Wednesday, July 25, 2018

Nature Communications - 25 July 2018

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25 July 2018 
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  Latest Editorial    
Data sharing and the future of science OPEN
19 July 2018 | doi: 10.1038/s41467-018-05227-z
  Latest Articles View all Articles  

Finite temperature quantum annealing solving exponentially small gap problem with non-monotonic success probability OPEN
Anurag Mishra, Tameem Albash & Daniel A. Lidar

The alternating sector chain Ising problem features an exponentially small energy gap in the sector size, so one would expect an exponential decrease in success probability on a quantum annealing device. Here, instead, the authors show a nonmonotonic behavior, explaining it in terms of thermally accessible states.

25 July 2018 | doi: 10.1038/s41467-018-05239-9
Quantum information  Quantum physics 

Polyaniline-intercalated manganese dioxide nanolayers as a high-performance cathode material for an aqueous zinc-ion battery OPEN
Jianhang Huang, Zhuo Wang, Mengyan Hou, Xiaoli Dong, Yao Liu, Yonggang Wang & Yongyao Xia

Zn-MnO2 batteries offer high energy density, but phase changes that lead to poor cathode stability hinder development of rechargeable versions. Here the authors report structurally reinforced polyaniline-intercalated MnO2 nanolayers that boost performance by eliminating phase transformation.

25 July 2018 | doi: 10.1038/s41467-018-04949-4
Batteries  Electrochemistry 

Unperturbed expression bias of imprinted genes in schizophrenia OPEN
Attila Gulyás-Kovács, Ifat Keydar, Eva Xia, Menachem Fromer, Gabriel Hoffman, Douglas Ruderfer, Ravi Sachidanandam & Andrew Chess

This study analyzes allelic expression bias in post-mortem brains of healthy individuals and those diagnosed with schizophrenia or bipolar disorder. The study shows that the number of imprinted genes is consistent with low estimates, and that allelic bias is independent of psychiatric disease status.

25 July 2018 | doi: 10.1038/s41467-018-04960-9
Gene expression  Risk factors  Statistical methods 

Structural and topological nature of plasticity in sheared granular materials OPEN
Yixin Cao, Jindong Li, Binquan Kou, Chengjie Xia, Zhifeng Li, Rongchang Chen, Honglan Xie, Tiqiao Xiao, Walter Kob, Liang Hong, Jie Zhang & Yujie Wang

It is a general consensus that the structural defects are the plasticity carriers in amorphous solids, but its microscopic view remains largely unknown. Cao et a. show that highly distorted coplanar tetrahedra act as defects in granular packings, which flip under shear to carry local plasticity.

25 July 2018 | doi: 10.1038/s41467-018-05329-8
Condensed-matter physics  Glasses 

Soluble RANKL contributes to osteoclast formation in adult mice but not ovariectomy-induced bone loss OPEN
Jinhu Xiong, Keisha Cawley, Marilina Piemontese, Yuko Fujiwara, Haibo Zhao, Joseph J. Goellner & Charles A. O’Brien

RANKL is a cytokine produced as a membrane-bound and a secreted protein. Here, using mice lacking soluble RANKL, the authors show that the secreted protein is important for osteoclast function, but not for mammary gland and lymphocyte development.

25 July 2018 | doi: 10.1038/s41467-018-05244-y
Bone  Bone remodelling 

A mosquito salivary gland protein partially inhibits Plasmodium sporozoite cell traversal and transmission OPEN
Tyler R. Schleicher, Jing Yang, Marianna Freudzon, Alison Rembisz, Samuel Craft, Madeleine Hamilton, Morven Graham, Godfree Mlambo, Abhai K. Tripathi, Yue Li, Peter Cresswell, Photini Sinnis, George Dimopoulos & Erol Fikrig

Mosquito saliva can affect transmission of Plasmodium to mammalian hosts, but active saliva components or mechanisms are poorly understood. Here, the authors identify a mosquito saliva protein that binds Plasmodium sporozoites and inhibits cell traversal in vitro and sporozoite speed in mice.

