Chen and Olivier Hyrien The physical origin and termination sites of DNA replication in human cells have remained elusive. Here the authors use Okazaki fragment sequencing to reveal global replication patterns and show how chromatin and transcription modulate the process. 11 January 2016 | doi: 10.1038/ncomms10208 Biological Sciences  Molecular biology  1,25D3 prevents CD8+Tc2 skewing and asthma development through VDR binding changes to the Cyp11a1 promoter OPEN Michaela Schedel, Yi Jia, Sven Michel, Katsuyuki Takeda, Joanne Domenico, Anthony Joetham, Fangkun Ning, Matthew Strand, Junyan Han, Meiqin Wang, Joseph J. Lucas, Christian Vogelberg, Michael Kabesch, Brian P. O’Connor and Erwin W. Gelfand Type 2 CD8+ T cells (Tc2) play a role in the development of experimental asthma. Here the authors show that 1,25D3, the active form of vitamin D3, can prevent conversion of CD8+T cells to a Tc2 phenotype, reducing asthma susceptibility. 11 January 2016 | doi: 10.1038/ncomms10213 Biological Sciences  Immunology  Medical research  High-efficiency robust perovskite solar cells on ultrathin flexible substrates OPEN Yaowen Li, Lei Meng, Yang (Michael) Yang, Guiying Xu, Ziruo Hong, Qi Chen, Jingbi You, Gang Li, Yang Yang and Yongfang Li Most efficiency values of flexible devices lag behind those on rigid substrates. Here, Li et al. fabricate a flexible perovskite solar cell on a silver-mesh/conducting polymer and demonstrate a power conversion efficiency of 14% and greater than 95% of its original efficiency after 5,000 times bending. 11 January 2016 | doi: 10.1038/ncomms10214 Physical Sciences  Materials science  Nanotechnology  Tellurium as a high-performance elemental thermoelectric OPEN Siqi Lin, Wen Li, Zhiwei Chen, Jiawen Shen, Binghui Ge and Yanzhong Pei Good thermoelectric materials are often complex compounds. Here, the authors reveal that elemental tellurium has a high thermoelectric figure of merit between 300 and 700 K when doped with As, with the potential advantages of easy preparation and relative isotropy. 11 January 2016 | doi: 10.1038/ncomms10287 Physical Sciences  Applied physics  Materials science  Three-dimensional controlled growth of monodisperse sub-50 nm heterogeneous nanocrystals OPEN Deming Liu, Xiaoxue Xu, Yi Du, Xian Qin, Yuhai Zhang, Chenshuo Ma, Shihui Wen, Wei Ren, Ewa M. Goldys, James A. Piper, Shixue Dou, Xiaogang Liu and Dayong Jin Atomic-level control over size, shape and surface composition of nanoparticles is vital for developing materials with integrated multiple functionalities. Here, the authors probe the different roles of oleate ions and oleic acid molecules and their effects on growth mechanisms for sub-50 nm nanoparticles. 08 January 2016 | doi: 10.1038/ncomms10254 Chemical Sciences  Materials science  Nanotechnology  Physical chemistry  Making hybrid [n]-rotaxanes as supramolecular arrays of molecular electron spin qubits OPEN Antonio Fernandez, Jesus Ferrando-Soria, Eufemio Moreno Pineda, Floriana Tuna, Iñigo J. Vitorica-Yrezabal, Christiane Knappke, Jakub Ujma, Christopher A. Muryn, Grigore A. Timco, Perdita E. Barran, Arzhang Ardavan and Richard E.P. Winpenny Paramagnetic heterometallic rings have long been considered as possible qubits within a quantum information processing system. Here, the authors employ supramolecular chemistry to fabricate multiple rings around multi-armed threads, as an important step towards generating useful qubit arrays. 08 January 2016 | doi: 10.1038/ncomms10240 Chemical Sciences  Inorganic chemistry  Materials science  Nanotechnology  A role of stochastic phenotype switching in generating mosaic endothelial cell heterogeneity OPEN Lei Yuan, Gary C. Chan, David Beeler, Lauren Janes, Katherine C. Spokes, Harita Dharaneeswaran, Anahita Mojiri, William J. Adams, Tracey Sciuto, Guillermo Garcia-Cardeña, Grietje Molema, Peter M. Kang, Nadia Jahroudi, Philip A. Marsden, Ann Dvorak, Erzsébet Ravasz Regan and William C. Aird Spontaneous phenotypic heterogeneity confers a population-level advantage to cells that are exposed to fluctuating environments. Here the authors show that the endothelium of some organs displays a dynamic mosaicism in expression of Von Willebrand factor, suggesting bet hedging as a strategy for adaptive homeostasis. 08 January 2016 | doi: 10.1038/ncomms10160 Biological Sciences  Cell biology  Medical research  Light Higgs channel of the resonant decay of magnon condensate in superfluid 3He-B OPEN V. V. Zavjalov, S. Autti, V. B. Eltsov, P. J. Heikkinen and G. E. Volovik The order parameter describing the spontaneous symmetry breaking which occurs when a system becomes a superfluid is analogous to the Higgs field in particle physics from which the Higgs boson arises. Here, the authors demonstrate the existence of a light Higgs boson in the B-phase of superfluid 3He. 08 January 2016 | doi: 10.1038/ncomms10294 Physical Sciences  Particle physics  Ciliated neurons lining the central canal sense both fluid movement and pH through ASIC3 OPEN Elham Jalalvand, Brita Robertson, Peter Wallén and Sten Grillner Cerebrospinal fluid-contacting (CSF-c) cells line the central canal of the vertebrate spinal cord yet their function remains unknown. Here, Javaland et al. show that CSF-c neurons in the lamprey respond to mechanical stimulation and lowered pH, effects likely mediated by ASIC3-channels. 08 January 2016 | doi: 10.1038/ncomms10002 Biological Sciences  Cell biology  Neuroscience  mTORC1-independent Raptor prevents hepatic steatosis by stabilizing PHLPP2 OPEN KyeongJin Kim, Li Qiang, Matthew S. Hayden, David P. Sparling, Nicole H. Purcell and Utpal B. Pajvani The protein raptor is a subunit of the mTORC signalling complex. Here the authors show that Raptor also exists in a free form, unbound to mTORC, and that this free Raptor negatively regulates hepatic Akt activity and lipid metabolism in mice via a mechanism involving the Akt phosphatase PHLPP2. 08 January 2016 | doi: 10.1038/ncomms10255 Biological Sciences  Cell biology  Medical research  Electromechanical control of nitrogen-vacancy defect emission using graphene NEMS OPEN Antoine Reserbat-Plantey, Kevin G. Schädler, Louis Gaudreau, Gabriele Navickaite, Johannes Güttinger, Darrick Chang, Costanza Toninelli, Adrian Bachtold and Frank H. L. Koppens Active control of optical fields at the nanoscale is difficult to achieve. Here, the authors fabricate an on-chip graphene NEMS suspended a few tens of nanometres above nitrogen vacancy centres and demonstrate electromechanical control of the photons emitted by electrostatic tuning of the graphene NEMS position. 