Wednesday, June 28, 2017

Nature Communications - 28 June 2017

Nature Communications

Animation: Amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder that primarily affects the motor system, resulting in progressive muscle weakness, which ultimately becomes fatal. This animation focuses on the mechanisms that drive ALS pathogenesis.

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Aging affects the balance of neural entrainment and top-down neural modulation in the listening brain OPEN
Molly J. Henry, Björn Herrmann, Dunja Kunke and Jonas Obleser
The changes that accompany age-related decreases in speech comprehension are not yet understood. Here, authors show that older adults are less able to entrain to speech-paced auditory rhythms and that the behavioural consequences can be counteracted by top-down neural modulation.
27 June 2017 | doi: 10.1038/ncomms15801

Caffeine inhibits hypothalamic A1R to excite oxytocin neuron and ameliorate dietary obesity in mice OPEN
Liufeng Wu, Jia Meng, Qing Shen, Yi Zhang, Susu Pan, Zhuo Chen, Ling-Qiang Zhu, Youming Lu, Yuan Huang and Guo Zhang
The mechanism by which caffeine, an antagonist of adenosine receptors, regulates metabolism is not clear. Here the authors show that adenosine A1R receptor expression is increased in the hypothalamus of diet-induced obesity mice, and that body weight can be alleviated by central administration of caffeine via its action on hypothalamic oxytocin neurons.
27 June 2017 | doi: 10.1038/ncomms15904

A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica OPEN
Michael Westbury, Sina Baleka, Axel Barlow, Stefanie Hartmann, Johanna L.A. Paijmans, Alejandro Kramarz, Analía M Forasiepi, Mariano Bond, Javier N. Gelfo, Marcelo A. Reguero, Patricio López-Mendoza, Matias Taglioretti, Fernando Scaglia, Andrés Rinderknecht, Washington Jones, Francisco Mena, Guillaume Billet, Christian de Muizon, José Luis Aguilar, Ross D.E. MacPhee et al.
Classification of the extinct South American native ungulates (SANUs) has posed a challenge given the absence of close, surviving relatives. Here, Westbury et al. sequence the mitochondrial genome of the extinct SANU Macrauchenia patachonica and reconstruct the evolutionary history of the lineage.
27 June 2017 | doi: 10.1038/ncomms15951

The increasing threat to stratospheric ozone from dichloromethane OPEN
Ryan Hossaini, Martyn P. Chipperfield, Stephen A. Montzka, Amber A. Leeson, Sandip S. Dhomse and John A. Pyle
Chlorine-containing species deplete stratospheric ozone and while chlorofluorocarbons have been drastically reduced, dichloromethane concentrations have recently increased rapidly. Hossaini et al. show that continued growth at this rate could result in important delays to Antarctic ozone recovery.
27 June 2017 | doi: 10.1038/ncomms15962

Engineering the thermal conductivity along an individual silicon nanowire by selective helium ion irradiation OPEN
Yunshan Zhao, Dan Liu, Jie Chen, Liyan Zhu, Alex Belianinov, Olga S. Ovchinnikova, Raymond R. Unocic, Matthew J. Burch, Songkil Kim, Hanfang Hao, Daniel S. Pickard, Baowen Li and John T. L. Thong
Manipulating the flow of heat at the nanoscale is difficult because it requires the ability to tune the thermal properties of tiny structures. Here, the authors locally change the thermal conductivity of an individual silicon nanowire by irradiating it with helium ions.
27 June 2017 | doi: 10.1038/ncomms15919

The structural and functional characterization of human RecQ4 reveals insights into its helicase mechanism OPEN
Sebastian Kaiser, Florian Sauer and Caroline Kisker
RecQ helicases are important for maintaining genomic integrity. Here, the authors present functional data and the crystal structure of human RecQ4, which exerts a helicase mechanism that may be more closely related to bacterial RecQ helicases than to its human family members.
27 June 2017 | doi: 10.1038/ncomms15907

Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability OPEN
Susan E. Tsutakawa, Mark J. Thompson, Andrew S. Arvai, Alexander J. Neil, Steven J. Shaw, Sana I. Algasaier, Jane C. Kim, L. David Finger, Emma Jardine, Victoria J.B. Gotham, Altaf H. Sarker, Mai Z. Her, Fahad Rashid, Samir M. Hamdan, Sergei M. Mirkin, Jane A. Grasby and John A. Tainer
Flap Endonuclease 1 is a DNA replication and repair enzyme indispensable for maintaining genomic stability. Here the authors provide mechanistic details on how FEN1 selects for 5′-flaps and promotes catalysis to avoid large-scale repeat expansion by a process termed ‘phosphate steering’.
27 June 2017 | doi: 10.1038/ncomms15855

