Nature Communications - 23 October 2013

Advertisement Changing geographic ranges of ticks and tick-borne pathogens: drivers, mechanisms and consequences for pathogen diversity (open access) In this review from Frontiers in Microbiology, Nicholas Ogden and colleagues explore current knowledge of the drivers for changes in the ranges of ticks and tick-borne pathogen species and strains via effects on their basic reproduction number (R0), and the mechanisms of dispersal that allow ticks and tick-borne pathogens to invade suitable environments.     Weekly Content Alert 23 October 2013  Featured image: Huang et al. sequence the kiwifruit genome and highlight evolutionary genetic features underlying agronomically important kiwifruit traits. Latest content: Articles Corrigenda Errata Journal homepage Recommend to library Web feed   Advertisement Nature Video in association with Scientific American present: Better living through chemistry Four debates from the 2013 Nobel Laureate Meeting in Lindau. We invited Nobel laureates and young researchers to discuss how chemistry can solve pressing world problems.  Access the videos.     Latest Articles View all Articles     Vortex magnetic structure in framboidal magnetite reveals existence of water droplets in an ancient asteroid Yuki Kimura, Takeshi Sato, Norihiro Nakamura, Jun Nozawa, Tomoki Nakamura, Katsuo Tsukamoto and Kazuo Yamamoto Meteorite mineralogy can provide a window into the conditions of the early Solar System, including how and when water disappeared from asteroids. Kimura et al. use nanometre-scale palaeomagnetics to reveal vestigial traces of water in the Type 2 Tagish Lake meteorite and unravel its formation history. 22 October 2013 | doi: 10.1038/ncomms3649 Earth Sciences  Materials science  Planetary sciences  Variation at 3p24.1 and 6q23.3 influences the risk of Hodgkin's lymphoma Matthew Frampton, Miguel Inacio da Silva Filho, Peter Broderick, Hauke Thomsen, Asta Försti, Jayaram Vijayakrishnan, Rosie Cooke, Victor Enciso-Mora, Per Hoffmann, Markus M. Nöthen, Amy Lloyd, Amy Holroyd, Lewin Eisele, Karl-Heinz Jöckel, Sabine Ponader, Elke Pogge von Strandmann, Tracy Lightfoot, Eve Roman, Annette Lake, Dorothy Montgomery et al. Hodgkin's lymphoma has a genetic component that is poorly understood. In this study, Frampton et al. perform a genome-wide association study in German patients and combine the results with a previously published UK genome-wide association study to identify susceptibility loci at 3p24.1 and 6q23.3. 22 October 2013 | doi: 10.1038/ncomms3549 Biological Sciences  Cancer  Genetics  Natural gold particles in Eucalyptus leaves and their relevance to exploration for buried gold deposits OPEN Melvyn Lintern, Ravi Anand, Chris Ryan and David Paterson The discovery of new gold deposits has declined by 45% over the past 10 years. Lintern et al. present new evidence for the occurrence of particulate gold in trees growing above buried mineral deposits, and propose vegetation sampling as a mineral exploration method. 22 October 2013 | doi: 10.1038/ncomms3614 Earth Sciences  Biogeochemistry  Geology and geophysics  Switch of glycolysis to gluconeogenesis by dexamethasone for treatment of hepatocarcinoma Ruihua Ma, Wanguang Zhang, Ke Tang, Huafeng Zhang, Yi Zhang, Dapeng Li, Yong Li, Pingwei Xu, Shunqun Luo, Wenqian Cai, Tiantian Ji, Foad Katirai, Duyun Ye and Bo Huang Hepatocytes use gluconeogenesis to produce glucose, but whether this process is altered in hepatocellular carcinoma (HCC) is unclear. Here, the loss of gluconeogenesis in HCC and altered glucocorticoid regulation is demonstrated and glucocorticoid treatment is shown to reduce tumour burden. 