08 January 2016 | doi: 10.1038/ncomms10218 Physical Sciences  Materials science  Nanotechnology  Optical physics  Protein-targeted corona phase molecular recognition OPEN Gili Bisker, Juyao Dong, Hoyoung D. Park, Nicole M. Iverson, Jiyoung Ahn, Justin T. Nelson, Markita P. Landry, Sebastian Kruss and Michael S. Strano Corona phase molecular recognition (CoPhMoRe) involves the deposition of a heteropolymer onto a nanoparticle surface, providing a recognition site for a given analyte. Here, the authors show that CoPhMoRe can be used to selectively detect proteins (fibrinogen) with high selectivity, including in a complex serum environment. 08 January 2016 | doi: 10.1038/ncomms10241 Chemical Sciences  Analytical chemistry  Biochemistry  Nanotechnology  Implementation of meiosis prophase I programme requires a conserved retinoid-independent stabilizer of meiotic transcripts OPEN Emilie Abby, Sophie Tourpin, Jonathan Ribeiro, Katrin Daniel, Sébastien Messiaen, Delphine Moison, Justine Guerquin, Jean-Charles Gaillard, Jean Armengaud, Francina Langa, Attila Toth, Emmanuelle Martini and Gabriel Livera Meiosis is a cell division program that produces haploid gametes and is initiated by a retinoic acid-dependent process. Here the authors report that a meiosis-specific protein, MEIOC, is upregulated in a retinoic acid-independent manner and is required to stabilise meiosis-specific transcripts. 08 January 2016 | doi: 10.1038/ncomms10324 Biological Sciences  Cell biology  Gs-coupled GPCR signalling in AgRP neurons triggers sustained increase in food intake OPEN Ken-ichiro Nakajima, Zhenzhong Cui, Chia Li, Jaroslawna Meister, Yinghong Cui, Ou Fu, Adam S. Smith, Shalini Jain, Bradford B. Lowell, Michael J. Krashes and Jürgen Wess Hypothalamic Agouti-related peptide (AgRP) neurons play a key role in regulating food intake. Here, the authors report a novel pathway in which activation of Gs-coupled receptors on AgRP neurons leads to robust, sustained increase in food intake. 08 January 2016 | doi: 10.1038/ncomms10268 Biological Sciences  Molecular biology  Neuroscience  Pre-vaccination inflammation and B-cell signalling predict age-related hyporesponse to hepatitis B vaccination OPEN Slim Fourati, Razvan Cristescu, Andrey Loboda, Aarthi Talla, Ali Filali, Radha Railkar, Andrea K. Schaeffer, David Favre, Dominic Gagnon, Yoav Peretz, I-Ming Wang, Chan R. Beals, Danilo R. Casimiro, Leonidas N. Carayannopoulos and Rafick-Pierre Sékaly Ageing is associated with poor responses to vaccines but the underlying mechanism remains unclear. Here the authors use a systems-based approach to define molecular signatures present before vaccination that correlate with non-responsiveness to hepatitis B vaccination in healthy, elderly adults. 08 January 2016 | doi: 10.1038/ncomms10369 Biological Sciences  Immunology  Systems biology  Repetitive magnetic stimulation induces plasticity of inhibitory synapses OPEN Maximilian Lenz, Christos Galanis, Florian Müller-Dahlhaus, Alexander Opitz, Corette J. Wierenga, Gábor Szabó, Ulf Ziemann, Thomas Deller, Klaus Funke and Andreas Vlachos Repetitive transcranial magnetic stimulation (rTMS) is widely used as a therapeutic tool yet its effect on inhibitory networks in the brain has not been studied. Here, the authors demonstrate that 10Hz rTMS specifically reduces dendritic inhibition onto pyramidal neurons accompanied by remodeling of postsynaptic gephyrin clusters. 08 January 2016 | doi: 10.1038/ncomms10020 Biological Sciences  Neuroscience  Superactivation of AMPA receptors by auxiliary proteins OPEN Anna L. Carbone and Andrew J. R. Plested Transmembrane AMPA receptor regulatory proteins (TARPs) exert a number of effects on fast glutamatergic synaptic transmission. Here, the authors model the interactions of two such proteins, Stargazin and γ-8, and propose a simple kinetic mechanism by which TARPs modulate channel opening reaction. 08 January 2016 | doi: 10.1038/ncomms10178 Biological Sciences  Cell biology  Neuroscience  Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells OPEN Sabine Klawitter, Nina V. Fuchs, Kyle R. Upton, Martin Muñoz-Lopez, Ruchi Shukla, Jichang Wang, Marta Garcia-Cañadas, Cesar Lopez-Ruiz, Daniel J. Gerhardt, Attila Sebe, Ivana Grabundzija, Sylvia Merkert, Patricia Gerdes, J. Andres Pulgarin, Anja Bock, Ulrike Held, Anett Witthuhn, Alexandra Haase, Balázs Sarkadi, Johannes Löwer et al. Genetic and epigenetic abnormalities have been found to result from reprogramming of differentiated cells into human induced pluripotent stem cells (hiPSCs). Here, Klawitter et al. identify endogenous L1, Alu and SVA mobilization during reprogramming, highlighting the risk of insertional mutagens in hiPSCs. 08 January 2016 | doi: 10.1038/ncomms10286 Biological Sciences  Cell biology  Developmental biology  Elevated glucose and oligomeric β-amyloid disrupt synapses via a common pathway of aberrant protein S-nitrosylation OPEN Mohd Waseem Akhtar, Sara Sanz-Blasco, Nima Dolatabadi, James Parker, Kevin Chon, Michelle S. Lee, Walid Soussou, Scott R. McKercher, Rajesh Ambasudhan, Tomohiro Nakamura and Stuart A. Lipton Alzheimer's disease is linked to metabolic syndrome and Type-2 diabetes, but the mechanism behind this association is unclear. Here, the authors show that elevated glucose and amyloid ß work together to increase nitrosative stress, leading to aberrant mitochondrial activity and synaptic dysfunction. 08 January 2016 | doi: 10.1038/ncomms10242 Biological Sciences  Cell biology  Neuroscience  Interplay of active processes modulates tension and drives phase transition in self-renewing, motor-driven cytoskeletal networks OPEN Michael Mak, Muhammad H. Zaman, Roger D. Kamm and Taeyoon Kim The actin cytoskeleton is a complex network of filaments, cross-linking proteins and motors; although the components are recognised, the behaviour of the network is less understood. Here Mak et al. use a Brownian dynamics model that reveals actin turnover dynamics as a key regulatory mechanism controlling cytoskeletal states. 