CDK4/6 and autophagy inhibitors synergistically induce senescence in Rb positive cytoplasmic cyclin E negative cancers OPEN
Smruthi Vijayaraghavan, Cansu Karakas, Iman Doostan, Xian Chen, Tuyen Bui, Min Yi, Akshara S. Raghavendra, Yang Zhao, Sami I. Bashour, Nuhad K. Ibrahim, Meghan Karuturi, Jing Wang, Jeffrey D. Winkler, Ravi K. Amaravadi, Kelly K. Hunt, Debu Tripathy and Khandan Keyomarsi
CDK4/6-Cyclin D pathway is often deregulated in cancer; therefore specific inhibitors have been developed. Here the authors show that treatment with CDK4/6 inhibitors activate autophagy in breast cancer cells; thus, combination of such inhibitors with autophagy inhibitors results in a synergistic effect on tumour growth.
27 June 2017 | doi: 10.1038/ncomms15916

Reminders of past choices bias decisions for reward in humans OPEN
Aaron M. Bornstein, Mel W. Khaw, Daphna Shohamy and Nathaniel D. Daw
Previous work has shown that learning models based on running averages of received rewards can account for sequential choices in value based decisions. Here the authors show that such choices can also be influenced by a process of sampling memories for individual past outcomes, and that the sampled memories are episodic in nature.
27 June 2017 | doi: 10.1038/ncomms15958

A dynamic and adaptive network of cytosolic interactions governs protein export by the T3SS injectisome OPEN
Andreas Diepold, Erdinc Sezgin, Miles Huseyin, Thomas Mortimer, Christian Eggeling and Judith P. Armitage
Bacterial type III secretion systems (T3SS) play important roles in pathogenesis. Here, Diepold et al. show the dynamic nature of complexes formed of essential T3SS components in live bacteria, and that extracellular calcium concentrations influence these cytosolic complexes likely via SctK/YscK.
27 June 2017 | doi: 10.1038/ncomms15940

Beam electrons as a source of Hα flare ribbons OPEN
Malcolm Druett, Eamon Scullion, Valentina Zharkova, Sarah Matthews, Sergei Zharkov and Luc Rouppe Van der Voort
The dynamic of plasma heating in solar flares can be effectively derived from observations of optical hydrogen H-α line emissions. Here the authors report the observation of a C1.5 class flare that produced two H-α ribbons, interpreted combining radiative models affected by an electron beam.
27 June 2017 | doi: 10.1038/ncomms15905

Prevalence of sexual dimorphism in mammalian phenotypic traits OPEN
Natasha A. Karp, Jeremy Mason, Arthur L. Beaudet, Yoav Benjamini, Lynette Bower, Robert E. Braun, Steve D.M. Brown, Elissa J. Chesler, Mary E. Dickinson, Ann M. Flenniken, Helmut Fuchs, Martin Hrabe de Angelis, Xiang Gao, Shiying Guo, Simon Greenaway, Ruth Heller, Yann Herault, Monica J. Justice, Natalja Kurbatova, Christopher J. Lelliott et al.
Systemic dissection of sexually dimorphic phenotypes in mice is lacking. Here, Karp and the International Mouse Phenotype Consortium show that approximately 10% of qualitative traits and 56% of quantitative traits in mice as measured in laboratory setting are sexually dimorphic.
26 June 2017 | doi: 10.1038/ncomms15475

Membrane-binding and activation of LKB1 by phosphatidic acid is essential for development and tumour suppression OPEN
Giada Dogliotti, Lars Kullmann, Pratibha Dhumale, Christian Thiele, Olga Panichkina, Gudrun Mendl, Roland Houben, Sebastian Haferkamp, Andreas W. Püschel and Michael P. Krahn
LKB1 regulates various cellular processes such as cell proliferation, energy homeostasis and cell polarity and is frequently downregulated in various tumours. Here the authors show that LKB1 activation requires direct binding to phospholipids and show this has an implication for carcinogenesis.
26 June 2017 | doi: 10.1038/ncomms15747

Characterizing sleep spindles in 11,630 individuals from the National Sleep Research Resource OPEN
S. M. Purcell, D. S. Manoach, C. Demanuele, B. E. Cade, S. Mariani, R. Cox, G. Panagiotaropoulou, R. Saxena, J. Q. Pan, J. W. Smoller, S. Redline and R. Stickgold
Sleep patterns vary and are associated with health and disease. Here Purcell et al characterize sleep spindle activity in 11,630 individuals and describe age-related changes, genetic influences, and possible confounding effects, serving as a resource for further understanding the physiology of sleep.
26 June 2017 | doi: 10.1038/ncomms15930

An L-threonine transaldolase is required for L-threo-β-hydroxy-α-amino acid assembly during obafluorin biosynthesis OPEN
Thomas A. Scott, Daniel Heine, Zhiwei Qin and Barrie Wilkinson
Obafluorin is a β-lactone antibiotic produced by Pseudomonas fluorescens. Here the authors present the biosynthetic gene cluster and biosynthetic pathway of obafluorin, which is characterized by a central transaldolase step catalysed by a rare L-threonine transaldolase.
26 June 2017 | doi: 10.1038/ncomms15935