22 October 2013 | doi: 10.1038/ncomms3508 Biological Sciences  Cancer  Medical research  Sequestration of Martian CO2 by mineral carbonation Tim Tomkinson, Martin R. Lee, Darren F. Mark and Caroline L. Smith The mechanism by which Mars lost its early dense and carbon dioxide-rich atmosphere remains relatively unknown. Here, via mineralogical analysis of the Lafayette Martian meteorite, Tomkinson et al. infer that carbonation was an effective carbon dioxide sequestration mechanism on an early, water-rich Mars. 22 October 2013 | doi: 10.1038/ncomms3662 Earth Sciences  Geology and geophysics  Planetary sciences  Harvesting singlet fission for solar energy conversion via triplet energy transfer John R. Tritsch, Wai-Lun Chan, Xiaoxi Wu, Nicholas R. Monahan and X-Y. Zhu The efficiency of organic solar cells may be increased by the incorporation of materials capable of singlet fission. Here, Tritsch and colleagues identify strategies to enhance the extraction of multiple excitons from the desirable singlet fission process. 22 October 2013 | doi: 10.1038/ncomms3679 Physical Sciences  Materials science  Optical physics  Flash freezing route to mesoporous polymer nanofibre networks OPEN Sadaki Samitsu, Rui Zhang, Xinsheng Peng, Mohan Raj Krishnan, Yoshihisa Fujii and Izumi Ichinose Mesoporous polymeric materials are good candidates for advanced separation materials, though their low-cost production remains challenging. Here, the authors report a microphase separation technique for the fabrication of nanoporous networks from frozen solutions of common polymers. 22 October 2013 | doi: 10.1038/ncomms3653 Chemical Sciences  Materials science  Nanotechnology  A solid–solid phase transition in carbon dioxide at high pressures and intermediate temperatures Jinjin Li, Olaseni Sode, Gregory A. Voth and So Hirata It is desirable for scientists to be able to predict the structures, spectra and phase diagrams of molecular crystals using ab initio computation. Li et al. demonstrate such an approach, which is able to determine the phase behaviour of solid carbon dioxide at a range of pressures and temperatures. 22 October 2013 | doi: 10.1038/ncomms3647 Chemical Sciences  Condensed matter  Materials science  Physical chemistry  Early adipogenesis is regulated through USP7-mediated deubiquitination of the histone acetyltransferase TIP60 Yuan Gao, Arjen Koppen, Maryam Rakhshandehroo, Ismayil Tasdelen, Stan F. van de Graaf, Jorg van Loosdregt, Olivier van Beekum, Nicole Hamers, Dik van Leenen, Celia R. Berkers, Ruud Berger, Frank C.P. Holstege, Paul J. Coffer, Arjan B. Brenkman, Huib Ovaa and Eric Kalkhoven Tip60 is a transcriptional coregulator that has an important role in differentiation. Here, Gao et al. demonstrate that the deubiquitination of Tip60 by USP7, a dominant deubiquitinating enzyme, is a key mechanism in early adipogenesis regulation. 21 October 2013 | doi: 10.1038/ncomms3656 Biological Sciences  Cell biology  Molecular biology  Electron correlations in MnxGa1-xAs as seen by resonant electron spectroscopy and dynamical mean field theory I. Di Marco, P. Thunström, M. I. Katsnelson, J. Sadowski, K. Karlsson, S. Lebègue, J. Kanski and O. Eriksson Although the discovery that manganese-doped gallium arsenide can be ferromagnetic has been made some time ago, its origin is still debated. To further clarify this issue, the authors use electron resonance spectroscopy and powerful numerical methods and study the compound's electronic structure. 21 October 2013 | doi: 10.1038/ncomms3645 Physical Sciences  Condensed matter  Materials science  Formation of nanodiamonds at near-ambient conditions via microplasma dissociation of ethanol vapour Ajay Kumar, Pin Ann Lin, Albert Xue, Boyi Hao, Yoke Khin Yap and R. Mohan Sankaran Nanodiamonds are small clusters of carbon that are of use in various nanotechnology applications such as spintronics, but are difficult to synthesize. Here, Kumar et al. achieve the fabrication of nanodiamonds 2–5 nm in size at near-ambient conditions by a microplasma process. 21 October 2013 | doi: 10.1038/ncomms3618 Physical Sciences  Applied physics  Nanotechnology  Plasmon-induced photonic and energy-transfer enhancement of solar water splitting by a hematite nanorod array Jiangtian Li, Scott K. Cushing, Peng Zheng, Fanke Meng, Deryn Chu and Nianqiang Wu Plasmonic nanostructures may enhance solar energy collection. Here, the authors exploit both plasmon-induced resonant energy transfer and surface plasmon polaritons in a hematite–gold nano-array, leading to a tenfold increase in the photocurrent at a bias of 0.23 V in a photoelectrochemical cell. 18 October 2013 | doi: 10.1038/ncomms3651 Chemical Sciences  Catalysis  Materials science  Nanotechnology  Physical chemistry  Site-selective electronic correlation in α-plutonium metal Jian-Xin Zhu, R. C. Albers, K. Haule, G. Kotliar and J. M. Wills Plutonium has unusual physical properties due to strong electronic correlation, but its α-phase has not been studied much in this respect. Using sophisticated numerical methods, Zhu et al. show that in this phase different atomic sites have different degrees of electronic correlation. 