Nature Communications - 18 June 2014

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Advertisement White Paper: Application of CRISPR/Cas-based Technology to the Rapid Generation of Genetically Engineered Mice  Over the past three decades, genetically engineered mice have become invaluable tools for the study of gene function in vivo. Learn more about:   -Gene Editing vs. Gene Manipulation -How CRISPR/Cas-based Gene Editing Works -The Advantages and Limitations of Gene Editing Technologies. Read More...     Weekly Content Alert 18 June 2014  Featured image: Steinhardt et al. present evidence for high-pressure phases in a meteorite and unravel the origin of metal phases found therein. Latest content: Articles Corrigendum Advertisement   An Atlas of Genetic Influences on Human Blood Metabolites   "Metabolomics...an excellent way of understanding individual uniqueness and..." - Craig Venter A new publication in Nature Genetics reveals how metabolomic profiling coupled with genomics data yields new insight into diseases, potential biomarkers and drug treatments.  Freely available here. Journal homepage Recommend to library Web feed   Advertisement Special on Synthetic Biology From Nature, Nature Methods & Nature Reviews Microbiology Since its debut almost 15 years ago, synthetic biology has evolved into a vibrant and productive field. This Nature special charts the progress of this multidisciplinary field through reports, reviews and commentaries from Nature, Nature Methods and Nature Reviews Microbiology.  Click here to access this Special!      Latest Articles View all Articles     Intensification of the meridional temperature gradient in the Great Barrier Reef following the Last Glacial Maximum OPEN Thomas Felis, Helen V. McGregor, Braddock K. Linsley, Alexander W. Tudhope, Michael K. Gagan, Atsushi Suzuki, Mayuri Inoue, Alexander L. Thomas, Tezer M. Esat, William G. Thompson, Manish Tiwari, Donald C. Potts, Manfred Mudelsee, Yusuke Yokoyama and Jody M. Webster The Great Barrier Reef (GBR) is under threat from rising ocean temperatures, yet its response to past temperature change is poorly known. Felis et al. show that the GBR experienced a much steeper temperature gradient during the last deglaciation, suggesting it may be more resilient than previously thought. 17 June 2014 | doi: 10.1038/ncomms5102 Earth Sciences  Climate science  Oceanography  Diminished hERG K+ channel activity facilitates strong human labour contractions but is dysregulated in obese women Helena C. Parkington, Janet Stevenson, Mary A. Tonta, Jonathan Paul, Trent Butler, Kaushik Maiti, Eng-Cheng Chan, Penelope M. Sheehan, Shaun P. Brennecke, Harold A. Coleman and Roger Smith Uterine muscle contracts rhythmically during labour but the underlying electrophysiological mechanisms are not fully understood. The authors of this study show that hERG1 potassium channels reduce human uterine contractions in pregnancy and are suppressed during labour in lean but not in obese women. 17 June 2014 | doi: 10.1038/ncomms5108 Biological Sciences  Medical research  2q36.3 is associated with prognosis for oestrogen receptor-negative breast cancer patients treated with chemotherapy OPEN Jingmei Li, Linda S. Lindström, Jia N. Foo, Sajjad Rafiq, Marjanka K. Schmidt, Paul D. P. Pharoah, Kyriaki Michailidou, Joe Dennis, Manjeet K. Bolla, Qin Wang, Laura J. Van 't Veer, Sten Cornelissen, Emiel Rutgers, Melissa C. Southey, Carmel Apicella, Gillian S. Dite, John L. Hopper, Peter A. Fasching, Lothar Haeberle, Arif B. Ekici et al. Studies have shown that breast cancer prognosis is hereditary. Here the authors show that a genetic variant in CCL20, a chemokine ligand involved in immune response, is significantly associated with breast cancer survival and may therefore represent an important therapeutic or prognostic target. 17 June 2014 | doi: 10.1038/ncomms5051 Biological Sciences  Cancer  Genetics  Predicting the risk of avian influenza A H7N9 infection in live-poultry markets across Asia OPEN Marius Gilbert, Nick Golding, Hang Zhou, G. R. William Wint, Timothy P. Robinson, Andrew J. Tatem, Shengjie Lai, Sheng Zhou, Hui Jiang, Danhuai Guo, Zhi Huang, Jane P. Messina, Xiangming Xiao, Catherine Linard, Thomas P. Van Boeckel, Vincent Martin, Samir Bhatt, Peter W. Gething, Jeremy J. Farrar, Simon I. Hay et al. An avian influenza virus of the H7N9 type, associated with live-poultry markets, has caused two human epidemics in China. Here, the authors develop a statistical model that predicts the risk of H7N9 infection in live-poultry markets across Asia, as a tool for disease surveillance and control. 