08 January 2016 | doi: 10.1038/ncomms10323 Biological Sciences  Biophysics  Cep57 is a Mis12-interacting kinetochore protein involved in kinetochore targeting of Mad1–Mad2 OPEN Haining Zhou, Tianning Wang, Tao Zheng, Junlin Teng and Jianguo Chen The spindle assembly checkpoint relies on the accumulation of Mad1-Mad2 at kinetochores, but the mechanism of regulation is not known. Here Zhou et al. show that the centrosomal protein Cep57 interacts with the kinetochore proteins Mis12 and Mad1, and regulates the recruitment of Mad1/Mad2 to kinetochores. 08 January 2016 | doi: 10.1038/ncomms10151 Biological Sciences  Cell biology  Genome-wide association study identifies variation at 6q25.1 associated with survival in multiple myeloma OPEN David C. Johnson, Niels Weinhold, Jonathan S. Mitchell, Bowang Chen, Martin Kaiser, Dil B. Begum, Jens Hillengass, Uta Bertsch, Walter A. Gregory, David Cairns, Graham H. Jackson, Asta Försti, Jolanta Nickel, Per Hoffmann, Markus M. Nöethen, Owen W. Stephens, Bart Barlogie, Faith E. Davis, Kari Hemminki, Hartmut Goldschmidt et al. The prognosis of multiple myeloma patients varies widely. Here, to identify genetic factors associated with differing prognoses, the authors carried out a meta-analysis of four genome-wide association studies and identified a risk variant associated with survival interval. 08 January 2016 | doi: 10.1038/ncomms10290 Biological Sciences  Cancer  Genetics  IL-7 signalling represses Bcl-6 and the TFH gene program OPEN Paul W. McDonald, Kaitlin A. Read, Chandra E. Baker, Ashlyn E. Anderson, Michael D. Powell, André Ballesteros-Tato and Kenneth J. Oestreich It remains incompletely understood how cytokines shape TH1 cell differentiation to central memory T (TCM) and follicular T helper (TFH) cells. Here the authors show that TH1 cells can co-initiate the expression of both TFH and TCM gene programs and that IL-7 signalling represses TFH-associated but not TCM-associated genes. 08 January 2016 | doi: 10.1038/ncomms10285 Biological Sciences  Immunology  Negative magnetoresistance in Dirac semimetal Cd3As2 OPEN Hui Li, Hongtao He, Hai-Zhou Lu, Huachen Zhang, Hongchao Liu, Rong Ma, Zhiyong Fan, Shun-Qing Shen and Jiannong Wang Materials with topologically non-trivial band structures promise applications exploiting exotic electronic transport behaviour. Here, the authors observe a large negative magnetoresistance in Cd3As2 nanoribbons, evidence for a chiral transport anomaly required for its status as a Dirac semi metal. 08 January 2016 | doi: 10.1038/ncomms10301 Physical Sciences  Condensed matter  Haematopoietic ESL-1 enables stem cell proliferation in the bone marrow by limiting TGFβ availability OPEN Magdalena Leiva, Juan A. Quintana, José M. Ligos and Andrés Hidalgo Hematopoietic stem and progenitor cell (HSPCs) proliferation is controlled by signals from the niche. Here, Leiva et al. show in vivo in mice that deletion of E-selectin ligand 1 causes quiescence of HSPCs and a reduction in niche size, which is mediated by changes of TGFß levels in the bone marrow. 08 January 2016 | doi: 10.1038/ncomms10222 Biological Sciences  Cell biology  Developmental biology  Computational multiqubit tunnelling in programmable quantum annealers OPEN Sergio Boixo, Vadim N. Smelyanskiy, Alireza Shabani, Sergei V. Isakov, Mark Dykman, Vasil S. Denchev, Mohammad H. Amin, Anatoly Yu Smirnov, Masoud Mohseni and Hartmut Neven Quantum tunnelling may be advantageous for quantum annealing, but multiqubit tunnelling has not yet been observed or characterized theoretically. Here, the authors demonstrate that 8-qubit tunnelling plays a role in a D-Wave Two device through a nonperturbative theory and experimental data. 07 January 2016 | doi: 10.1038/ncomms10327 Physical Sciences  Applied physics  Theoretical physics  Molar tooth carbonates and benthic methane fluxes in Proterozoic oceans OPEN Bing Shen, Lin Dong, Shuhai Xiao, Xianguo Lang, Kangjun Huang, Yongbo Peng, Chuanming Zhou, Shan Ke and Pengju Liu Molar tooth structures are common in early- to mid-Proterozoic carbonates but extremely rare in rocks younger than 750 Ma. Here, the authors show molar tooth carbonate formation is related to benthic methane fluxes. 07 January 2016 | doi: 10.1038/ncomms10317 Earth Sciences  Biogeochemistry  Geology and geophysics  Ice-sheet-driven methane storage and release in the Arctic OPEN Alexey Portnov, Sunil Vadakkepuliyambatta, Jürgen Mienert and Alun Hubbard Methane release across the Arctic continental shelf has been attributed to modern dissociation of gas hydrate, accelerated by ocean warming. Here, the authors show that thermogenic methane was stored as subglacial gas hydrate during the last glaciation, and subsequently released following ice sheet retreat. 07 January 2016 | doi: 10.1038/ncomms10314 Earth Sciences  Climate science  Geology and geophysics  Confining energy migration in upconversion nanoparticles towards deep ultraviolet lasing OPEN Xian Chen, Limin Jin, Wei Kong, Tianying Sun, Wenfei Zhang, Xinhong Liu, Jun Fan, Siu Fung Yu and Feng Wang A general approach to maximize upconversion luminescence in stoichiometric lanthanide lattices is lacking. Here, Chen et al. report a NaYbF4:Tm lattice and demonstrate fine-tuning of energy migration by controlling dimensions of the crystal lattice, highlighting their potential for deep ultraviolet lasing. 07 January 2016 | doi: 10.1038/ncomms10304 Physical Sciences  Materials science  Optical physics  BAP1/ASXL1 recruitment and activation for H2A deubiquitination OPEN Danny D. Sahtoe, Willem J. van Dijk, Reggy Ekkebus, Huib Ovaa and Titia K. Sixma The tumor suppressor BAP1 is activated by ASXL1 to deubiquitinate mono-ubiquitinated H2A at K119 in Polycomb gene repression. Here, the authors show how BAP1’s C-terminal extension auto-recruits it to nucleosomes, where the DEUBAD domain of ASXL1 increases BAP1’s affinity for ubiquitin to drive deubiquitination. 07 January 2016 | doi: 10.1038/ncomms10292 Biological Sciences  Biochemistry  Molecular biology  Label-free cell cycle analysis for high-throughput imaging flow cytometry OPEN Thomas Blasi, Holger Hennig, Huw D. Summers, Fabian J. Theis, Joana Cerveira, James O. Patterson, Derek Davies, Andrew Filby, Anne E. Carpenter and Paul Rees Imaging flow cytometry enables high-throughput acquisition of fluorescence, brightfield and darkfield images of biological cells. Here, Blasi et al. demonstrate that applying machine learning algorithms on brightfield and darkfield images can detect cellular phenotypes without the need for fluorescent stains, enabling label-free assays. 