Iron-mediated soil carbon response to water-table decline in an alpine wetland OPEN
Yiyun Wang, Hao Wang, Jin-Sheng He and Xiaojuan Feng
The response of soil organic carbon in wetlands to water-table decline remains uncertain. Here, the authors examine the role of iron in mediating soil enzyme activity and lignin stabilization and find that iron protecting lignin phenols in soils exposed to air acts as an iron gate against the enzyme latch.
26 June 2017 | doi: 10.1038/ncomms15972

A practical and catalyst-free trifluoroethylation reaction of amines using trifluoroacetic acid OPEN
Keith G. Andrews, Radmila Faizova and Ross M. Denton
Amino and trifluoromethyl groups are ubiquitous within medicinal chemistry, but synthesis of fluoroalkylamines normally requires harsh conditions or sensitive reagents. Here the authors report an operationally simple, catalyst-free procedure for the trifluoroethylation of primary and secondary amines.
26 June 2017 | doi: 10.1038/ncomms15913

Rewritable ghost floating gates by tunnelling triboelectrification for two-dimensional electronics OPEN
Seongsu Kim, Tae Yun Kim, Kang Hyuck Lee, Tae-Ho Kim, Francesco Arturo Cimini, Sung Kyun Kim, Ronan Hinchet, Sang-Woo Kim and Christian Falconi
Once fabricated, the gates of conventional electronic devices are spatially fixed. Here, the authors introduce tunnelling triboelectrification to create, modify and destroy on-demand ghost floating gates underneath 2D materials, with the spatial resolution of an atomic force microscope.
26 June 2017 | doi: 10.1038/ncomms15891

A PPARγ transcriptional cascade directs adipose progenitor cell-niche interaction and niche expansion OPEN
Yuwei Jiang, Daniel C. Berry, Ayoung Jo, Wei Tang, Robert W. Arpke, Michael Kyba and Jonathan M. Graff
Adipocyte progenitor cells (APCs) are found tethered to adipose tissue blood vessel walls and can differentiate into adipocytes. Here the authors show that PPARγ controls angiogenesis by stimulating APC–blood vessel interaction and retention via a transcriptional network that includes PDGFRβ and VEGF.
26 June 2017 | doi: 10.1038/ncomms15926

Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis OPEN
Xiaowen Zhang, Huai-Chin Chiang, Yao Wang, Chi Zhang, Sabrina Smith, Xiayan Zhao, Sreejith J. Nair, Joel Michalek, Ismail Jatoi, Meeghan Lautner, Boyce Oliver, Howard Wang, Anna Petit, Teresa Soler, Joan Brunet, Francesca Mateo, Miguel Angel Pujana, Elizabeth Poggi, Krysta Chaldekas, Claudine Isaacs et al.
The vast majority of BRCA1-driven breast cancers derive from luminal progenitor cells but the mechanisms of this lineage specificity are unclear. Here the authors show that dangerous accumulation of DNA-RNA hybrid structures due to RNA polymerase II pausing, occurs specifically in luminal epithelial cells.
26 June 2017 | doi: 10.1038/ncomms15908

Structural and regulatory diversity shape HLA-C protein expression levels OPEN
Gurman Kaur, Stephanie Gras, Jesse I. Mobbs, Julian P. Vivian, Adrian Cortes, Thomas Barber, Subita Balaram Kuttikkatte, Lise Torp Jensen, Kathrine E. Attfield, Calliope A. Dendrou, Mary Carrington, Gil McVean, Anthony W. Purcell, Jamie Rossjohn and Lars Fugger
HLA-C expression levels correlate with immune responses to pathogens and autoimmunity, and vary in an allele-specific manner across individuals. Here the authors identify factors that drive differential expression of HLA-C allomorphs at the cell surface, and influence the structure of the peptide-binding cleft and diversity of peptides bound by HLA-C molecules.
26 June 2017 | doi: 10.1038/ncomms15924

The social inefficiency of regulating indirect land use change due to biofuels OPEN
Madhu Khanna, Weiwei Wang, Tara W. Hudiburg and Evan H. DeLucia
A Low Carbon Fuel Standard seeks to regulate indirect land use change by including its related carbon emissions in the carbon intensity of biofuels. Khanna et al. show the economic cost of abatement achieved by including this factor is much larger than the social cost of carbon.
26 June 2017 | doi: 10.1038/ncomms15513

A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay OPEN
Zhiyuan Hu, Christopher Yau and Ahmed Ashour Ahmed
Nonsense-mediated decay (NMD) eliminates transcripts with premature stop codons and has been linked to cancer genesis. Here, the authors develop an algorithm to predict NMD and perform a pan-cancer analysis that finds that some hypermutated cancers are dependent on mutations that elicit NMD.
26 June 2017 | doi: 10.1038/ncomms15943