17 June 2014 | doi: 10.1038/ncomms5116 Biological Sciences  Ecology  Virology  Evidence for global cooling in the Late Cretaceous OPEN Christian Linnert, Stuart A. Robinson, Jackie A. Lees, Paul R. Bown, Irene Pérez-Rodríguez, Maria Rose Petrizzo, Francesca Falzoni, Kate Littler, José Antonio Arz and Ernest E. Russell The Late Cretaceous experienced significant cooling, yet a lack of low-latitude records mean the regional extent of this cooling is poorly constrained. Linnert et al. present a TEX86 sea surface temperature record from a palaeolatitude of ~35 °N and show that Late Cretaceous cooling was global in nature. 17 June 2014 | doi: 10.1038/ncomms5194 Earth Sciences  Climate science  Oceanography  Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor Amy D. Migliori, Nicholas Keller, Tanfis I. Alam, Marthandan Mahalingam, Venigalla B. Rao, Gaurav Arya and Douglas E. Smith Viral DNA packaging motors must generate large forces to package the viral capsid. Here, Migliori et al. provide functional and computational evidence that electrostatic interactions between subdomains of the T4 packaging motor provide the driving force for DNA packaging. 17 June 2014 | doi: 10.1038/ncomms5173 Biological Sciences  Biochemistry  Biophysics  Microbiology  Electrochemical mechanism of ion current rectification of polyelectrolyte gel diodes Tetsuya Yamamoto and Masao Doi Polyelectrolyte gel diodes rectify ion currents in electrolyte solutions and the rectification mechanism is believed to be similar to that of conventional semiconductor p–n diodes. Here, Yamamoto and Doi predict a very different mechanism, which is attributable to their electrochemical nature. 17 June 2014 | doi: 10.1038/ncomms5162 Physical Sciences  Condensed matter  Physical chemistry  Theoretical physics  Encapsulation kinetics and dynamics of carbon monoxide in clathrate hydrate OPEN Jinlong Zhu, Shiyu Du, Xiaohui Yu, Jianzhong Zhang, Hongwu Xu, Sven C. Vogel, Timothy C. Germann, Joseph S. Francisco, Fujio Izumi, Koichi Momma, Yukihiko Kawamura, Changqing Jin and Yusheng Zhao Carbon monoxide clathrate hydrate has been widely studied and although the structure-II gas hydrate is predicted to be thermodynamically favourable, it is the structure-I hydrate that has been observed. Here, the authors synthesize the structure-II carbon monoxide hydrate and probe its structure and formation. 17 June 2014 | doi: 10.1038/ncomms5128 Chemical Sciences  Materials science  Physical chemistry  Visible-frequency asymmetric transmission devices incorporating a hyperbolic metamaterial Ting Xu and Henri J. Lezec Optical devices with asymmetric transmission are desirable for many applications, but fabrication difficulties impede visible frequency operation. Xu and Lezec overcome this by combining nonsymmetric subwavelength gratings with a hyperbolic metamaterial to realize efficient asymmetric transmission. 17 June 2014 | doi: 10.1038/ncomms5141 Physical Sciences  Applied physics  Materials science  Optical physics  Evidence for interacting two-level systems from the 1/f noise of a superconducting resonator J. Burnett, L. Faoro, I. Wisby, V. L. Gurtovoi, A. V. Chernykh, G. M. Mikhailov, V. A. Tulin, R. Shaikhaidarov, V. Antonov, P. J. Meeson, A. Ya. Tzalenchuk and T. Lindström The quantum noise generated as multiple two-level systems switch state is usually described by the standard tunnelling model. By studying superconducting resonators, Burnett et al. show that this model fails at low temperatures, and propose a new model to accurately describe the noise in quantum circuits. 17 June 2014 | doi: 10.1038/ncomms5119 Physical Sciences  Condensed matter  Theoretical physics  A synthetic biochemistry molecular purge valve module that maintains redox balance Paul H. Opgenorth, Tyler P. Korman and James U. Bowie In vitro biochemical pathways could provide the high yields required for economical commodity chemical production, but require circuitry development to regulate high-energy cofactors. Here, the authors design and test a simple purge valve system to maintain NADP+/NADPH balance in E. coli. 17 June 2014 | doi: 10.1038/ncomms5113 Biological Sciences  Systems biology  Senescence impairs direct conversion of human somatic cells to neurons Chong-kui Sun, Di Zhou, Zhen Zhang, Liming He, Fan Zhang, Xiaowei Wang, Jie Yuan, Qianming Chen, Ling-Gang Wu and Qin Yang Cellular senescence has been shown to inhibit reprogramming of fibroblasts to induced pluripotent stem cells. Here, the authors show that senescence pathways also impair the direct conversion of human fibroblasts into neurons. 