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Nature Communications

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https://www.readbyqxmd.com/read/28098255/annual-time-series-analysis-of-aqueous-edna-reveals-ecologically-relevant-dynamics-of-lake-ecosystem-biodiversity
#1
Iliana Bista, Gary R Carvalho, Kerry Walsh, Mathew Seymour, Mehrdad Hajibabaei, Delphine Lallias, Martin Christmas, Simon Creer
The use of environmental DNA (eDNA) in biodiversity assessments offers a step-change in sensitivity, throughput and simultaneous measures of ecosystem diversity and function. There remains, however, a need to examine eDNA persistence in the wild through simultaneous temporal measures of eDNA and biota. Here, we use metabarcoding of two markers of different lengths, derived from an annual time series of aqueous lake eDNA to examine temporal shifts in ecosystem biodiversity and in an ecologically important group of macroinvertebrates (Diptera: Chironomidae)...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098238/expression-of-the-novel-maternal-centrosome-assembly-factor-wdr8-is-required-for-vertebrate-embryonic-mitoses
#2
Daigo Inoue, Manuel Stemmer, Thomas Thumberger, Thomas Ruppert, Felix Bärenz, Joachim Wittbrodt, Oliver J Gruss
The assembly of the first centrosome occurs upon fertilisation when male centrioles recruit pericentriolar material (PCM) from the egg cytoplasm. The mechanisms underlying the proper assembly of centrosomes during early embryogenesis remain obscure. We identify Wdr8 as a novel maternally essential protein that is required for centrosome assembly during embryonic mitoses of medaka (Oryzias latipes). By CRISPR-Cas9-mediated knockout, maternal/zygotic Wdr8-null (m/zWdr8(-/-)) blastomeres exhibit severe defects in centrosome structure that lead to asymmetric division, multipolar mitotic spindles and chromosome alignment errors...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098184/infrared-laser-induced-gene-expression-for-tracking-development-and-function-of-single-c-elegans-embryonic-neurons
#3
Anupriya Singhal, Shai Shaham
Visualizing neural-circuit assembly in vivo requires tracking growth of optically resolvable neurites. The Caenorhabditis elegans embryonic nervous system, comprising 222 neurons and 56 glia, is attractive for comprehensive studies of development; however, embryonic reporters are broadly expressed, making single-neurite tracking/manipulation challenging. We present a method, using an infrared laser, for reproducible heat-dependent gene expression in small sublineages (one to four cells) without radiation damage...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098164/uncovering-the-sumoylation-and-ubiquitylation-crosstalk-in-human-cells-using-sequential-peptide-immunopurification
#4
Frédéric Lamoliatte, Francis P McManus, Ghizlane Maarifi, Mounira K Chelbi-Alix, Pierre Thibault
Crosstalk between the SUMO and ubiquitin pathways has recently been reported. However, no approach currently exists to determine the interrelationship between these modifications. Here, we report an optimized immunoaffinity method that permits the study of both protein ubiquitylation and SUMOylation from a single sample. This method enables the unprecedented identification of 10,388 SUMO sites in HEK293 cells. The sequential use of SUMO and ubiquitin remnant immunoaffinity purification facilitates the dynamic profiling of SUMOylated and ubiquitylated proteins in HEK293 cells treated with the proteasome inhibitor MG132...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098163/erratum-global-gain-modulation-generates-time-dependent-urgency-during-perceptual-choice-in-humans
#5
Peter R Murphy, Evert Boonstra, Sander Nieuwenhuis
No abstract text is available yet for this article.