Uniform electroactive fibre-like micelle nanowires for organic electronics OPEN
Xiaoyu Li, Piotr J. Wolanin, Liam R. MacFarlane, Robert L. Harniman, Jieshu Qian, Oliver E. C. Gould, Thomas G. Dane, John Rudin, Martin J. Cryan, Thomas Schmaltz, Holger Frauenrath, Mitchell A. Winnik, Charl F. J. Faul and Ian Manners
The self-assembly of block copolymers to form micelles has been used in applications such as drug delivery and composite reinforcement. Here the authors explore the use of fibre-like micelles of controlled length in the active layer of field-effect transistor devices.
26 June 2017 | doi: 10.1038/ncomms15909

Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma OPEN
Sam Behjati, Patrick S. Tarpey, Kerstin Haase, Hongtao Ye, Matthew D. Young, Ludmil B. Alexandrov, Sarah J. Farndon, Grace Collord, David C. Wedge, Inigo Martincorena, Susanna L. Cooke, Helen Davies, William Mifsud, Mathias Lidgren, Sancha Martin, Calli Latimer, Mark Maddison, Adam P. Butler, Jon W. Teague, Nischalan Pillay et al.
Osteosarcoma is a primary malignancy of bone that affects children and adults. Here, the authors sequence childhood and adult osteosarcomas, identifying mutations in insulin-like growth factor signalling genes and distinct genomic rearrangement profiles characterized by chromothripsis-amplification.
23 June 2017 | doi: 10.1038/ncomms15936

Optogenetic rewiring of thalamocortical circuits to restore function in the stroke injured brain OPEN
Kelly A. Tennant, Stephanie L. Taylor, Emily R. White and Craig E. Brown
Stroke recovery requires circuit reorganization and therapeutic efforts have focused on rewiring cortical circuits after stroke, but what about thalamic inputs? Here, the authors examine how thalamocortical axons are affected by stroke and use optogenetic stimulation to promote recovery.
23 June 2017 | doi: 10.1038/ncomms15879

Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations OPEN
Yali Xue, Massimo Mezzavilla, Marc Haber, Shane McCarthy, Yuan Chen, Vagheesh Narasimhan, Arthur Gilly, Qasim Ayub, Vincenza Colonna, Lorraine Southam, Christopher Finan, Andrea Massaia, Himanshu Chheda, Priit Palta, Graham Ritchie, Jennifer Asimit, George Dedoussis, Paolo Gasparini, Aarno Palotie, Samuli Ripatti et al.
Isolated populations often have special genetic compositions that can be leveraged for genetic association studies. Here, Xue and colleagues generate and analyse 3,059 low-depth whole-genome sequences from eight European isolated populations and two matched general populations.
23 June 2017 | doi: 10.1038/ncomms15927

A decoherence-free subspace in a charge quadrupole qubit OPEN
Mark Friesen, Joydip Ghosh, M. A. Eriksson and S. N. Coppersmith
Robust implementations of semiconducting qubits require overcoming the effects of charge noise, which limits coherence times. Here the authors propose a decoherence-free subspace for charge qubits to protect them from uniform electric field fluctuations, proposing an implementation in a triple quantum dot.
23 June 2017 | doi: 10.1038/ncomms15923

A unified model of Hymenopteran preadaptations that trigger the evolutionary transition to eusociality OPEN
Andrés E. Quiñones and Ido Pen
The Hymenoptera are thought to have preadaptations responsible for the repeated evolution of eusociality in ants, bees, and wasps. Here, Quiñones and Pen model the evolution of primitively social insects and identify factors that synergistically promote the transition to eusociality.
23 June 2017 | doi: 10.1038/ncomms15920

Voltage controlled interfacial magnetism through platinum orbits OPEN
Shinji Miwa, Motohiro Suzuki, Masahito Tsujikawa, Kensho Matsuda, Takayuki Nozaki, Kazuhito Tanaka, Takuya Tsukahara, Kohei Nawaoka, Minori Goto, Yoshinori Kotani, Tadakatsu Ohkubo, Frédéric Bonell, Eiiti Tamura, Kazuhiro Hono, Tetsuya Nakamura, Masafumi Shirai, Shinji Yuasa and Yoshishige Suzuki
Electric field control of magnetization is usually weak and this hampers its application for the ultralow-power-consumption spintronic devices. Here, the authors demonstrate a mechanism to enhance the control of magnetic anisotropy by voltage-induced electric quadrupole in a metal–dielectric interface.
23 June 2017 | doi: 10.1038/ncomms15848