18 October 2013 | doi: 10.1038/ncomms3644 Physical Sciences  Condensed matter  Materials science  Theoretical physics  Separation of a functional deubiquitylating module from the SAGA complex by the proteasome regulatory particle Sungsu Lim, Jaechan Kwak, Minhoo Kim and Daeyoup Lee The SAGA transcriptional coactivator is modulated by the 19S proteasome to increase the interaction of SAGA with transcription activators. Here, Lim et al. show that the 19S proteasome mediates dissociation of a submodule of the SAGA complex in a non-proteolytic manner, which is implicated in mRNA export in yeast. 18 October 2013 | doi: 10.1038/ncomms3641 Biological Sciences  Cell biology  Molecular biology  Draft genome of the kiwifruit Actinidia chinensis OPEN Shengxiong Huang, Jian Ding, Dejing Deng, Wei Tang, Honghe Sun, Dongyuan Liu, Lei Zhang, Xiangli Niu, Xia Zhang, Meng Meng, Jinde Yu, Jia Liu, Yi Han, Wei Shi, Danfeng Zhang, Shuqing Cao, Zhaojun Wei, Yongliang Cui, Yanhua Xia, Huaping Zeng et al. The kiwifruit is an economically and nutritionally important fruit crop with high vitamin C content. Here, the authors report the draft genome sequence of a heterozygous kiwifruit and through comparative genomic analysis provide valuable insight into kiwifruit evolution. 18 October 2013 | doi: 10.1038/ncomms3640 Biological Sciences  Evolution  Genetics  Crossreactivity of a human autoimmune TCR is dominated by a single TCR loop Dhruv K. Sethi, Susana Gordo, David A. Schubert and Kai W. Wucherpfennig Autoimmune T cell receptors can interact with both self and microbial antigens, but the structural basis for crossreactivity is not fully understood. Here, the authors provide structural insights into binding characteristics of the autoreactive T cell receptor Hy.1B11 to both self and pathogen-derived peptides. 18 October 2013 | doi: 10.1038/ncomms3623 Biological Sciences  Immunology  Characterization of the LCROSS impact plume from a ground-based imaging detection Paul D. Strycker, Nancy J. Chanover, Charles Miller, Ryan T. Hamilton, Brendan Hermalyn, Robert M. Suggs and Michael Sussman The 2009 LCROSS mission detected water in a debris plume ejected from the Moon's southern pole, but poor viewing angles limited essential data regarding plume dynamics. Strycker et al. provide independent observations of the debris plume from Earth and ascertain much needed morphological information. 18 October 2013 | doi: 10.1038/ncomms3620 Earth Sciences  Planetary sciences  Reconstructing targetable pathways in lung cancer by integrating diverse omics data O. Alejandro Balbin, John R. Prensner, Anirban Sahu, Anastasia Yocum, Sunita Shankar, Rohit Malik, Damian Fermin, Saravana M. Dhanasekaran, Benjamin Chandler, Dafydd Thomas, David G. Beer, Xuhong Cao, Alexey I. Nesvizhskii and Arul M. Chinnaiyan Non-small cell lung cancers (NSCLC) that harbour mutations in KRas can be separated into KRas-dependent and -independent subsets. By analysing transcriptome, proteome and phosphoproteome data from NSCLC cell lines, Balbin et al. show that KRas-dependent cell lines activate the Lck pathway. 18 October 2013 | doi: 10.1038/ncomms3617 Biological Sciences  Cancer  Sharply autofocused ring-Airy beams transforming into non-linear intense light bullets P. Panagiotopoulos, D.G. Papazoglou, A. Couairon and S. Tzortzakis The propagation of high-intensity light beams through transparent media can lead to unusual non-linear effects. Here, Panagiotopoulos et al. show that a high-intensity ring-Airy beam transforms into a robust non-linear light bullet. 