07 January 2016 | doi: 10.1038/ncomms10256 Biological Sciences  Bioinformatics  Biotechnology  TIA1 oxidation inhibits stress granule assembly and sensitizes cells to stress-induced apoptosis OPEN Kyoko Arimoto-Matsuzaki, Haruo Saito and Mutsuhiro Takekawa Cytoplasmic stress granules (SG) are intracellular aggregates that suppress translation and sequester apoptosis regulatory factors. Here the authors show that reactive oxygen species oxidise the SG-nucleating protein TIA1, preventing SG formation and promoting apoptosis in the presence of additional stress. 07 January 2016 | doi: 10.1038/ncomms10252 Biological Sciences  Cell biology  Multi-reporter selection for the design of active and more specific zinc-finger nucleases for genome editing OPEN Benjamin L. Oakes, Danny F. Xia, Elizabeth F. Rowland, Denise J. Xu, Irina Ankoudinova, Jennifer S. Borchardt, Lei Zhang, Patrick Li, Jeffrey C. Miller, Edward J. Rebar and Marcus B. Noyes Zinc finger nucleases have an established role in genome editing. Here, the authors report a strategy for identifying zinc finger nucleases that discriminate between desired targets and provide genome-wide specificity. 07 January 2016 | doi: 10.1038/ncomms10194 Biological Sciences  Biotechnology  Molecular biology  Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes OPEN Hernan Lorenzi, Asis Khan, Michael S. Behnke, Sivaranjani Namasivayam, Lakshmipuram S. Swapna, Michalis Hadjithomas, Svetlana Karamycheva, Deborah Pinney, Brian P. Brunk, James W. Ajioka, Daniel Ajzenberg, John C. Boothroyd, Jon P. Boyle, Marie L. Dardé, Maria A. Diaz-Miranda, Jitender P. Dubey, Heather M. Fritz, Solange M. Gennari, Brian D. Gregory, Kami Kim et al. Toxoplasma gondii is a parasite that causes zoonotic infections in humans. Here, the authors identify tandem amplification and diversification of secretory pathogenesis determinants in the T. gondii genome and show that clade-specific inheritance of conserved haploblocks enriched for these determinants shapes population structure. 07 January 2016 | doi: 10.1038/ncomms10147 Biological Sciences  Genetics  Microbiology  Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system OPEN Mainak Guharoy, Pallab Bhowmick, Mohamed Sallam and Peter Tompa Degrons are determinants within proteins that direct programmed degradation by the ubiquitinproteasome system. Here, the authors propose a three-part degron architecture which contains an E3-ligase recognition motif, a ubiquitination site(s), and a disordered site to initiate degradation. 06 January 2016 | doi: 10.1038/ncomms10239 Biological Sciences  Biochemistry  Bioinformatics  Molecular biology  Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment OPEN Christian L. Vestergaard, Morten Bo Mikkelsen, Walter Reisner, Anders Kristensen and Henrik Flyvbjerg Transition state theory has proven to be a powerful tool for the analysis of a number of processes, perhaps most commonly chemical reactions. Here, the authors use transition state theory to model a directly observable, micron scale process—the transport of DNA molecules in a confined environment. 06 January 2016 | doi: 10.1038/ncomms10227 Physical Sciences  Atomic and molecular physics  Biophysics  Physical chemistry  Genetically engineering self-organization of human pluripotent stem cells into a liver bud-like tissue using Gata6 OPEN Patrick Guye, Mohammad R. Ebrahimkhani, Nathan Kipniss, Jeremy J. Velazquez, Eldi Schoenfeld, Samira Kiani, Linda G. Griffith and Ron Weiss There has been limited success in generating tissues from human induced pluripotent stem cells (hiPSCs). Here, the authors genetically engineer expression of the transcription factor Gata6 in a single isogenic hiPSC population resulting in complex tissue structures that exhibit liver bud-like properties. 06 January 2016 | doi: 10.1038/ncomms10243 Biological Sciences  Cell biology  Developmental biology  Sequence variants in the PTCH1 gene associate with spine bone mineral density and osteoporotic fractures OPEN Unnur Styrkarsdottir, Gudmar Thorleifsson, Sigurjon A. Gudjonsson, Asgeir Sigurdsson, Jacqueline R. Center, Seung Hun Lee, Tuan V. Nguyen, Timothy C.Y. Kwok, Jenny S.W. Lee, Suzanne C. Ho, Jean Woo, Ping-C. Leung, Beom-Jun Kim, Thorunn Rafnar, Lambertus A. Kiemeney, Thorvaldur Ingvarsson, Jung-Min Koh, Nelson L.S. Tang, John A. Eisman, Claus Christiansen et al. Bone mineral density (BMD) is the best predictor of osteoporotic fracture risk. Here, the authors perform a genome wide association study in Icelanders and people of European and East-Asian descent, and identify a new allele in intron 15 of the PTCH1 gene that associates with reduced BMD. 06 January 2016 | doi: 10.1038/ncomms10129 Biological Sciences  Genetics  Reconciling diverse mammalian pigmentation patterns with a fundamental mathematical model OPEN Richard L. Mort, Robert J. H. Ross, Kirsten J. Hainey, Olivia J. Harrison, Margaret A. Keighren, Gabriel Landini, Ruth E. Baker, Kevin J. Painter, Ian J. Jackson and Christian A. Yates How embryonic melanoblast behaviour influences adult pigmentation patterns and causes patterning defects is unclear. Here, Mort et al. construct a stochastic model parameterised experimentally to show that melanoblast migration is undirected and that reduced proliferation causes patterning defects. 06 January 2016 | doi: 10.1038/ncomms10288 Biological Sciences  Cell biology  Developmental biology  Electrochemically driven mechanical energy harvesting OPEN Sangtae Kim, Soon Ju Choi, Kejie Zhao, Hui Yang, Giorgia Gobbi, Sulin Zhang and Ju Li There is intensive research underway into the development of various mechanical energy harvesters. Here, the authors report an electrochemically driven mechanical energy harvester that uses the stress-induced potential difference of lithiated silicon electrodes to generate continuous electricity. 06 January 2016 | doi: 10.1038/ncomms10146 Chemical Sciences  Materials science  Physical chemistry  Reverse transduction measured in the living cochlea by low-coherence heterodyne interferometry OPEN Tianying Ren, Wenxuan He and Peter G. Barr-Gillespie Mammalian hearing is remarkable for its sensitivity and frequency selectivity. Here, the authors show that outer hair cell-generated force, which amplifies sound-induced vibrations inside the cochlea, is responsible for these traits. 