Ezrin enhances line tension along transcellular tunnel edges via NMIIa driven actomyosin cable formation OPEN
Caroline Stefani, David Gonzalez-Rodriguez, Yosuke Senju, Anne Doye, Nadia Efimova, Sébastien Janel, Justine Lipuma, Meng Chen Tsai, Daniel Hamaoui, Madhavi P. Maddugoda, Olivier Cochet-Escartin, Coline Prévost, Frank Lafont, Tatyana Svitkina, Pekka Lappalainen, Patricia Bassereau and Emmanuel Lemichez
Holes in endothelial barriers, called transendothelial cell macroapertures (TEMs), are predicted to be limited by line tension of unknown origin. Here the authors identify an actomyosin cable encircling TEMs and establish a role for ezrin in stabilising F-actin bundles, allowing their crosslinking by non-muscle myosin IIa.
23 June 2017 | doi: 10.1038/ncomms15839

Cdt1 stabilizes an open MCM ring for helicase loading OPEN
Jordi Frigola, Jun He, Kerstin Kinkelin, Valerie E. Pye, Ludovic Renault, Max E. Douglas, Dirk Remus, Peter Cherepanov, Alessandro Costa and John F. X. Diffley
The loading and activation of the Mcm2-7 replicative helicase couples cell cycle progression to DNA replication. Here the authors use X-ray crystallography and single-particle electron microscopy to demonstrate how Ctd1 functions to promote MCM loading onto DNA.
23 June 2017 | doi: 10.1038/ncomms15720

Single-virus genomics reveals hidden cosmopolitan and abundant viruses OPEN
Francisco Martinez-Hernandez, Oscar Fornas, Monica Lluesma Gomez, Benjamin Bolduc, Maria Jose de la Cruz Peña, Joaquín Martínez Martínez, Josefa Anton, Josep M. Gasol, Riccardo Rosselli, Francisco Rodriguez-Valera, Matthew B. Sullivan, Silvia G. Acinas and Manuel Martinez-Garcia
Viruses play an important role in microbial communities but, due to limitations of available techniques, our understanding of viral diversity is limited. Here, the authors use SVGs and identify highly abundant viruses in marine communities that have been previously overlooked.
23 June 2017 | doi: 10.1038/ncomms15892

Zika virus pathogenesis in rhesus macaques is unaffected by pre-existing immunity to dengue virus OPEN
Petraleigh Pantoja, Erick X. Pérez-Guzmán, Idia V. Rodríguez, Laura J. White, Olga González, Crisanta Serrano, Luis Giavedoni, Vida Hodara, Lorna Cruz, Teresa Arana, Melween I. Martínez, Mariah A. Hassert, James D. Brien, Amelia K. Pinto, Aravinda de Silva and Carlos A. Sariol
Antibodies against dengue virus (DENV) can increase Zika virus (ZIKV) infection in vitro, but their role in vivo remains largely unknown. Here, the authors show that pre-existing immunity from a 2.8 years earlier DENV infection does not affect ZIKV pathogenesis in macaques but instead shortens Zika viremia.
23 June 2017 | doi: 10.1038/ncomms15674

Long noncoding RNA LncHIFCAR/MIR31HG is a HIF-1α co-activator driving oral cancer progression OPEN
Jing-Wen Shih, Wei-Fan Chiang, Alexander T. H. Wu, Ming-Heng Wu, Ling-Yu Wang, Yen-Ling Yu, Yu-Wen Hung, Wen-Chang Wang, Cheng-Ying Chu, Chiu-Lien Hung, Chun A. Changou, Yun Yen and Hsing-Jien Kung
Cancer cells adapt to the changing microenvironment by activating different pathways through multiple mechanisms. Here the authors identify long noncoding RNA MIR31HG as a HIF-1α co-activator required for the induction of the hypoxic response and show its oncogenic role in oral carcinogenesis.
22 June 2017 | doi: 10.1038/ncomms15874

HTLV-1-induced leukotriene B4 secretion by T cells promotes T cell recruitment and virus propagation OPEN
Florent Percher, Céline Curis, Eléonore Pérès, Maria Artesi, Nicolas Rosewick, Patricia Jeannin, Antoine Gessain, Olivier Gout, Renaud Mahieux, Pierre-Emmanuel Ceccaldi, Anne Van den Broeke, Madeleine Duc Dodon and Philippe V. Afonso
HTLV-1 predominantly spreads through direct cell-cell contacts, but mechanisms of target cell recruitment are unclear. Here, the authors show that HTLV-1 infected T-cells secrete leukotriene B4, which recruits T-cells, facilitates HTLV-1 transmission in vitro, and increases the number of infected clones in mice.
22 June 2017 | doi: 10.1038/ncomms15890