17 October 2013 | doi: 10.1038/ncomms3622 Physical Sciences  Applied physics  Optical physics  Molecular mechanism of strigolactone perception by DWARF14 Hidemitsu Nakamura, You-Lin Xue, Takuya Miyakawa, Feng Hou, Hui-Min Qin, Kosuke Fukui, Xuan Shi, Emi Ito, Shinsaku Ito, Seung-Hyun Park, Yumiko Miyauchi, Atsuko Asano, Naoya Totsuka, Takashi Ueda, Masaru Tanokura and Tadao Asami Both strigolactone and DELLA plant signalling pathways have a role in shoot branching. In this study, Nakamura et al. show that DWARF14 cleaves strigolactones creating a binding surface for the DELLA protein SLR1, thereby providing a mechanism for pathway crosstalk. 17 October 2013 | doi: 10.1038/ncomms3613 Biological Sciences  Plant sciences  Horizontal gene transfer converts non-toxigenic Clostridium difficile strains into toxin producers OPEN Michael S.M. Brouwer, Adam P. Roberts, Haitham Hussain, Rachel J. Williams, Elaine Allan and Peter Mullany Clostridium difficile produces potent toxins that are encoded by its pathogenicity locus. Here, Brouwer et al. demonstrate surprising bacterial genome plasticity whereby the pathogenicity locus is transferred from toxigenic to non-toxigenic strains of C. difficile by conjugational transfer. 17 October 2013 | doi: 10.1038/ncomms3601 Biological Sciences  Microbiology  Programming adaptive control to evolve increased metabolite production Howard H. Chou and Jay D. Keasling Cells can adapt rapidly to survive and efficiently exploit constantly changing environments by varying their mutation rate. Here, the authors construct an in silico system to modulate mutation rate, and demonstrate that this method can be used in the laboratory to create specific phenotypes. 17 October 2013 | doi: 10.1038/ncomms3595 Biological Sciences  Bioengineering  Evolution  Genetics  Ultrafast modulation of polarization amplitude by terahertz fields in electronic-type organic ferroelectrics OPEN Tatsuya Miyamoto, Hiroyuki Yada, Hiromichi Yamakawa and Hiroshi Okamoto Controlling ferroelectric polarization on a terahertz timescale is a challenge, because typically the domain-wall motion occurs on much longer time scales. Here, the authors achieve control over the electronic ferroelectricity in an organic material using a terahertz pump–probe technique. 17 October 2013 | doi: 10.1038/ncomms3586 Physical Sciences  Condensed matter  Optical physics  Cross-talk between KLF4 and STAT3 regulates axon regeneration Song Qin, Yuhua Zou and Chun-Li Zhang Axon regeneration is controlled by both positive and negative regulators. In this study, Qin et al. show that KLF4 acts as an intrinsic inhibitor of axon regeneration by antagonizing the cytokine JAK–STAT3 pathway, and that deletion of KLF4 can greatly enhance cytokine-induced axon regeneration. 16 October 2013 | doi: 10.1038/ncomms3633 Biological Sciences  Cell biology  Neuroscience  Microbial biosynthesis of the anticoagulant precursor 4-hydroxycoumarin Yuheng Lin, Xiaolin Shen, Qipeng Yuan and Yajun Yan 4-hydroxycoumarin (4HC), a precursor for anticoagulant drugs such as warfarin, has a major role in the treatment of thromboembolic diseases. Here, the authors present an artificial biosynthetic pathway for 4HC production in E. coli and demonstrate its potential for large-scale microbial production. 16 October 2013 | doi: 10.1038/ncomms3603 Biological Sciences  Bioengineering  Biotechnology  Three-dimensional self-assembled photonic crystals with high temperature stability for thermal emission modification Kevin A. Arpin, Mark D. Losego, Andrew N. Cloud, Hailong Ning, Justin Mallek, Nicholas P. Sergeant, Linxiao Zhu, Zongfu Yu, Berç Kalanyan, Gregory N. Parsons, Gregory S. Girolami, John R. Abelson, Shanhui Fan and Paul V. Braun Photonic crystal structures can be used to control the spectral distribution of thermal emission. Here, Arpin et al. demonstrate three-dimensional tungsten and hafnium diboride photonic crystals to control high-temperature thermal emission for solar thermophotovoltaic energy devices. 