06 January 2016 | doi: 10.1038/ncomms10282 Biological Sciences  Neuroscience  Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics OPEN Erik Malmström, Ola Kilsgård, Simon Hauri, Emanuel Smeds, Heiko Herwald, Lars Malmström and Johan Malmström Sepsis can lead to multiple organ failure that could potentially be reflected by change in plasma protein abundance. Here the authors describe a proteomics strategy that allows the determination of plasma proteins tissue origin in a quantitative manner for use as biomarkers—illustrated in a mouse model of sepsis. 06 January 2016 | doi: 10.1038/ncomms10261 Biological Sciences  Medical research  Systems biology  Direct observation of mineral–organic composite formation reveals occlusion mechanism OPEN Kang Rae Cho, Yi-Yeoun Kim, Pengcheng Yang, Wei Cai, Haihua Pan, Alexander N. Kulak, Jolene L. Lau, Prashant Kulshreshtha, Steven P. Armes, Fiona C. Meldrum and James J. De Yoreo The occlusion of biomacromolecules can endow biominerals with enhanced mechanical properties. Here, the authors use in situ atomic force microscopy and micromechanical simulations to trace micelle incorporation in calcite to shed light on the mechanism of occlusion and cavity formation. 06 January 2016 | doi: 10.1038/ncomms10187 Physical Sciences  Bioengineering  Materials science  Physical chemistry  A shear gradient-activated microfluidic device for automated monitoring of whole blood haemostasis and platelet function OPEN Abhishek Jain, Amanda Graveline, Anna Waterhouse, Andyna Vernet, Robert Flaumenhaft and Donald E. Ingber The current hemostasis assays are unable to predict thrombotic or bleeding risk in clinics. Here, Jain et al. present a novel microfluidic device mimicking stenosed arterioles that determines clotting times in vitro and in extracorporeal circuits, offering a simple and reliable monitoring of blood homeostasis and platelet function. 06 January 2016 | doi: 10.1038/ncomms10176 Biological Sciences  Medical research  Human pancreatic beta-like cells converted from fibroblasts OPEN Saiyong Zhu, Holger A. Russ, Xiaojing Wang, Mingliang Zhang, Tianhua Ma, Tao Xu, Shibing Tang, Matthias Hebrok and Sheng Ding Insulin-producing pancreatic beta cells, generated in vitro, could lead to new anti-diabetic therapies. Here, Zhu et al. convert human fibroblasts into endodermal progenitors that differentiate in vitro into glucose-responsive beta-like cells that, following transplantation in mice, protect from diabetes. 06 January 2016 | doi: 10.1038/ncomms10080 Biological Sciences  Cell biology  Developmental biology  Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping OPEN Kevin J. Freedman, Lauren M. Otto, Aleksandar P. Ivanov, Avijit Barik, Sang-Hyun Oh and Joshua B. Edel Nanopore sensors have shown tremendous potential for biomolecule sensing, though the diffusion-controlled capture can limit the speed of analysis. Here, the authors report a dielectrophoretic method to concentrate DNA near the tip of a nanopore, reducing the limit of detection by three orders of magnitude. 06 January 2016 | doi: 10.1038/ncomms10217 Chemical Sciences  Analytical chemistry  Biophysics  Nanotechnology  A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages OPEN Robert J. Kimmerling, Gregory Lee Szeto, Jennifer W. Li, Alex S. Genshaft, Samuel W. Kazer, Kristofor R. Payer, Jacob de Riba Borrajo, Paul C. Blainey, Darrell J. Irvine, Alex K. Shalek and Scott R. Manalis Existing single-cell RNA-seq methods provide the transcriptome of a cellular phenotype at a single time point. Here, Kimmerling et al. present a microfluidic platform that enables off-chip single-cell RNA-seq after multigenerational lineage tracking under controlled culture conditions. 06 January 2016 | doi: 10.1038/ncomms10220 Biological Sciences  Biotechnology  Molecular biology  A polymer scaffold for self-healing perovskite solar cells OPEN Yicheng Zhao, Jing Wei, Heng Li, Yin Yan, Wenke Zhou, Dapeng Yu and Qing Zhao Perovskite solar cells exhibit large conversion efficiencies, but their stability still represents a bottleneck. Here, the authors integrate a hygroscopic polymer scaffold to the perovskite active layer and fabricate efficient and stable devices that recover after being exposed to a humid environment. 06 January 2016 | doi: 10.1038/ncomms10228 Chemical Sciences  Applied physics  Materials science  DCAF1 controls T-cell function via p53-dependent and -independent mechanisms OPEN Zengli Guo, Qing Kong, Cui Liu, Song Zhang, Liyun Zou, Feng Yan, Jason K. Whitmire, Yue Xiong, Xian Chen and Yisong Y. Wan DCAF1 (VprBP), an HIV target protein, is a component of an ubiquitin ligase complex involved in developmental processes in plants and animals. Here, DCAF1 is shown to be vital for activation-induced T cell growth and proliferation, partly by being required for p53’s ubiquitination and degradation. 05 January 2016 | doi: 10.1038/ncomms10307 Biological Sciences  Immunology  Molecular biology  Overlap microtubules link sister k-fibres and balance the forces on bi-oriented kinetochores OPEN Janko Kajtez, Anastasia Solomatina, Maja Novak, Bruno Polak, Kruno Vukušić, Jonas Rüdiger, Gheorghe Cojoc, Ana Milas, Ivana Šumanovac Šestak, Patrik Risteski, Federica Tavano, Anna H. Klemm, Emanuele Roscioli, Julie Welburn, Daniela Cimini, Matko Glunčić, Nenad Pavin and Iva M. Tolić During metaphase, k-fibre microtubules exert force on kinetochores, but there are also non-kinetochore microtubules close to kinetochores without a known function. Here the authors show that these microtubules, which they call bridging fibres, balance interkinetochore tension by bridging sister k-fibres. 05 January 2016 | doi: 10.1038/ncomms10298 Biological Sciences  Cell biology  The KDM3A–KLF2–IRF4 axis maintains myeloma cell survival OPEN Hiroto Ohguchi, Teru Hideshima, Manoj K. Bhasin, Gullu T. Gorgun, Loredana Santo, Michele Cea, Mehmet K. Samur, Naoya Mimura, Rikio Suzuki, Yu-Tzu Tai, Ruben D. Carrasco, Noopur Raje, Paul G. Richardson, Nikhil C. Munshi, Hideo Harigae, Takaomi Sanda, Juro Sakai and Kenneth C. Anderson Several histone modifiers have been implicated in the survival of multiple myeloma cells. Here, the authors reveal a role for the histone demethylase KDM3A in the survival of this haematologic cancer, and show that mechanistically KDM3A removes H3K9 methylation from the promoters of KLF2 and IRF4, genes essential for myeloma cell survival. 