MicroRNA-34a dependent regulation of AXL controls the activation of dendritic cells in inflammatory arthritis OPEN
Mariola Kurowska-Stolarska, Stefano Alivernini, Emma Garcia Melchor, Aziza Elmesmari, Barbara Tolusso, Clare Tange, Luca Petricca, Derek S. Gilchrist, Gabriele Di Sante, Chantal Keijzer, Lynn Stewart, Clara Di Mario, Vicky Morrison, James M. Brewer, Duncan Porter, Simon Milling, Ronald D. Baxter, David McCarey, Elisa Gremese, Greg Lemke et al.
Axl is a TAM receptor that can inhibit Toll-like receptor (TLR) -induced pro-inflammatory production by dendritic cells (DC). Here the authors show that miR-34a targets Axl to control CD1c+ DC activity in mice, and that miR-34a-deficient mice are resistant to collagen-induced arthritis, whereas DCs from patients with rheumatoid arthritis have high levels of miR- 34a.
22 June 2017 | doi: 10.1038/ncomms15877

A coherent quantum annealer with Rydberg atoms OPEN
A. W. Glaetzle, R. M. W. van Bijnen, P. Zoller and W. Lechner
It is an open challenge to implement a coherent quantum annealer with fully programmable all-to-all connectivity. Here the authors present a scheme based on enhanced Rydberg-dressed interactions between neutral atoms in an optical lattice which is programmable by individual addressing of local fields.
22 June 2017 | doi: 10.1038/ncomms15813

Poly(4-styrenesulfonate)-induced sulfur vacancy self-healing strategy for monolayer MoS2 homojunction photodiode OPEN
Xiankun Zhang, Qingliang Liao, Shuo Liu, Zhuo Kang, Zheng Zhang, Junli Du, Feng Li, Shuhao Zhang, Jiankun Xiao, Baishan Liu, Yang Ou, Xiaozhi Liu, Lin Gu and Yue Zhang
Two-dimensional MoS2 homojunctions, considered potential building blocks for next generation flexible electronics, currently suffer from quick degradation. Here, Zhang and co-workers use a self-healing sulfur vacancy mechanism to produce a MoS2 photodiode that possesses long term stability.
22 June 2017 | doi: 10.1038/ncomms15881

Nearest-neighbour resonating valence bonds in YbMgGaO4 OPEN
Yuesheng Li, Devashibhai Adroja, David Voneshen, Robert I. Bewley, Qingming Zhang, Alexander A. Tsirlin and Philipp Gegenwart
The signature of short range resonating valence bonds (RVB) to understand quantum spin liquids is yet to be explored. Here, Li et al. observe the putative RVB correlations restricted to nearest neighbours in YbMgGaO4, responsible for the high-energy spin excitations.
22 June 2017 | doi: 10.1038/ncomms15814

Imaging quasiperiodic electronic states in a synthetic Penrose tiling OPEN
Laura C. Collins, Thomas G. Witte, Rochelle Silverman, David B. Green and Kenjiro K. Gomes
Quasicrystals possess long-range order but lack translational symmetry. Here, the authors use atomic manipulation and scanning tunnelling microscopy to assemble a Penrose tiling quasicrystal and observe that its electronic density of states has a quasiperiodic order, linked to the quasicrystal topology.
22 June 2017 | doi: 10.1038/ncomms15961

Adaptive and freeze-tolerant heteronetwork organohydrogels with enhanced mechanical stability over a wide temperature range OPEN
Hainan Gao, Ziguang Zhao, Yudong Cai, Jiajia Zhou, Wenda Hua, Lie Chen, Li Wang, Jianqi Zhang, Dong Han, Mingjie Liu and Lei Jiang
Several living organisms can survive subzero temperatures without cell damage. Here, the authors show a heteronetwork organohydrogel with improved elasticity and mechanical features in a wide range of temperatures.
22 June 2017 | doi: 10.1038/ncomms15911

Electronic metal-support interaction enhanced oxygen reduction activity and stability of boron carbide supported platinum OPEN
Colleen Jackson, Graham T. Smith, David W. Inwood, Andrew S. Leach, Penny S. Whalley, Mauro Callisti, Tomas Polcar, Andrea E. Russell, Pieter Levecque and Denis Kramer
D-band engineering via alloying platinum is a leading design principle for advanced oxygen reduction electrocatalysts, but stability remains a concern. Here the authors make Pt nanoparticles supported on graphite-rich boron carbide for enhanced activity and stability, isolating and optimizing the electronic metal-support interactions.
22 June 2017 | doi: 10.1038/ncomms15802

Mechanical properties of atomically thin boron nitride and the role of interlayer interactions OPEN
Aleksey Falin, Qiran Cai, Elton J.G. Santos, Declan Scullion, Dong Qian, Rui Zhang, Zhi Yang, Shaoming Huang, Kenji Watanabe, Takashi Taniguchi, Matthew R. Barnett, Ying Chen, Rodney S. Ruoff and Lu Hua Li
Atomically thin boron nitride remains undercharacterized in terms of their mechanical properties. Here authors test high-quality mono- and few-layer BN and show it to be one of the strongest electrically insulating materials and dramatically better in interlayer integrity than graphene under indentation.
22 June 2017 | doi: 10.1038/ncomms15815

Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms OPEN
Axel von Kamp and Steffen Klamt
Coupling of growth and product synthesis is an important principle in metabolic engineering, but its range of applicability is unclear. Here, the authors use a dedicated computational framework to study the feasibility of coupling the production of metabolites to growth in the genome-scale metabolic models of five production organisms, and show that coupling can be achieved for most metabolites.
22 June 2017 | doi: 10.1038/ncomms15956

Current rates and mechanisms of subsea permafrost degradation in the East Siberian Arctic Shelf OPEN
Natalia Shakhova, Igor Semiletov, Orjan Gustafsson, Valentin Sergienko, Leopold Lobkovsky, Oleg Dudarev, Vladimir Tumskoy, Michael Grigoriev, Alexey Mazurov, Anatoly Salyuk, Roman Ananiev, Andrey Koshurnikov, Denis Kosmach, Alexander Charkin, Nicolay Dmitrevsky, Victor Karnaukh, Alexey Gunar, Alexander Meluzov and Denis Chernykh
The rate of subsea permafrost degradation is a key factor controlling marine methane emissions in the Arctic. Here, using re-drilled boreholes, the authors show that the ice-bonded permafrost table in the near-shore East Siberian Arctic Shelf has deepened by ∼14 cm per year over the past 31–32 years.
22 June 2017 | doi: 10.1038/ncomms15872

ITK signalling via the Ras/IRF4 pathway regulates the development and function of Tr1 cells OPEN
Weishan Huang, Sabrina Solouki, Nicholas Koylass, Song-Guo Zheng and Avery August
IL-10+ Tr1 cells, which do not express stable Foxp3 like conventional Treg cells, are associated with various diseases, but little is known about how their differentiation and function are regulated. Here the authors show that ITK is a central TCR signalling effector of the differentiation and function of Tr1 cells.
21 June 2017 | doi: 10.1038/ncomms15871

Elastically driven intermittent microscopic dynamics in soft solids OPEN
Mehdi Bouzid, Jader Colombo, Lucas Vieira Barbosa and Emanuela Del Gado
Soft solids have important applications in industry but their material properties can be compromised by aging. Here Bouzid et al. present a large-scale study of a model gel to investigate the aging of soft matter which can help unravel the microscopic dynamics in a range of soft solids.
21 June 2017 | doi: 10.1038/ncomms15846

Hypoxia-induced mobilization of NHE6 to the plasma membrane triggers endosome hyperacidification and chemoresistance OPEN
Fabrice Lucien, Pierre-Paul Pelletier, Roxane R. Lavoie, Jean-Michel Lacroix, Sébastien Roy, Jean-Luc Parent, Dominique Arsenault, Kelly Harper and Claire M. Dubois
Sodium/proton exchangers (NHEs) are critical regulators of pH within the cell and the extracellular microenvironment. Here, the authors show that hypoxia induces mobilization of NHE6 from endosomal compartment to the plasma membrane in a PKC-dependent manner inducing hyper acidification of endosomes and drug resistance.
21 June 2017 | doi: 10.1038/ncomms15884

Munc13-1 and Munc18-1 together prevent NSF-dependent de-priming of synaptic vesicles OPEN
Enqi He, Keimpe Wierda, Rhode van Westen, Jurjen H. Broeke, Ruud F. Toonen, L. Niels Cornelisse and Matthijs Verhage
The molecular mechanism underlying the generation and maintenance of the readily releasable pool composed of primed synaptic vesicles is only partially known. Here the authors show that in mouse primary neurons, Munc13-1 and Munc18-1 stabilize primed synaptic vesicles by preventing NSF-dependent de-priming.
21 June 2017 | doi: 10.1038/ncomms15915

Origin of fast ion diffusion in super-ionic conductors OPEN
Xingfeng He, Yizhou Zhu and Yifei Mo
Ab initio atomistic modelling reveals that fast ion diffusion in super-ionic conductors is mediated by concerted migration of multiple ions. On the basis of this understanding, a universal strategy for designing fast ion conductors is proposed and demonstrated.
21 June 2017 | doi: 10.1038/ncomms15893

Expansion of the Tibetan Plateau during the Neogene OPEN
Weitao Wang, Wenjun Zheng, Peizhen Zhang, Qiang Li, Eric Kirby, Daoyang Yuan, Dewen Zheng, Caicai Liu, Zhicai Wang, Huiping Zhang and Jianzhang Pang
The timing of mountain building along the Tibetan Plateau remains unclear. Here, the authors present new magnetostratigraphic and mammalian biostratigraphic data from sediments to show that mountain building at the edge of the Tibetan Plateau commenced at 25.5 Ma with a separate emergence in the north at 12 Ma.
21 June 2017 | doi: 10.1038/ncomms15887