17 June 2014 | doi: 10.1038/ncomms5112 Biological Sciences  Neuroscience  Biomimetic block copolymer particles with gated nanopores and ultrahigh protein sorption capacity Haizhou Yu, Xiaoyan Qiu, Suzana P. Nunes and Klaus-Viktor Peinemann Porous particles can be capable of selectivity encapsulating various guests. Here, the authors report a strategy to make block copolymer microparticles with pH-responsive pores, study and rationalize their assembly process and furthermore demonstrate separation of differently charged proteins. 17 June 2014 | doi: 10.1038/ncomms5110 Chemical Sciences  Materials science  Nanotechnology  Plasticity and redundancy among AMA–RON pairs ensure host cell entry of Toxoplasma parasites Mauld H. Lamarque, Magali Roques, Marie Kong-Hap, Michelle L. Tonkin, George Rugarabamu, Jean-Baptiste Marq, Diana M. Penarete-Vargas, Martin J. Boulanger, Dominique Soldati-Favre and Maryse Lebrun Apicomplexan parasites such as Toxoplasma gondii and Plasmodium form a tight, moving junction with host cells before invading them. Here the authors show that the proteins AMA1 and RON2 of T. gondii cooperate during junction formation and identify additional proteins that have a role in this process. 17 June 2014 | doi: 10.1038/ncomms5098 Biological Sciences  Cell biology  Microbiology  Lamb-Dicke spectroscopy of atoms in a hollow-core photonic crystal fibre OPEN Shoichi Okaba, Tetsushi Takano, Fetah Benabid, Tom Bradley, Luca Vincetti, Zakhar Maizelis, Valery Yampol'skii, Franco Nori and Hidetoshi Katori Atoms lose coherence via interactions with each other and the walls of their environment, which degrades the performance of atomic systems. As a route to minimize such effects, Okaba et al. use kagome-lattice hollow-core photonic crystal fibres to confine atoms, preventing them interacting with the wall. 17 June 2014 | doi: 10.1038/ncomms5096 Physical Sciences  Atomic and molecular physics  Optical physics  Using nanoscale and mesoscale anisotropy to engineer the optical response of three-dimensional plasmonic metamaterials Michael B. Ross, Martin G. Blaber and George C. Schatz The geometry of periodic plasmonic nanostructures in three dimensions can be exploited to give tailored optical properties. Here, the authors study the role of anisotropy on the nano- and mesoscale to provide a framework for designing the optical response of metamaterials formed from plasmonic building blocks. 17 June 2014 | doi: 10.1038/ncomms5090 Physical Sciences  Materials science  Nanotechnology  Optical physics  Stiff filamentous virus translocations through solid-state nanopores Angus McMullen, Hendrick W. de Haan, Jay X. Tang and Derek Stein Nanopores are promising tools for the detection and characterization of biomolecules. Here, the authors combine experiments and simulations to study how the passage of rigid viruses through solid-state nanopores differs from more flexible biomolecules. 16 June 2014 | doi: 10.1038/ncomms5171 Physical Sciences  Biophysics  Virology  Multi-peaked adaptive landscape for chikungunya virus evolution predicts continued fitness optimization in Aedes albopictus mosquitoes Konstantin A. Tsetsarkin, Rubing Chen, Ruimei Yun, Shannan L. Rossi, Kenneth S. Plante, Mathilde Guerbois, Naomi Forrester, Guey Chuen Perng, Easwaran Sreekumar, Grace Leal, Jing Huang, Suchetana Mukhopadhyay and Scott C. Weaver The ability of a pathogen to adapt to new hosts affects its ability to spread in new environments. Here, Tsetsarkin et al. analysed mutations that enabled the chikungunya virus to adapt to a mosquito vector and predict that specific mutations will result in greater transmission efficiency. 16 June 2014 | doi: 10.1038/ncomms5084 Biological Sciences  Evolution  Genetics  Interfacial mobility scale determines the scale of collective motion and relaxation rate in polymer films Paul Z. Hanakata, Jack F. Douglas and Francis W. Starr Interfacial mobility in thin polymer films is crucial for their technological applications. Here, Hanakata et al. provide computational evidence for a general relationship between the scale of interfacial mobility and collective motion within the films, which explains their glass transition behaviour. 