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098162/novel-genetic-loci-associated-with-hippocampal-volume
#6
Derrek P Hibar, Hieab H H Adams, Neda Jahanshad, Ganesh Chauhan, Jason L Stein, Edith Hofer, Miguel E Renteria, Joshua C Bis, Alejandro Arias-Vasquez, M Kamran Ikram, Sylvane Desrivières, Meike W Vernooij, Lucija Abramovic, Saud Alhusaini, Najaf Amin, Micael Andersson, Konstantinos Arfanakis, Benjamin S Aribisala, Nicola J Armstrong, Lavinia Athanasiu, Tomas Axelsson, Ashley H Beecham, Alexa Beiser, Manon Bernard, Susan H Blanton, Marc M Bohlken, Marco P Boks, Janita Bralten, Adam M Brickman, Owen Carmichael, M Mallar Chakravarty, Qiang Chen, Christopher R K Ching, Vincent Chouraki, Gabriel Cuellar-Partida, Fabrice Crivello, Anouk Den Braber, Nhat Trung Doan, Stefan Ehrlich, Sudheer Giddaluru, Aaron L Goldman, Rebecca F Gottesman, Oliver Grimm, Michael E Griswold, Tulio Guadalupe, Boris A Gutman, Johanna Hass, Unn K Haukvik, David Hoehn, Avram J Holmes, Martine Hoogman, Deborah Janowitz, Tianye Jia, Kjetil N Jørgensen, Nazanin Karbalai, Dalia Kasperaviciute, Sungeun Kim, Marieke Klein, Bernd Kraemer, Phil H Lee, David C M Liewald, Lorna M Lopez, Michelle Luciano, Christine Macare, Andre F Marquand, Mar Matarin, Karen A Mather, Manuel Mattheisen, David R McKay, Yuri Milaneschi, Susana Muñoz Maniega, Kwangsik Nho, Allison C Nugent, Paul Nyquist, Loes M Olde Loohuis, Jaap Oosterlaan, Martina Papmeyer, Lukas Pirpamer, Benno Pütz, Adaikalavan Ramasamy, Jennifer S Richards, Shannon L Risacher, Roberto Roiz-Santiañez, Nanda Rommelse, Stefan Ropele, Emma J Rose, Natalie A Royle, Tatjana Rundek, Philipp G Sämann, Arvin Saremi, Claudia L Satizabal, Lianne Schmaal, Andrew J Schork, Li Shen, Jean Shin, Elena Shumskaya, Albert V Smith, Emma Sprooten, Lachlan T Strike, Alexander Teumer, Diana Tordesillas-Gutierrez, Roberto Toro, Daniah Trabzuni, Stella Trompet, Dhananjay Vaidya, Jeroen Van der Grond, Sven J Van der Lee, Dennis Van der Meer, Marjolein M J Van Donkelaar, Kristel R Van Eijk, Theo G M Van Erp, Daan Van Rooij, Esther Walton, Lars T Westlye, Christopher D Whelan, Beverly G Windham, Anderson M Winkler, Katharina Wittfeld, Girma Woldehawariat, Christiane Wolf, Thomas Wolfers, Lisa R Yanek, Jingyun Yang, Alex Zijdenbos, Marcel P Zwiers, Ingrid Agartz, Laura Almasy, David Ames, Philippe Amouyel, Ole A Andreassen, Sampath Arepalli, Amelia A Assareh, Sandra Barral, Mark E Bastin, Diane M Becker, James T Becker, David A Bennett, John Blangero, Hans van Bokhoven, Dorret I Boomsma, Henry Brodaty, Rachel M Brouwer, Han G Brunner, Randy L Buckner, Jan K Buitelaar, Kazima B Bulayeva, Wiepke Cahn, Vince D Calhoun, Dara M Cannon, Gianpiero L Cavalleri, Ching-Yu Cheng, Sven Cichon, Mark R Cookson, Aiden Corvin, Benedicto Crespo-Facorro, Joanne E Curran, Michael Czisch, Anders M Dale, Gareth E Davies, Anton J M De Craen, Eco J C De Geus, Philip L De Jager, Greig I De Zubicaray, Ian J Deary, Stéphanie Debette, Charles DeCarli, Norman Delanty, Chantal Depondt, Anita DeStefano, Allissa Dillman, Srdjan Djurovic, Gary Donohoe, Wayne C Drevets, Ravi Duggirala, Thomas D Dyer, Christian Enzinger, Susanne Erk, Thomas Espeseth, Iryna O Fedko, Guillén Fernández, Luigi Ferrucci, Simon E Fisher, Debra A Fleischman, Ian Ford, Myriam Fornage, Tatiana M Foroud, Peter T Fox, Clyde Francks, Masaki Fukunaga, J Raphael Gibbs, David C Glahn, Randy L Gollub, Harald H H Göring, Robert C Green, Oliver Gruber, Vilmundur Gudnason, Sebastian Guelfi, Asta K Håberg, Narelle K Hansell, John Hardy, Catharina A Hartman, Ryota Hashimoto, Katrin Hegenscheid, Andreas Heinz, Stephanie Le Hellard, Dena G Hernandez, Dirk J Heslenfeld, Beng-Choon Ho, Pieter J Hoekstra, Wolfgang Hoffmann, Albert Hofman, Florian Holsboer, Georg Homuth, Norbert Hosten, Jouke-Jan Hottenga, Matthew Huentelman, Hilleke E Hulshoff Pol, Masashi Ikeda, Clifford R Jack, Mark Jenkinson, Robert Johnson, Erik G Jönsson, J Wouter Jukema, René S Kahn, Ryota Kanai, Iwona Kloszewska, David S Knopman, Peter Kochunov, John B Kwok, Stephen M Lawrie, Hervé Lemaître, Xinmin Liu, Dan L Longo, Oscar L Lopez, Simon Lovestone, Oliver Martinez, Jean-Luc Martinot, Venkata S Mattay, Colm McDonald, Andrew M McIntosh, Francis J McMahon, Katie L McMahon, Patrizia Mecocci, Ingrid Melle, Andreas Meyer-Lindenberg, Sebastian Mohnke, Grant W Montgomery, Derek W Morris, Thomas