In situ dynamic observations of perovskite crystallisation and microstructure evolution intermediated from [PbI6]4− cage nanoparticles OPEN
Qin Hu, Lichen Zhao, Jiang Wu, Ke Gao, Deying Luo, Yufeng Jiang, Ziyi Zhang, Chenhui Zhu, Eric Schaible, Alexander Hexemer, Cheng Wang, Yi Liu, Wei Zhang, Michael Grätzel, Feng Liu, Thomas P. Russell, Rui Zhu and Qihuang Gong
The photovoltaic performances of perovskite materials are strongly influenced by their crystallinity and film morphology. Here, the authors investigate the formation and morphology evolution mechanisms of lead halide perovskites and reveal that bulk polycrystals grow from intermediate [PbI6]4 cage nanoparticles.
21 June 2017 | doi: 10.1038/ncomms15688

Single-molecule analysis of steroid receptor and cofactor action in living cells OPEN
Ville Paakinaho, Diego M. Presman, David A. Ball, Thomas A. Johnson, R. Louis Schiltz, Peter Levitt, Davide Mazza, Tatsuya Morisaki, Tatiana S. Karpova and Gordon L. Hager
Transcription factors (TFs) are thought to regulate gene expression by stably binding to target DNA elements. Here, the authors use single-molecule tracking to analyse the dynamic behaviour of steroid receptors TFs and show that most specific interactions with chromatin are transient and dynamic.
21 June 2017 | doi: 10.1038/ncomms15896

Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis OPEN
P. Savola, T. Kelkka, H. L. Rajala, A. Kuuliala, K. Kuuliala, S. Eldfors, P. Ellonen, S. Lagström, M. Lepistö, T. Hannunen, E. I. Andersson, R. K. Khajuria, T. Jaatinen, R. Koivuniemi, H. Repo, J. Saarela, K. Porkka, M. Leirisalo-Repo and S. Mustjoki
Accumulation of somatic mutations in lymphocytes is a feature of some cancers. Here the authors show that patients with recent onset of rheumatoid arthritis also accumulate mutations in their expanded CD8+ effector memory T cell pool independent of cancer association.
21 June 2017 | doi: 10.1038/ncomms15869

Self-assembled three dimensional network designs for soft electronics OPEN
Kyung-In Jang, Kan Li, Ha Uk Chung, Sheng Xu, Han Na Jung, Yiyuan Yang, Jean Won Kwak, Han Hee Jung, Juwon Song, Ce Yang, Ao Wang, Zhuangjian Liu, Jong Yoon Lee, Bong Hoon Kim, Jae-Hwan Kim, Jungyup Lee, Yongjoon Yu, Bum Jun Kim, Hokyung Jang, Ki Jun Yu et al.
Many low modulus systems, such as sensors, circuits and radios, are in 2D formats that interface with soft human tissue in order to form health monitors or bioelectronic therapeutics. Here the authors produce 3D architectures, which bypass engineering constraints and performance limitations experienced by their 2D counterparts.
21 June 2017 | doi: 10.1038/ncomms15894

Optogenetic activation of Plexin-B1 reveals contact repulsion between osteoclasts and osteoblasts OPEN
Abhijit Deb Roy, Taofei Yin, Shilpa Choudhary, Vladimir Rodionov, Carol C. Pilbeam and Yi I. Wu
Osteoclasts induce chemotaxis of osteoblasts during bone remodelling, but maintain spatial segregation. Here the authors show that osteoclasts repel osteoblasts via contact inhibition of locomotion mediated by Semaphorin-Plexin signalling and develop an optogenetic tool for Plexin-B1 to show how this signalling axis induces cell repolarization.
21 June 2017 | doi: 10.1038/ncomms15831

Growth of organic crystals via attachment and transformation of nanoscopic precursors OPEN
Yuan Jiang, Matthias Kellermeier, Denis Gebaue, Zihao Lu, Rose Rosenberg, Adrian Moise, Michael Przybylski and Helmut Cölfen
Multistage crystallization pathways involving nanoscopic precursors or intermediates have been proposed for various systems. Here, the authors find compelling evidence that nanoscopic species participate in the crystallization of glutamic acid monohydrate, extending this non-classical growth mechanism to organic crystals.
21 June 2017 | doi: 10.1038/ncomms15933
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  Latest Corrigendum  
Corrigendum: Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy OPEN
Niclas E. Bengtsson, John K. Hall, Guy L. Odom, Michael P. Phelps, Colin R. Andrus, R. David Hawkins, Stephen D. Hauschka, Joel R. Chamberlain and Jeffrey S. Chamberlain
23 June 2017 | doi: 10.1038/ncomms16007
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Erratum: Organocatalytic atroposelective synthesis of axially chiral styrenes OPEN
Sheng-Cai Zheng, San Wu, Qinghai Zhou, Lung Wa Chung, Liu Ye and Bin Tan
27 June 2017 | doi: 10.1038/ncomms16119

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