16 June 2014 | doi: 10.1038/ncomms5163 Physical Sciences  Materials science  Physical chemistry  The impact of the metabotropic glutamate receptor and other gene family interaction networks on autism OPEN Dexter Hadley, Zhi-liang Wu, Charlly Kao, Akshata Kini, Alisha Mohamed-Hadley, Kelly Thomas, Lyam Vazquez, Haijun Qiu, Frank Mentch, Renata Pellegrino, Cecilia Kim, John Connolly, Joseph Glessner, Hakon Hakonarson, AGP Consortium, Dalila Pinto, Alison Merikangas, Lambertus Klei, Jacob A.S. Vorstman, Ann Thompson et al. The autism spectrum disorders are complex genetic traits characterized by various neurodevelopmental deficits. Here, the authors analyse defective gene family interaction networks in autism cases and healthy controls and identify potential gene family interactions that may contribute to autism aetiology. 13 June 2014 | doi: 10.1038/ncomms5074 Biological Sciences  Genetics  Neuroscience  Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris Alexander A. Navarini, Michael A. Simpson, Michael Weale, Jo Knight, Isabelle Carlavan, Pascale Reiniche, David A. Burden, Alison Layton, Veronique Bataille, Michael Allen, Robert Pleass, Andrew Pink, Daniel Creamer, John English, Stephanie Munn, Shernaz Walton, Carolyn Willis, The Acne Genetic Study Group, Sophie Déret, Johannes J. Voegel, Tim Spector et al. Acne vulgaris is a common, inflammatory skin disorder. Here the authors carry out a genome-wide association study and identify three genetic variants that associate with an increased risk of developing acne, which together suggest a mechanistic role for the TGFβ cell signalling pathway in acne development and progression. 13 June 2014 | doi: 10.1038/ncomms5020 Biological Sciences  Genetics  Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel Olivier Delaneau, Jonathan Marchini, The 1000 Genomes Project Consortium, Gil A. McVean, Peter Donnelly, Gerton Lunter, Jonathan L. Marchini, Simon Myers, Anjali Gupta-Hinch, Zamin Iqbal, Iain Mathieson, Andy Rimmer, Dionysia K. Xifara, Angeliki Kerasidou, Claire Churchhouse, Olivier Delaneau, David M. Altshuler, Stacey B. Gabriel, Eric S. Lander, Namrata Gupta et al. 1000 Genomes imputation can increase the power of genome-wide association studies to detect genetic variants associated with human traits and diseases. Here, the authors develop a method to integrate and analyse low-coverage sequence data and SNP array data, and show that it improves imputation performance. 13 June 2014 | doi: 10.1038/ncomms4934 Biological Sciences  Genetics  Tonic inhibition in dentate gyrus impairs long-term potentiation and memory in an Alzhiemer's disease model Zheng Wu, Ziyuan Guo, Marla Gearing and Gong Chen Altered GABAergic synaptic transmission is implicated in Alzheimer's disease pathology. Here, Wu et al. show that GABA content is increased in brain samples from human patients and that in mouse models of the disease, the increase in GABA leads to an increase in tonic inhibition in the dentate gyrus. 13 June 2014 | doi: 10.1038/ncomms5159 Biological Sciences  Neuroscience  A mutation burst during the acute phase of Helicobacter pylori infection in humans and rhesus macaques Bodo Linz, Helen M. Windsor, John J. McGraw, Lori M. Hansen, John P. Gajewski, Lynn P. Tomsho, Caylie M. Hake, Jay V. Solnick, Stephan C. Schuster and Barry J. Marshall Helicobacter pylori chronically infects humans, and this is associated with high mutation and recombination rates in the bacterium. Here the authors provide evidence that genome evolution in H. pylori during acute infection of the host is orders of magnitude faster than any previously determined mutation rates in bacteria. 13 June 2014 | doi: 10.1038/ncomms5165 Biological Sciences  Evolution  Microbiology  Cell division and targeted cell cycle arrest opens and stabilizes basement membrane gaps David Q. Matus, Emily Chang, Sasha C. Makohon-Moore, Mary A. Hagedorn, Qiuyi Chi and David R. Sherwood The mechanisms that open and stabilize basement membrane (BM) gaps are poorly understood. Here the authors combine evolutionary and cell biological studies of nematode uterine–vulval attachment to show that BM gaps are widened by cell division and stabilized in their position by attachment to non-dividing cells. 