16 October 2013 | doi: 10.1038/ncomms3630 Physical Sciences  Materials science  Optical physics  ArabidopsisWAT1 is a vacuolar auxin transport facilitator required for auxin homoeostasis OPEN Philippe Ranocha, Oana Dima, Réka Nagy, Judith Felten, Claire Corratgé-Faillie, Ondřej Novák, Kris Morreel, Benoît Lacombe, Yves Martinez, Stephanie Pfrunder, Xu Jin, Jean-Pierre Renou, Jean-Baptiste Thibaud, Karin Ljung, Urs Fischer, Enrico Martinoia, Wout Boerjan and Deborah Goffner The plant hormone auxin is essential for plant development and growth and is transported across cellular membranes via specialized transporter proteins. In this study, Ranocha et al. identify the first vacuolar auxin transporter, WAT1, suggesting an involvement of the vacuole in auxin signalling. 16 October 2013 | doi: 10.1038/ncomms3625 Biological Sciences  Plant sciences  A plasma-treated chalcogenide switch device for stackable scalable 3D nanoscale memory Myoung-Jae Lee, Dongsoo Lee, Seong-Ho Cho, Ji-Hyun Hur, Sang-Moon Lee, David H. Seo, Dong-Sik Kim, Moon-Seung Yang, Sunghun Lee, Euichul Hwang, Mohammad Rakib Uddin, Hojung Kim, U-In Chung, Youngsoo Park and In-Kyeong Yoo To reach terabit density in random access memory devices, the select switching and storage components need to be improved. Here, the authors fabricate a fully stackable switching device based on chalcogenides, which reaches an exceptional performance following reactive nitrogen and nitrogen plasma treatments. 16 October 2013 | doi: 10.1038/ncomms3629 Physical Sciences  Applied physics  Nanotechnology    Nature Communications JOBS of the week Research Support Assistant Medical Research Council Postdoctoral Researchers John Innes Centre Postdoctoral Fellow Baylor College of Medicine PhD position Synchrotron SOLEIL PhD Researcher KU Leuven Research Assistant I The Scripps Reseach Institute Postdoctoral Fellow Western University (The University of Western Ontario) Bioinformaticist Washington University School of Medicine Postdoctoral Research Assistant University of Oxford Postdoctoral Research Associate BOKU - University of Natural Resources and Applied Life Sciences, Vienna More Science jobs from Nature Communications EVENT Diet, gut microbiology and human health 11.12.13 London, UK More science events from       Latest Corrigenda     Corrigendum: Critical fictive temperature for plasticity in metallic glasses Golden Kumar, Pascal Neibecker, Yan Hui Liu and Jan Schroers 17 October 2013 | doi: 10.1038/ncomms3357 Physical Sciences  Materials science      Corrigendum: Regulation of histone modification and chromatin structure by the p53–PADI4 pathway Chizu Tanikawa, Martha Espinosa, Akari Suzuki, Ken Masuda, Kazuhiko Yamamoto, Eiju Tsuchiya, Koji Ueda, Yataro Daigo, Yusuke Nakamura and Koichi Matsuda 16 October 2013 | doi: 10.1038/ncomms3638 Biological Sciences  Cancer  Cell biology  Medical research  Molecular biology      Corrigendum: Cancer cells that survive radiation therapy acquire HIF-1 activity and translocate toward tumour blood vessels Hiroshi Harada, Masahiro Inoue, Satoshi Itasaka, Kiichi Hirota, Akiyo Morinibu, Kazumi Shinomiya, Lihua Zeng, Guangfei Ou, Yuxi Zhu, Michio Yoshimura, W. Gillies Mckenna, Ruth J. Muschel and Masahiro Hiraoka 16 October 2013 | doi: 10.1038/ncomms3314 Biological Sciences  Cancer  Medical research  Molecular biology        Latest Errata     Erratum: A small molecule modulates Jumonji histone demethylase activity and selectively inhibits cancer growth Lei Wang, Jianjun Chang, Diana Varghese, Michael Dellinger, Subodh Kumar, Anne M. Best, Julio Ruiz, Richard Bruick, Samuel Penã-Llopis, Junjie Xu, David J. Babinski, Doug E. Frantz, Rolf A. Brekken, Amy M. Quinn, Anton Simeonov, Johnny Easmon and Elisabeth D. Martinez 22 October 2013 | doi: 10.1038/ncomms3639 Biological Sciences  Cancer  Medical research      Erratum: TREX exposes the RNA-binding domain of Nxf1 to enable mRNA export Nicolas Viphakone, Guillaume M. Hautbergue, Matthew Walsh, Chung-Te Chang, Arthur Holland, Eric G. Folco, Robin Reed and Stuart A. Wilson 17 October 2013 | doi: 10.1038/ncomms3377 Biological Sciences  Cell biology  Molecular biology      Advertisement Scientific Reports WE launched in 2011 YOU published 2000 papers with us OUR impact factor is 2.927* Discover what we can do together.  nature.com/scientificreports  *2012 Journal Citation Reports® (Thomson Reuters, 2013)   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. 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