25 July 2018 | doi: 10.1038/s41467-018-05374-3
Malaria  Parasite biology  Pathogens 

Toroidal diamond anvil cell for detailed measurements under extreme static pressures OPEN
Agnès Dewaele, Paul Loubeyre, Florent Occelli, Olivier Marie & Mohamed Mezouar

Extreme static pressures exceeding a million atmospheres exist in a variety of natural environments, but obtaining such pressures in a laboratory is still a challenge. Here, the authors develop a toroidal diamond anvil design that allows for the generation of 600 GPa (6 million atmospheres) in routinely used diamond anvil cells.

25 July 2018 | doi: 10.1038/s41467-018-05294-2
Characterization and analytical techniques  Structure of solids and liquids 

PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity OPEN
Jessica van Setten, Jennifer A. Brody, Yalda Jamshidi, Brenton R. Swenson, Anne M. Butler, Harry Campbell, Fabiola M. Del Greco, Daniel S. Evans, Quince Gibson, Daniel F. Gudbjartsson, Kathleen F. Kerr, Bouwe P. Krijthe, Leo-Pekka Lyytikäinen, Christian Müller, Martina Müller-Nurasyid, Ilja M. Nolte, Sandosh Padmanabhan, Marylyn D. Ritchie, Antonietta Robino, Albert V. Smith et al.

Abnormal PR interval duration is associated with risk for atrial fibrillation and heart block. Here, van Setten et al. identify 44 PR interval loci in a genome-wide association study of over 92,000 individuals and find genetic overlap with QRS duration, heart rate and atrial fibrillation.

25 July 2018 | doi: 10.1038/s41467-018-04766-9
Atrial fibrillation  Cardiovascular genetics  Genetic association study 

Electrically driven three-dimensional solitary waves as director bullets in nematic liquid crystals OPEN
Bing-Xiang Li, Volodymyr Borshch, Rui-Lin Xiao, Sathyanarayana Paladugu, Taras Turiv, Sergij V. Shiyanovskii & Oleg D. Lavrentovich

Solitary waves which maintain their shape have many fascinating physical and mathematical properties. Here the authors observe waves trapped along three spatial dimensions in nematic liquid crystals due to an electric field and show that these director bullets can re-form after collisions.

25 July 2018 | doi: 10.1038/s41467-018-05101-y
Fluid dynamics  Liquid crystals 

Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins OPEN
Alexander P. Hynes, Geneviève M. Rousseau, Daniel Agudelo, Adeline Goulet, Beatrice Amigues, Jeremy Loehr, Dennis A. Romero, Christophe Fremaux, Philippe Horvath, Yannick Doyon, Christian Cambillau & Sylvain Moineau

Some phages carry genes coding for anti-CRISPR (Acr) proteins that interfere with the activity of bacterial CRISPR-Cas systems. Here, Hynes et al. characterize a new Acr family from streptococcal phages and investigate its potential in genome-editing applications.

25 July 2018 | doi: 10.1038/s41467-018-05092-w
CRISPR-Cas9 genome editing  Phage biology 

Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks OPEN
Richard C. Pelikan, Jennifer A. Kelly, Yao Fu, Caleb A. Lareau, Kandice L. Tessneer, Graham B. Wiley, Mandi M. Wiley, Stuart B. Glenn, John B. Harley, Joel M. Guthridge, Judith A. James, Martin J. Aryee, Courtney Montgomery & Patrick M. Gaffney

Disease risk variants can exert their influence on phenotypes by altering epigenome function. Here, Pelikan et al. show that variants inducing allelic imbalance in histone marks in lymphoblastoid cell lines from lupus patients are enriched in autoimmune disease haplotypes and influence gene expression.

25 July 2018 | doi: 10.1038/s41467-018-05328-9
Autoimmune diseases  Chromatin structure  Epigenomics  Quantitative trait loci 

Suppression of atom motion and metal deposition in mixed ionic electronic conductors OPEN
Pengfei Qiu, Matthias T. Agne, Yongying Liu, Yaqin Zhu, Hongyi Chen, Tao Mao, Jiong Yang, Wenqing Zhang, Sossina M. Haile, Wolfgang G. Zeier, Jürgen Janek, Ctirad Uher, Xun Shi, Lidong Chen & G. Jeffrey Snyder

Mixed ionic–electronic conductors are limited by material decomposition. Here the authors reveal the mechanism for atom migration and deposition in Cu2–δ(S,Se) materials based on a critical chemical potential difference and propose electronically conducting, ion-blocking interfaces to enhance stability.