13 June 2014 | doi: 10.1038/ncomms5184 Biological Sciences  Cell biology  Developmental biology  Evolution  RNA-binding proteins regulate the expression of the immune activating ligand MICB Daphna Nachmani, Tony Gutschner, Adi Reches, Sven Diederichs and Ofer Mandelboim The expression of stress-induced ligands and their recognition by the NKG2D-activating receptor is important for the elimination of virally infected and cancerous cells by cytotoxic lymphocytes. Here, the authors provide insights into the post-transcriptional mechanism regulating the expression of the NKG2D ligand, MICB. 13 June 2014 | doi: 10.1038/ncomms5186 Biological Sciences  Cell biology  Immunology  Imaging intraorganellar Ca2+ at subcellular resolution using CEPIA OPEN Junji Suzuki, Kazunori Kanemaru, Kuniaki Ishii, Masamichi Ohkura, Yohei Okubo and Masamitsu Iino The use of intracellular calcium sensors provides important information about the dynamics of calcium signalling in cells. Here Suzuki et al. develop organelle-targeted sensors to simultaneously measure calcium concentrations in ER and mitochondria, and uncover novel insights into calcium flux in mitochondria. 13 June 2014 | doi: 10.1038/ncomms5153 Biological Sciences  Cell biology  Coordinated DNA dynamics during the human telomerase catalytic cycle Joseph W. Parks and Michael D. Stone Telomerase reverse transcriptase extends the ends of linear chromosomes with the aid of an integral RNA subunit. Here, Parks and Stone characterize the translocation kinetics of telomerase identifying distinct steps important for the processivity of the enzyme. 13 June 2014 | doi: 10.1038/ncomms5146 Biological Sciences  Biophysics  A source of the single-stranded DNA substrate for activation-induced deaminase during somatic hypermutation Xiaohua Wang, Manxia Fan, Susan Kalis, Lirong Wei and Matthew D. Scharff The process of somatic hypermutation, used by B cells to increase antibody diversity, is catalysed by the activation-induced deaminase (AID), which needs to access single-stranded DNA to mediate its function. Here, the authors propose a mechanism for the generation of single-stranded DNA substrate required for AID activity. 13 June 2014 | doi: 10.1038/ncomms5137 Biological Sciences  Immunology  Molecular biology  Direct observation of spin-forbidden transitions through the use of suitably polarized light Camille Lévêque, Daniel Peláez, Horst Köppel and Richard Taïeb The study of excited triplet states in molecular systems is in some cases hindered by the difficulty in accessing them and the intense signals of singlet states. Here, the authors show that the combination of polarized light and molecular alignment can enhance the triplet absorption for sulphur dioxide. 13 June 2014 | doi: 10.1038/ncomms5126 Chemical Sciences  Physical chemistry  Large-scale complementary macroelectronics using hybrid integration of carbon nanotubes and IGZO thin-film transistors Haitian Chen, Yu Cao, Jialu Zhang and Chongwu Zhou Carbon nanotubes and metal-oxide semiconductors are widely used in thin-film transistors, but integrating the two technologies is challenging. Here, the authors report a hybrid integration of p-type carbon nanotubes and n-type IGZO transistors, resulting in a large-area complementary circuit. 13 June 2014 | doi: 10.1038/ncomms5097 Physical Sciences  Materials science  Nanotechnology  Cluster synchronization and isolated desynchronization in complex networks with symmetries Louis M. Pecora, Francesco Sorrentino, Aaron M. Hagerstrom, Thomas E. Murphy and Rajarshi Roy Many networks exhibit patterns of synchronized clusters, but the conditions under which this occurs are poorly understood. Pecora et al. develop an analytical approach based on computational group theory to predict the emergence and disappearance of synchrony among local clusters in complex networks. 13 June 2014 | doi: 10.1038/ncomms5079 Physical Sciences  Theoretical physics  Structural basis for catalysis in a CDP-alcohol phosphotransferase Giuliano Sciara, Oliver B. Clarke, David Tomasek, Brian Kloss, Shantelle Tabuso, Rushelle Byfield, Raphael Cohn, Surajit Banerjee, Kanagalaghatta R. Rajashankar, Vesna Slavkovic, Joseph H. Graziano, Lawrence Shapiro and Filippo Mancia The transfer of a phosphate group from a CDP-linked donor to an acceptor alcohol is catalysed by CDP-alcohol phosphotransferases. Here, Sciara et al. report crystal structures of a CDP-alcohol phosphotransferase, define roles of conserved residues and propose a mechanism of action for this protein family. 13 June 2014 | doi: 10.1038/ncomms5068 Biological Sciences  Biochemistry  A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains Mark D. Preston, Susana Campino, Samuel A. Assefa, Diego F. Echeverry, Harold Ocholla, Alfred Amambua-Ngwa, Lindsay B. Stewart, David J. Conway, Steffen Borrmann, Pascal Michon, Issaka Zongo, Jean-Bosco Ouédraogo, Abdoulaye A. Djimde, Ogobara K. Doumbo, Francois Nosten, Arnab Pain, Teun Bousema, Chris J. Drakeley, Rick M. Fairhurst, Colin J. Sutherland et al. Tracing the source of malarial infections is an important step towards monitoring and controlling the disease. Here, Preston et al. analyse sequence data from 711 isolates and design a genetic barcode based on combined mitochondrial and apicoplast genomes that is able to distinguish between malaria parasites isolated from different geographical regions. 