H Mosley, Thomas W Mühleisen, Bertram Müller-Myhsok, Michael A Nalls, Matthias Nauck, Thomas E Nichols, Wiro J Niessen, Markus M Nöthen, Lars Nyberg, Kazutaka Ohi, Rene L Olvera, Roel A Ophoff, Massimo Pandolfo, Tomas Paus, Zdenka Pausova, Brenda W J H Penninx, G Bruce Pike, Steven G Potkin, Bruce M Psaty, Simone Reppermund, Marcella Rietschel, Joshua L Roffman, Nina Romanczuk-Seiferth, Jerome I Rotter, Mina Ryten, Ralph L Sacco, Perminder S Sachdev, Andrew J Saykin, Reinhold Schmidt, Helena Schmidt, Peter R Schofield, Sigurdur Sigursson, Andrew Simmons, Andrew Singleton, Sanjay M Sisodiya, Colin Smith, Jordan W Smoller, Hilkka Soininen, Vidar M Steen, David J Stott, Jessika E Sussmann, Anbupalam Thalamuthu, Arthur W Toga, Bryan J Traynor, Juan Troncoso, Magda Tsolaki, Christophe Tzourio, Andre G Uitterlinden, Maria C Valdés Hernández, Marcel Van der Brug, Aad van der Lugt, Nic J A van der Wee, Neeltje E M Van Haren, Dennis van 't Ent, Marie-Jose Van Tol, Badri N Vardarajan, Bruno Vellas, Dick J Veltman, Henry Völzke, Henrik Walter, Joanna M Wardlaw, Thomas H Wassink, Michael E Weale, Daniel R Weinberger, Michael W Weiner, Wei Wen, Eric Westman, Tonya White, Tien Y Wong, Clinton B Wright, Ronald H Zielke, Alan B Zonderman, Nicholas G Martin, Cornelia M Van Duijn, Margaret J Wright, W T Longstreth, Gunter Schumann, Hans J Grabe, Barbara Franke, Lenore J Launer, Sarah E Medland, Sudha Seshadri, Paul M Thompson, M Arfan Ikram
The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098159/fluid-shear-stress-activates-yap1-to-promote-cancer-cell-motility
#7
Hyun Jung Lee, Miguel F Diaz, Katherine M Price, Joyce A Ozuna, Songlin Zhang, Eva M Sevick-Muraca, John P Hagan, Pamela L Wenzel
Mechanical stress is pervasive in egress routes of malignancy, yet the intrinsic effects of force on tumour cells remain poorly understood. Here, we demonstrate that frictional force characteristic of flow in the lymphatics stimulates YAP1 to drive cancer cell migration; whereas intensities of fluid wall shear stress (WSS) typical of venous or arterial flow inhibit taxis. YAP1, but not TAZ, is strictly required for WSS-enhanced cell movement, as blockade of YAP1, TEAD1-4 or the YAP1-TEAD interaction reduces cellular velocity to levels observed without flow...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098156/sixfold-improved-single-particle-measurement-of-the-magnetic-moment-of-the-antiproton
#8
H Nagahama, C Smorra, S Sellner, J Harrington, T Higuchi, M J Borchert, T Tanaka, M Besirli, A Mooser, G Schneider, K Blaum, Y Matsuda, C Ospelkaus, W Quint, J Walz, Y Yamazaki, S Ulmer
Our current understanding of the Universe comes, among others, from particle physics and cosmology. In particle physics an almost perfect symmetry between matter and antimatter exists. On cosmological scales, however, a striking matter/antimatter imbalance is observed. This contradiction inspires comparisons of the fundamental properties of particles and antiparticles with high precision. Here we report on a measurement of the g-factor of the antiproton with a fractional precision of 0.8 parts per million at 95% confidence level...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098155/the-geometric-nature-of-weights-in-real-complex-networks
#9
Antoine Allard, M Ángeles Serrano, Guillermo García-Pérez, Marián Boguñá
The topology of many real complex networks has been conjectured to be embedded in hidden metric spaces, where distances between nodes encode their likelihood of being connected. Besides of providing a natural geometrical interpretation of their complex topologies, this hypothesis yields the recipe for sustainable Internet's routing protocols, sheds light on the hierarchical organization of biochemical pathways in cells, and allows for a rich characterization of the evolution of international trade. Here we present empirical evidence that this geometric interpretation also applies to the weighted organization of real complex networks...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098154/structural-basis-of-ligand-interaction-with-atypical-chemokine-receptor-3
#10
Martin Gustavsson, Liwen Wang, Noortje van Gils, Bryan S Stephens, Penglie Zhang, Thomas J Schall, Sichun Yang, Ruben Abagyan, Mark R Chance, Irina Kufareva, Tracy M Handel
Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098153/mecp2-regulates-cortical-plasticity-underlying-a-learned-behaviour-in-adult-female-mice
#11
Keerthi Krishnan, Billy Y B Lau, Gabrielle Ewall, Z Josh Huang, Stephen D Shea
Neurodevelopmental disorders are marked by inappropriate synaptic connectivity early in life, but how disruption of experience-dependent plasticity contributes to cognitive and behavioural decline in adulthood is unclear. Here we show that pup gathering behaviour and associated auditory cortical plasticity are impaired in female Mecp2(het) mice, a model of Rett syndrome. In response to learned maternal experience, Mecp2(het) females exhibited transient changes to cortical inhibitory networks typically associated with limited plasticity...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098152/human-farnesyl-pyrophosphate-synthase-is-allosterically-inhibited-by-its-own-product
#12
Jaeok Park, Michal Zielinski, Alexandr Magder, Youla S Tsantrizos, Albert M Berghuis
Farnesyl pyrophosphate synthase (FPPS) is an enzyme of the mevalonate pathway and a well-established therapeutic target. Recent research has focused around a newly identified druggable pocket near the enzyme's active site. Pharmacological exploitation of this pocket is deemed promising; however, its natural biological function, if any, is yet unknown. Here we report that the product of FPPS, farnesyl pyrophosphate (FPP), can bind to this pocket and lock the enzyme in an inactive state. The Kd for this binding is 5-6 μM, within a catalytically relevant range...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098147/nanoparticle-induced-unusual-melting-and-solidification-behaviours-of-metals
#13
Chao Ma, Lianyi Chen, Chezheng Cao, Xiaochun Li
Effective control of melting and solidification behaviours of materials is significant for numerous applications. It has been a long-standing challenge to increase the melted zone (MZ) depth while shrinking the heat-affected zone (HAZ) size during local melting and solidification of materials. In this paper, nanoparticle-induced unusual melting and solidification behaviours of metals are reported that effectively solve this long-time dilemma. By introduction of Al2O3 nanoparticles, the MZ depth of Ni is increased by 68%, while the corresponding HAZ size is decreased by 67% in laser melting at a pulse energy of 0...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098146/metal-oxide-interfacial-effects-on-the-selective-oxidation-of-primary-alcohols
#14
Guofeng Zhao, Fan Yang, Zongjia Chen, Qingfei Liu, Yongjun Ji, Yi Zhang, Zhiqiang Niu, Junjie Mao, Xinhe Bao, Peijun Hu, Yadong Li
A main obstacle in the rational development of heterogeneous catalysts is the difficulty in identifying active sites. Here we show metal/oxide interfacial sites are highly active for the oxidation of benzyl alcohol and other industrially important primary alcohols on a range of metals and oxides combinations. Scanning tunnelling microscopy together with density functional theory calculations on FeO/Pt(111) reveals that benzyl alcohol enriches preferentially at the oxygen-terminated FeO/Pt(111) interface and undergoes readily O-H and C-H dissociations with the aid of interfacial oxygen, which is also validated in the model study of Cu2O/Ag(111)...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098145/highly-thermal-stable-ferromagnetism-by-a-natural-composite
#15
Tianyu Ma, Junming Gou, Shanshan Hu, Xiaolian Liu, Chen Wu, Shuai Ren, Hui Zhao, Andong Xiao, Chengbao Jiang, Xiaobing Ren, Mi Yan
All ferromagnetic materials show deterioration of magnetism-related properties such as magnetization and magnetostriction with increasing temperature, as the result of gradual loss of magnetic order with approaching Curie temperature TC. However, technologically, it is highly desired to find a magnetic material that can resist such magnetism deterioration and maintain stable magnetism up to its TC, but this seems against the conventional wisdom about ferromagnetism. Here we show that a Fe-Ga alloy exhibits highly thermal-stable magnetization up to the vicinity of its TC, 880 K...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098143/efficient-dna-free-genome-editing-of-bread-wheat-using-crispr-cas9-ribonucleoprotein-complexes
#16
Zhen Liang, Kunling Chen, Tingdong Li, Yi Zhang, Yanpeng Wang, Qian Zhao, Jinxing Liu, Huawei Zhang, Cuimin Liu, Yidong Ran, Caixia Gao