05 January 2016 | doi: 10.1038/ncomms10258 Biological Sciences  Cancer  Molecular biology  Stepwise B-cell-dependent expansion of T helper clonotypes diversifies the T-cell response OPEN Julia Merkenschlager, Mickaël J. Ploquin, Urszula Eksmond, Rakieb Andargachew, Georgina Thorborn, Andrew Filby, Marion Pepper, Brian Evavold and George Kassiotis During an immune response, CD4+ T cell repertoire is thought to increase in avidity at the expense of diversity. Here the authors show that B cells act as antigen-presenting cells to boost the development of low-avidity T cell clones, diversifying the T cell repertoire at late stages of the response. 05 January 2016 | doi: 10.1038/ncomms10281 Biological Sciences  Immunology  A series connection architecture for large-area organic photovoltaic modules with a 7.5% module efficiency OPEN Soonil Hong, Hongkyu Kang, Geunjin Kim, Seongyu Lee, Seok Kim, Jong-Hoon Lee, Jinho Lee, Minjin Yi, Junghwan Kim, Hyungcheol Back, Jae-Ryoung Kim and Kwanghee Lee The fabrication of organic photovoltaic modules usually relies on patterning techniques which limit their efficiencies. Here, the authors propose a module structure that avoids the patterning steps, and use doctor-blade printing and slot-die coating to fabricate large-area modules reaching 7.5% efficiencies. 05 January 2016 | doi: 10.1038/ncomms10279 Physical Sciences  Applied physics  Materials science  Optical physics  A liquid-crystalline hexagonal columnar phase in highly-dilute suspensions of imogolite nanotubes OPEN Erwan Paineau, Marie-Eve M. Krapf, Mohamed-Salah Amara, Natalia V. Matskova, Ivan Dozov, Stéphan Rouzière, Antoine Thill, Pascale Launois and Patrick Davidson Liquid crystals are grouped into four main classes—nematic, lamellar, cubic and columnar—depending on their symmetries. Here, the authors show for the first time that a columnar phase can form in suspensions of imogolite nanotubes at very low concentrations. 05 January 2016 | doi: 10.1038/ncomms10271 Physical Sciences  Condensed matter  Materials science  HSP90 regulates temperature-dependent seedling growth in Arabidopsis by stabilizing the auxin co-receptor F-box protein TIR1 OPEN Renhou Wang, Yi Zhang, Martin Kieffer, Hong Yu, Stefan Kepinski and Mark Estelle A moderate increase in temperature promotes hypocotyl elongation in Arabidopsis. Here, Wang et al. show that elevated temperature not only increases auxin biosynthesis but also acts via the co-chaperones HSP90 and SGT1 to stabilize the TIR1 auxin receptor. 05 January 2016 | doi: 10.1038/ncomms10269 Biological Sciences  Plant sciences  Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames OPEN Céline M. Laumont, Tariq Daouda, Jean-Philippe Laverdure, Éric Bonneil, Olivier Caron-Lizotte, Marie-Pierre Hardy, Diana P. Granados, Chantal Durette, Sébastien Lemieux, Pierre Thibault and Claude Perreault Cryptic translation of the 'non-coding' genome is increasingly recognised, however its biological significance remains unclear. Laumont et al. employ proteogenomic techniques to map the human immunoproteome, and find that approximately 10% of MHC class I-associated peptides are cryptic. 05 January 2016 | doi: 10.1038/ncomms10238 Biological Sciences  Immunology  Systems biology  Detection of nanoscale electron spin resonance spectra demonstrated using nitrogen-vacancy centre probes in diamond OPEN L. T. Hall, P. Kehayias, D. A. Simpson, A. Jarmola, A. Stacey, D. Budker and L. C. L. Hollenberg The application of resonant electron spin ensembles to the study electronic systems can be limited in spatial resolution above the micrometre scale. Here, the authors use nitrogen vacancies to probe the paramagnetic background in diamond via spin resonance spectra dominated by single local spins. 05 January 2016 | doi: 10.1038/ncomms10211 Physical Sciences  Condensed matter  A cell cycle-dependent BRCA1–UHRF1 cascade regulates DNA double-strand break repair pathway choice OPEN Haoxing Zhang, Hailong Liu, Yali Chen, Xu Yang, Panfei Wang, Tongzheng Liu, Min Deng, Bo Qin, Cristina Correia, Seungbaek Lee, Jungjin Kim, Melanie Sparks, Asha A. Nair, Debra L. Evans, Krishna R. Kalari, Pumin Zhang, Liewei Wang, Zhongsheng You, Scott H. Kaufmann, Zhenkun Lou et al. BRCA1 is a key regulator of DNA double-strand break repair, functioning to promote homologous recombination and repress non-homologous end-joining. Here the authors show that the ubiquitin ligase UHRF1 is recruited to breaks by BRCA1, where it targets RIF1 and thereby facilitates recombination. 05 January 2016 | doi: 10.1038/ncomms10201 Biological Sciences  Molecular biology  Crystal structure of E. coli lipoprotein diacylglyceryl transferase OPEN Guotao Mao, Yan Zhao, Xusheng Kang, Zhijie Li, Yan Zhang, Xianping Wang, Fei Sun, Krishnan Sankaran and Xuejun C. Zhang Bacterial lipoproteins have important biological functions, and the lipoprotien biogenesis enzyme Lgt is essential in most gram-negative bacteria. Here, the authors use structural and biochemical techniques to shed light on the function of Lgt in post-translational transacylation modification. 05 January 2016 | doi: 10.1038/ncomms10198 Biological Sciences  Biochemistry  Mouse strains to study cold-inducible beige progenitors and beige adipocyte formation and function OPEN Daniel C. Berry, Yuwei Jiang and Jonathan M. Graff Beige adipocytes are formed in response to cold and thought to contribute to organismal energy homeostasis. Here, the authors study a range of conditional and inducible RFP-expressing Cre mouse strains and find that SMA-based lines are the most useful for mapping beige adipocyte progenitor cells. 05 January 2016 | doi: 10.1038/ncomms10184 Biological Sciences  Medical research  Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis OPEN Chiara Ardiccioni, Oliver B. Clarke, David Tomasek, Habon A. Issa, Desiree C. von Alpen, Heather L. Pond, Surajit Banerjee, Kanagalaghatta R. Rajashankar, Qun Liu, Ziqiang Guan, Chijun Li, Brian Kloss, Renato Bruni, Edda Kloppmann, Burkhard Rost, M. Chiara Manzini, Lawrence Shapiro and Filippo Mancia Polyisoprenyl-glycosyltransferases (PI-GTs) catalyse the addition of sugar to lipid carriers, which is the first step in the production of sugar donors for glycosylation. Here Ardiccioni et al. present the structure of a bacterial PI-GT and propose a mechanistic basis for sugar transfer. 