13 June 2014 | doi: 10.1038/ncomms5052 Biological Sciences  Genetics  Impact-induced shock and the formation of natural quasicrystals in the early solar system Lincoln S. Hollister, Luca Bindi, Nan Yao, Gerald R. Poirier, Christopher L. Andronicos, Glenn J. MacPherson, Chaney Lin, Vadim V. Distler, Michael P. Eddy, Alexander Kostin, Valery Kryachko, William M. Steinhardt, Marina Yudovskaya, John M. Eiler, Yunbin Guan, Jamil J. Clarke and Paul J. Steinhardt The first-reported natural quasicrystal, found in the meteorite Khatyrka, has posed many questions regarding the extraterrestrial processes that led to its formation. Here, the authors suggest how the metallic Al- and Cu-bearing phases formed and report the discovery of other new minerals. 13 June 2014 | doi: 10.1038/ncomms5040 Earth Sciences  Geology and geophysics  Reversing the pump dependence of a laser at an exceptional point OPEN M. Brandstetter, M. Liertzer, C. Deutsch, P. Klang, J. Schöberl, H. E. Türeci, G. Strasser, K. Unterrainer and S. Rotter Exceptional points are singularities that occur when two resonant modes coalesce both in their frequency and width, giving rise to counterintuitive behaviour. Brandstetter et al. demonstrate how to induce such an exceptional point in a coupled pair of lasers, causing a reversal in their pump characteristics. 13 June 2014 | doi: 10.1038/ncomms5034 Physical Sciences  Applied physics  Optical physics  Selective fishing induces density-dependent growth OPEN Henrik Svedäng and Sara Hornborg The effects of fishing policies that adjust selectivity are unclear. Here, Svedäng and Hornborg show that fishing practices that increase selectivity of the Eastern Baltic cod have negatively affected its productivity, suggesting that fishing policies should prioritize catch rates over yield. 12 June 2014 | doi: 10.1038/ncomms5152 Biological Sciences  Ecology  Silicate deposition during decomposition of cyanobacteria may promote export of picophytoplankton to the deep ocean Tiantian Tang, Kim Kisslinger and Cindy Lee The contribution of picophytoplankton to particle transport in the marine environment is relatively unknown. Here, the authors perform incubation experiments and show that decomposing picophytoplankton provides an efficient transport pathway for silica-enriched marine particles. 12 June 2014 | doi: 10.1038/ncomms5143 Earth Sciences  Biogeochemistry  Oceanography  Incorporation and redistribution of impurities into silicon nanowires during metal-particle-assisted growth Wanghua Chen, Linwei Yu, Soumyadeep Misra, Zheng Fan, Philippe Pareige, Gilles Patriarche, Sophie Bouchoule and Pere Roca i Cabarrocas Understanding the incorporation of metal atoms into silicon nanowires during metal-catalysed growth is of importance. Here, the authors find that the metal atom concentration dissolved into the silicon nanowires increases with growth rate and is two orders of magnitude higher than their equilibrium solubility. 12 June 2014 | doi: 10.1038/ncomms5134 Physical Sciences  Materials science  Steric hindrance between S4 and S5 of the KCNQ1/KCNE1 channel hampers pore opening Koichi Nakajo and Yoshihiro Kubo KCNQ1 is a voltage-gated K+ channel and gating is modulated by auxiliary subunit KCNE proteins. Here, Nakajo and Kubo identify KCNQ1 phenylalanine residues in the voltage sensor and pore domains that are responsible for the gating modulation by KCNE1. 12 June 2014 | doi: 10.1038/ncomms5100 Biological Sciences  Biochemistry  A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus W. Cozen, M. N. Timofeeva, D. Li, A. Diepstra, D. Hazelett, M. Delahaye-Sourdeix, C. K. Edlund, L. Franke, K. Rostgaard, D. J. Van Den Berg, V. K. Cortessis, K. E. Smedby, S. L. Glaser, H.-J. Westra, L. L. Robison, T. M. Mack, H. Ghesquieres, A. E. Hwang, A. Nieters, S. de Sanjose et al. While Hodgkin lymphoma (HL) is a common cancer affecting young adults in Western countries, its genetic basis is poorly understood. Here, the authors carry out a genome-wide association analysis in HL patients and healthy controls; identifying a new HL risk locus and implicating TCF3 in the disease aetiology. 