Substantial efforts are being made to optimize the CRISPR/Cas9 system for precision crop breeding. The avoidance of transgene integration and reduction of off-target mutations are the most important targets for optimization. Here, we describe an efficient genome editing method for bread wheat using CRISPR/Cas9 ribonucleoproteins (RNPs). Starting from RNP preparation, the whole protocol takes only seven to nine weeks, with four to five independent mutants produced from 100 immature wheat embryos. Deep sequencing reveals that the chance of off-target mutations in wheat cells is much lower in RNP mediated genome editing than in editing with CRISPR/Cas9 DNA...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098142/carbon-translocation-from-a-plant-to-an-insect-pathogenic-endophytic-fungus
#17
Scott W Behie, Camila C Moreira, Irina Sementchoukova, Larissa Barelli, Paul M Zelisko, Michael J Bidochka
Metarhizium robertsii is a common soil fungus that occupies a specialized ecological niche as an endophyte and an insect pathogen. Previously, we showed that the endophytic capability and insect pathogenicity of Metarhizium are coupled to provide an active method of insect-derived nitrogen transfer to a host plant via fungal mycelia. We speculated that in exchange for this insect-derived nitrogen, the plant would provide photosynthate to the fungus. By using (13)CO2, we show the incorporation of (13)C into photosynthate and the subsequent translocation of (13)C into fungal-specific carbohydrates (trehalose and chitin) in the root/endophyte complex...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098141/one-million-years-of-glaciation-and-denudation-history-in-west-greenland
#18
Astrid Strunk, Mads Faurschou Knudsen, David L Egholm, John D Jansen, Laura B Levy, Bo H Jacobsen, Nicolaj K Larsen
The influence of major Quaternary climatic changes on growth and decay of the Greenland Ice Sheet, and associated erosional impact on the landscapes, is virtually unknown beyond the last deglaciation. Here we quantify exposure and denudation histories in west Greenland by applying a novel Markov-Chain Monte Carlo modelling approach to all available paired cosmogenic (10)Be-(26)Al bedrock data from Greenland. We find that long-term denudation rates in west Greenland range from >50 m Myr(-1) in low-lying areas to ∼2 m Myr(-1) at high elevations, hereby quantifying systematic variations in denudation rate among different glacial landforms caused by variations in ice thickness across the landscape...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098140/dynamical-observations-on-the-crack-tip-zone-and-stress-corrosion-of-two-dimensional-mos2
#19
Thuc Hue Ly, Jiong Zhao, Magdalena Ola Cichocka, Lain-Jong Li, Young Hee Lee
Whether and how fracture mechanics needs to be modified for small length scales and in systems of reduced dimensionality remains an open debate. Here, employing in situ transmission electron microscopy, atomic structures and dislocation dynamics in the crack tip zone of a propagating crack in two-dimensional (2D) monolayer MoS2 membrane are observed, and atom-to-atom displacement mapping is obtained. The electron beam is used to initiate the crack; during in situ observation of crack propagation the electron beam effect is minimized...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098138/scimp-is-a-transmembrane-non-tir-tlr-adaptor-that-promotes-proinflammatory-cytokine-production-from-macrophages
#20
Lin Luo, Nilesh J Bokil, Adam A Wall, Ronan Kapetanovic, Natalie M Lansdaal, Faustine Marceline, Belinda J Burgess, Samuel J Tong, Zhong Guo, Kirill Alexandrov, Ian L Ross, Margaret L Hibbs, Jennifer L Stow, Matthew J Sweet
Danger signals activate Toll-like receptors (TLRs), thereby initiating inflammatory responses. Canonical TLR signalling, via Toll/Interleukin-1 receptor domain (TIR)-containing adaptors and proinflammatory transcription factors such as NF-κB, occurs in many cell types; however, additional mechanisms are required for specificity of inflammatory responses in innate immune cells. Here we show that SCIMP, an immune-restricted, transmembrane adaptor protein (TRAP), promotes selective proinflammatory cytokine responses by direct modulation of TLR4...
January 18, 2017: Nature Communications
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