05 January 2016 | doi: 10.1038/ncomms10175 Biological Sciences  Biochemistry  The histone demethylase JMJD2A/KDM4A links ribosomal RNA transcription to nutrients and growth factors availability OPEN Kader Salifou, Swagat Ray, Laure Verrier, Marion Aguirrebengoa, Didier Trouche, Konstantin I. Panov and Marie Vandromme Histone methylation regulates gene expression. Here, Salifou et al. show that KDM4A, a histone lysine demethylase, regulates RNA polymerase I-driven transcription in a PI3K dependent manner, therefore linking nutrients and growth factors availability to ribosomal RNA transcription. 05 January 2016 | doi: 10.1038/ncomms10174 Biological Sciences  Cell biology  Molecular biology  BPTF is required for c-MYC transcriptional activity and in vivo tumorigenesis OPEN Laia Richart, Enrique Carrillo-de Santa Pau, Ana Río-Machín, Mónica P. de Andrés, Juan C. Cigudosa, Víctor J. Sánchez-Arévalo Lobo and Francisco X. Real c-MYC genomic distribution is dictated by the epigenetic context but the mechanisms are unknown. Here, the authors show that c-MYC requires the chromatin reader BPTF to activate its transcriptional program and promote tumour development in vivo, suggesting that BPTF is a potential target for cancer therapy. 05 January 2016 | doi: 10.1038/ncomms10153 Biological Sciences  Cancer  Molecular biology  Local viscoelasticity of living cells measured by rotational magnetic spectroscopy OPEN J.-F. Berret Cells are recognized as having viscoelastic properties, but whether the cytoplasm resembles a viscoelastic liquid or an elastic gel is still debated. Here the authors use micron-sized wires rotating at variable speeds to show that the cytoplasm has properties of a viscoelastic liquid. 05 January 2016 | doi: 10.1038/ncomms10134 Biological Sciences  Biophysics  Computational ligand design in enantio- and diastereoselective ynamide [5+2] cycloisomerization OPEN R. N. Straker, Q. Peng, A. Mekareeya, R. S. Paton and E. A. Anderson Using a chiral catalyst to override the innate stereochemical outcome of a diastereoselective process is a challenging task. Here, the authors use theory and experiment to develop a cycloisomerization where the enantioselectivity is driven by the electronic nature of the ligand regardless of the reaction's inherent diastereoselectivity. 05 January 2016 | doi: 10.1038/ncomms10109 Chemical Sciences  Catalysis  Organic chemistry  Controlling the screening process of a nanoscaled space charge region by minority carriers OPEN Philipp Kloth, Katharina Kaiser and Martin Wenderoth Understanding the dynamics of bound and free charges and local electric fields on a nanometre scale are important in scanning tunnelling microscopy and nanoscale electronics. Here, the authors present a model system—a metallic tip near a gallium arsenide surface—for studying such electrostatic interactions. 05 January 2016 | doi: 10.1038/ncomms10108 Physical Sciences  Applied physics  Nanotechnology  Proteomic maps of breast cancer subtypes OPEN Stefka Tyanova, Reidar Albrechtsen, Pauliina Kronqvist, Juergen Cox, Matthias Mann and Tamar Geiger Breast cancers have been extensively studied at the genomic and transcriptomic levels in the hope of tailoring therapeutic regimens. Here the authors generate deep coverage proteomes from several clinical breast cancer samples, and use machine learning techniques to uncover biological processes altered in specific cancer subtypes. 04 January 2016 | doi: 10.1038/ncomms10259 Biological Sciences  Cancer  Systems biology  F-actin mechanics control spindle centring in the mouse zygote OPEN Agathe Chaigne, Clément Campillo, Raphaël Voituriez, Nir S. Gov, Cécile Sykes, Marie-Hélène Verlhac and Marie-Emilie Terret How the mitotic spindle is positioned in the centre of the cell during the first mitotic division is not clear. Here Chaigne et al. show that the pronucleus coarsely centres using F-actin/Myosin-Vb dynamics, and the metaphase plate is finely centred by an F-actin cage influenced by high cortical tension. 04 January 2016 | doi: 10.1038/ncomms10253 Biological Sciences  Biophysics  Cell biology  Mechanism of FGF receptor dimerization and activation OPEN Sarvenaz Sarabipour and Kalina Hristova Different fibroblast growth factor (fgf) ligands elicit specific biological responses, but the mechanism directing this specificity is unknown. Here the authors show that fgf1 and fgf2 impose specific reorganizations on the fgf receptor dimer trans-membrane helices that result in distinct level of receptor activation. 04 January 2016 | doi: 10.1038/ncomms10262 Biological Sciences  Biochemistry  Biophysics  Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles OPEN Frederick S. Varn, Erik H. Andrews, David W. Mullins and Chao Cheng Tumour samples are heterogeneous and are comprised of multiple cell types in addition to cancer cells. Here, the authors devised a method to estimate the relative levels of haematopoietic cells in breast cancer samples and demonstrate that this correlates with prognosis. 04 January 2016 | doi: 10.1038/ncomms10248 Biological Sciences  Cancer  Immunology  Controlling Gaussian and mean curvatures at microscale by sublimation and condensation of smectic liquid crystals OPEN Dae Seok Kim, Yun Jeong Cha, Mun Ho Kim, Oleg D. Lavrentovich and Dong Ki Yoon The self-assembly of soft matter is sensitive to their morphology, which is changeable. Here, Kim et al. show how evaporation and condensation at high temperature modify the surface of a smectic liquid crystal film in a way controlled by the local Gaussian and mean curvature of its layered structure. 04 January 2016 | doi: 10.1038/ncomms10236 Physical Sciences  Condensed matter  Materials science  Surface-enabled propulsion and control of colloidal microwheels OPEN T. O. Tasci, P. S. Herson, K. B. Neeves and D. W. M. Marr Most artificial microdevices include biomimetic features, but existing systems do not yet match living microorganisms in speed and direction control. Here, Tasci et al. use a rotating magnetic field to reversibly assemble colloidal particles into wheels that translate at velocities approaching 100 μm s−1. 