12 June 2014 | doi: 10.1038/ncomms4856 Biological Sciences  Cancer  Genetics  Sub-micron phase coexistence in small-molecule organic thin films revealed by infrared nano-imaging OPEN Christian Westermeier, Adrian Cernescu, Sergiu Amarie, Clemens Liewald, Fritz Keilmann and Bert Nickel The grain boundaries between two coexisting phases in organic semiconductor pentacene are expected to obstruct charge transport in its thin-film devices. Westermeier et al. use infrared-spectroscopic nano-imaging to show an interlocking morphology, which is uncorrelated with its grain structures. 11 June 2014 | doi: 10.1038/ncomms5101 Physical Sciences  Condensed matter  Materials science  A 3D insight on the catalytic nanostructuration of few-layer graphene OPEN G. Melinte, I. Florea, S. Moldovan, I. Janowska, W. Baaziz, R. Arenal, A. Wisnet, C. Scheu, S. Begin-Colin, D. Begin, C. Pham-Huu and O. Ersen The nanostructuration of graphene by catalytic cutting using iron oxide nanoparticles leads to the formation of well-defined trenches and tunnels. Here, the authors use electron microscopy to investigate this process in three dimensions and to gain insight into the formation and nature of these nanostructures. 11 June 2014 | doi: 10.1038/ncomms5109 Chemical Sciences  Catalysis  Materials science  Physical chemistry  A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals Giovanni Strona, Domenico Nappo, Francesco Boccacci, Simone Fattorini and Jesus San-Miguel-Ayanz Available methods to randomize binary matrices with fixed row and column sums are computationally intensive and tend to generate matrix configurations with unequal frequency. Here, the authors introduce a fast and unbiased procedure that requires reduced computational effort and produces uniformly distributed null matrices. 11 June 2014 | doi: 10.1038/ncomms5114 Biological Sciences  Ecology  Carbon storage and potential methane production in the Hudson Bay Lowlands since mid-Holocene peat initiation Maara S. Packalen, Sarah A. Finkelstein and James W. McLaughlin Peatlands both store and emit potent greenhouse gases, yet their contribution to carbon dynamics during the past is poorly constrained. Here, Packalen et al. present new age constraints for peat development in the Hudson Bay Lowlands and quantify carbon storage and methane emissions during the Holocene. 11 June 2014 | doi: 10.1038/ncomms5078 Earth Sciences  Climate science  Correlated motions are a fundamental property of β-sheets R. Bryn Fenwick, Laura Orellana, Santi Esteban-Martín, Modesto Orozco and Xavier Salvatella Functional changes in protein structures are involved in a large number of biochemical processes. Here, the authors perform a simulation study of known protein structures to show how β-sheets possess the ability to facilitate concerted backbone motions. 11 June 2014 | doi: 10.1038/ncomms5070 Biological Sciences  Biophysics  Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors Tuhin Bhowmick, Soumitra Ghosh, Karuna Dixit, Varsha Ganesan, Udupi A. Ramagopal, Debayan Dey, Siddhartha P. Sarma, Suryanarayanarao Ramakumar and Valakunja Nagaraja Histone-like HU proteins play roles in chromatin architecture and DNA-dependent processes in bacteria. Here, the authors describe the crystal structure of the DNA-binding domain of HU from Mycobacterium tuberculosis, and show that the pathogen's growth can be inhibited using HU-targeting small molecules. 11 June 2014 | doi: 10.1038/ncomms5124 Biological Sciences  Biochemistry  Biophysics  Microbiology  Isolation and reversible dimerization of a selenium–selenium three-electron σ-bond Senwang Zhang, Xingyong Wang, Yuanting Su, Yunfan Qiu, Zaichao Zhang and Xinping Wang Three-electron σ-bonds are known as intermediates in chemical reactions, but they typically are unstable and transient. Here, the authors observe, isolate and characterize a room-temperature-stable organic compound with a three-electron selenium–selenium σ-bond. 11 June 2014 | doi: 10.1038/ncomms5127 Chemical Sciences  Inorganic chemistry  Organic chemistry  Physical chemistry  Forests fuel fish growth in freshwater deltas OPEN Andrew J. Tanentzap, Erik J. Szkokan-Emilson, Brian W. Kielstra, Michael T. Arts, Norman D. Yan and John M. Gunn Vegetation close to streams and lakes provides organic matter to aquatic ecosystems. Here, the authors show that the dense forest cover around lakes feeds the near-shore lake food web through organic matter subsidies, leading to faster growth in planktivorous fish. 11 June 2014 | doi: 10.1038/ncomms5077 Biological Sciences  Ecology  An ultralow power athermal silicon modulator OPEN Erman Timurdogan, Cheryl M. Sorace-Agaskar, Jie Sun, Ehsan Shah Hosseini, Aleksandr Biberman and Michael R. Watts Optical modulators on silicon promise to deliver ultralow power communication networks between or within computer chips. Here, the authors demonstrate a silicon modulator operating with less than one femtojoule energy and are able to compensate for thermal drift over a 7.5 °C temperature range. 11 June 2014 | doi: 10.1038/ncomms5008 Physical Sciences  Nanotechnology  Optical physics  Membrane deformation and scission by the HSV-1 nuclear egress complex Janna M. Bigalke, Thomas Heuser, Daniela Nicastro and Ekaterina E. Heldwein Two viral proteins form the nuclear egress complex of herpesviruses, which is essential for the exit of nascent viral capsids from the cell nucleus. Here, the authors use synthetic lipid vesicles to show that the complex can mediate membrane budding in the absence of other cellular factors. 11 June 2014 | doi: 10.1038/ncomms5131 Biological Sciences  Biophysics  Cell biology  Virology  Picometre-precision analysis of scanning transmission electron microscopy images of platinum nanocatalysts Andrew B. Yankovich, Benjamin Berkels, W. Dahmen, P. Binev, S. I. Sanchez, S. A. Bradley, Ao Li, Izabela Szlufarska and Paul M. Voyles The structural characterization of materials with picometre precision is vital for the development of structure–property relationships. Here, the authors present results demonstrating sub-picometre precision measurements of atomic position based on a non-rigid registration technique. 11 June 2014 | doi: 10.1038/ncomms5155 Chemical Sciences  Catalysis  Materials science  Nanotechnology  Nothosaur foraging tracks from the Middle Triassic of southwestern China Qiyue Zhang, Wen Wen, Shixue Hu, Michael J. Benton, Changyong Zhou, Tao Xie, Tao Lü, Jinyuan Huang, Brian Choo, Zhong-Qiang Chen, Jun Liu and Qican Zhang The seas of the Mesozoic were populated by marine reptiles, yet their modes of locomotion remain unknown. Here, Zhang et al. describe seabed tracks made by the paddles of Middle Triassic nothosaurs in southwestern China, which shows that these marine reptiles used their forelimbs for propulsion. 11 June 2014 | doi: 10.1038/ncomms4973 Biological Sciences  Palaeontology  Haemodynamic and extracellular matrix cues regulate the mechanical phenotype and stiffness of aortic endothelial cells Caitlin Collins, Lukas D. Osborne, Christophe Guilluy, Zhongming Chen, E. Tim O'Brien III, John S. Reader, Keith Burridge, Richard Superfine and Ellie Tzima Endothelial cells at the inner surface of blood vessels are exposed to mechanical forces as a result of blood flow. Here the authors show that the interaction of extracellular matrix proteins with adhesion molecules on the endothelial cell surface determines cellular stiffness and sensitivity to mechanical forces. 11 June 2014 | doi: 10.1038/ncomms4984 Biological Sciences  Cell biology    Nature Communications JOBS of the week Group leader positions in Development & Stem Cells IGBMC (Institute of Genetics & Molecular & Cellular Biology)/ CERBM GIE Postdoctoral Research Scientist Wellcome Trust Centre for Human Genetics Wissenschaftliche / r Mitarbeiter / in / Postdoctoral research fellow Robert Koch - Institut Professor Helmholtz Institute Erlangen-Nürnberg Scientific employees (Postdoctoral Positions) Philipps-University Clinical Research Fellow in Surgery University of Glasgow Volunteer Studies and Clinical Services / Research Manager Medical Research Council - Human Nutrition Research Volunteer Studies and Clinical Services / Research Manager Medical Research Council - Human Nutrition Research Research Associate in Statistical Population Genetics University College London (UCL) Research Fellow, Synthetic Biology (Biological Sciences) University of Essex More Science jobs from Nature Communications EVENT Paediatric Drug Development 08.07.14 London, UK More science events from       Latest Corrigendum     Corrigendum: Evolutionary instability of zero-determinant strategies demonstrates that winning is not everything Christoph Adami and Arend Hintze 16 June 2014 | doi: 10.1038/ncomms4764 Biological Sciences  Ecology  Evolution      Advertisement An open access online-only multidisciplinary journal publishing high-quality research in all areas of primary care management of respiratory and respiratory-related allergic diseases. 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