04 January 2016 | doi: 10.1038/ncomms10225 Physical Sciences  Applied physics  Condensed matter  Nanotechnology  Quasi one-dimensional band dispersion and surface metallization in long-range ordered polymeric wires OPEN Guillaume Vasseur, Yannick Fagot-Revurat, Muriel Sicot, Bertrand Kierren, Luc Moreau, Daniel Malterre, Luis Cardenas, Gianluca Galeotti, Josh Lipton-Duffin, Federico Rosei, Marco Di Giovannantonio, Giorgio Contini, Patrick Le Fèvre, François Bertran, Liangbo Liang, Vincent Meunier and Dmitrii F. Perepichka Polymerization on surfaces is an emerging approach for producing graphene nanoribbons with a tunable bandgap, a promising material for carbon-based electronics. Here, Vasseur et al. show quasi-one-dimensional band structure of a model semiconducting polymer synthesized directly on a supporting surface. 04 January 2016 | doi: 10.1038/ncomms10235 Physical Sciences  Condensed matter  Materials science  Bio-recognitive photonics of a DNA-guided organic semiconductor OPEN Seung Hyuk Back, Jin Hyuk Park, Chunzhi Cui and Dong June Ahn BioLEDs is an emerging group of light-emitting diodes that use duplex-strand DNA to enhance luminescence intensity. Here, Back et al. show that only the specific binding between a pair of single-strand DNA can trigger the enhancement, which potentially makes BioLEDs an easy platform for DNA recognition. 04 January 2016 | doi: 10.1038/ncomms10234 Physical Sciences  Applied physics  Biotechnology  Nanotechnology  Multistep assembly of DNA condensation clusters by SMC OPEN HyeongJun Kim and Joseph J. Loparo The Structural Maintenance of Chromosomes (SMC) proteins are essential for chromosome condensation, cohesion and DNA repair. Here the authors use single molecule imaging to visualise how Bacillus subtilis SMC interacts with and condenses DNA. 04 January 2016 | doi: 10.1038/ncomms10200 Biological Sciences  Molecular biology  The hydrogen-bond network of water supports propagating optical phonon-like modes OPEN Daniel C. Elton and Marivi Fernández-Serra How the local structure of water varies as a function of temperature is a long-studied topic, which is still under debate. Here, the authors show that dielectric susceptibility measurements might be used to probe and identify propagating optical phonon-like modes in the hydrogen-bond network of water. 04 January 2016 | doi: 10.1038/ncomms10193 Physical Sciences  Fluids and plasma physics  Physical chemistry  Unlocking new contrast in a scanning helium microscope OPEN M. Barr, A. Fahy, J. Martens, A. P. Jardine, D. J. Ward, J. Ellis, W. Allison and P. C. Dastoor Scanning helium microscopy uses neutral atoms to image traditionally challenging materials (e.g. delicate, insulating and magnetic samples) non-destructively with absolute surface sensitivity. This work reports the first observation of chemical contrast in helium microscopy via inelastic scattering. 04 January 2016 | doi: 10.1038/ncomms10189 Physical Sciences  Applied physics  Nanotechnology  ROR1 sustains caveolae and survival signalling as a scaffold of cavin-1 and caveolin-1 OPEN Tomoya Yamaguchi, Can Lu, Lisa Ida, Kiyoshi Yanagisawa, Jiro Usukura, Jinglei Cheng, Naoe Hotta, Yukako Shimada, Hisanori Isomura, Motoshi Suzuki, Toyoshi Fujimoto and Takashi Takahashi Resistance to receptor tyrosine kinase inhibitors is a major obstacle in treatment of lung adenocarcinoma. Yamaguchi et al. identify the orphan receptor ROR1 as a potential target to overcome this resistance, by virtue of its role in promoting cell survival through stabilisation of caveolae. 04 January 2016 | doi: 10.1038/ncomms10060 Biological Sciences  Cancer  Cell biology  Regulation of miR-200c/141 expression by intergenic DNA-looping and transcriptional read-through OPEN Luciana Batista, Brigitte Bourachot, Bogdan Mateescu, Fabien Reyal and Fatima Mechta-Grigoriou The miR-141/200 familly of micro RNAs control oxidative stress and impact on ovarian tumorigenesis. Here the authors show that the transcription of miR-200c/141 is regulated through transcriptional read-through of the upstream gene PTPN6, and DNA looping linking the PTPN6 and miR-200c/141 promoters. 04 January 2016 | doi: 10.1038/ncomms9959 Biological Sciences  Molecular biology    Nature Communications JOBS of the week MRC Postdoctoral Scientist (CSC 74) Medical Research Council Biostatistician The Henry M.Jackson Foundation Postdoctoral Fellow / Doctoral Student Helmholtz Association Research Associate University College London (UCL) Charity Officer Myrovlytis Trust Research Associate (Fixed Term) University of Cambridge Postdoctoral Fellow Wellcome Trust Sanger Institute Postdoc Position Weill Cornell College of Medicine Postdoctoral Researcher INSERM U1100 Research Scientist MIT More Science jobs from Nature Communications EVENT AAI Advanced Course in Immunology 31.07.16 Boston, USA More science events from       Latest Corrigenda     Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression OPEN Jong Kyoung Kim, Aleksandra A. Kolodziejczyk, Tomislav Ilicic, Sarah A. Teichmann and John C. Marioni 11 January 2016 | doi: 10.1038/ncomms10415 Biological Sciences  Bioinformatics  Molecular biology      Corrigendum: Artemisinin-resistant Plasmodium falciparum clinical isolates can infect diverse mosquito vectors of Southeast Asia and Africa OPEN Brandyce St. Laurent, Becky Miller, Timothy A. Burton, Chanaki Amaratunga, Sary Men, Siv Sovannaroth, Michael P. Fay, Olivo Miotto, Robert W. Gwadz, Jennifer M. Anderson and Rick M. Fairhurst 08 January 2016 | doi: 10.1038/ncomms10345 Biological Sciences  Microbiology        Latest Erratum     Erratum: A biomimetic hybrid nanoplatform for encapsulation and precisely controlled delivery of theranostic agents OPEN Hai Wang, Pranay Agarwal, Shuting Zhao, Jianhua Yu, Xiongbin Lu and Xiaoming He 07 January 2016 | doi: 10.1038/ncomms10350 Biological Sciences  Bioengineering  Cancer  Nanotechnology      Advertisement All content now open 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 physics. Visit the website to explore ALL the content available within your field.   Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com  More Nature Events You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at:www.nature.com/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For other enquiries, please contact our customer feedback department Nature Publishing Group | One New York Plaza, Suite 4500 | New York | NY 10004-1562 | USA Nature Publishing Group's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.