25 July 2018 | doi: 10.1038/s41467-018-05248-8
Electrochemistry  Thermodynamics  Thermoelectric devices and materials  Thermoelectrics 

Higher activation barriers can lift exothermic rate restrictions in electron transfer and enable faster reactions OPEN
Kamila K. Mentel, Arménio Serra, Paulo E. Abreu & Luis G. Arnaut

A widely-assumed principle of chemical reactivity is that, for elementary reactions, higher activation barriers lead to slower reactions. Here, the authors show that some intramolecular electron transfer processes become faster as their apparent activation energies increase, contradicting chemical intuition.

25 July 2018 | doi: 10.1038/s41467-018-05267-5
Electron transfer  Reaction kinetics and dynamics 

Saccade metrics reflect decision-making dynamics during urgent choices OPEN
Joshua A. Seideman, Terrence R. Stanford & Emilio Salinas

Saccades have been extensively used to report choices in perceptual decision making studies yet little is known about the influence of covert decision-related processes on saccade metrics. Here, the authors demonstrate that saccade kinematics is a reliable tell about the degree of decision certainty.

25 July 2018 | doi: 10.1038/s41467-018-05319-w
Cortex  Decision  Neural encoding  Perception  Saccades 

Direct observation of polymer surface mobility via nanoparticle vibrations OPEN
Hojin Kim, Yu Cang, Eunsoo Kang, Bartlomiej Graczykowski, Maria Secchi, Maurizio Montagna, Rodney D. Priestley, Eric M. Furst & George Fytas

Measuring polymer surface dynamics is a challenge of importance to applications ranging from pressure-sensitive adhesives to nanopatterning. Here, the authors introduce a methodology of Brillouin light spectroscopy to reveal polymer surface mobility via nanoparticle vibrations.

25 July 2018 | doi: 10.1038/s41467-018-04854-w
Chemistry  Engineering  Nanoscience and technology 

Abp1 promotes Arp2/3 complex-dependent actin nucleation and stabilizes branch junctions by antagonizing GMF OPEN
Siyang Guo, Olga S. Sokolova, Johnson Chung, Shae Padrick, Jeff Gelles & Bruce L. Goode

Abp1, a type II actin nucleation promoting factor, is a known component of branched actin networks but its mechanism remains poorly understood. Here, the authors find that Abp1 enhances Arp2/3-mediated actin branch formation, and blocks ‘debranching’ by GMF, making it a pro-branching factor.

24 July 2018 | doi: 10.1038/s41467-018-05260-y
Actin  Cytoskeletal proteins 

Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer OPEN
Aurélie S. Cazet, Mun N. Hui, Benjamin L. Elsworth, Sunny Z. Wu, Daniel Roden, Chia-Ling Chan, Joanna N. Skhinas, Raphaël Collot, Jessica Yang, Kate Harvey, M. Zahied Johan, Caroline Cooper, Radhika Nair, David Herrmann, Andrea McFarland, Niantao Deng, Manuel Ruiz-Borrego, Federico Rojo, José M. Trigo, Susana Bezares et al.

Stromal cell recruitment, activation and crosstalk with cancer cells is poorly understood. Here, the authors demonstrate that cancer cell-derived Hedgehog ligand  triggers stromal remodeling that in turn induces a cancer-stem-cell like, drug-resistant phenotype of nearby cancer cells while treatment with smoothened inhibitors reverses these phenotypes.

24 July 2018 | doi: 10.1038/s41467-018-05220-6
Breast cancer  Cancer microenvironment  Cancer stem cells 

Interferon gene therapy reprograms the leukemia microenvironment inducing protective immunity to multiple tumor antigens OPEN
Giulia Escobar, Luigi Barbarossa, Giulia Barbiera, Margherita Norelli, Marco Genua, Anna Ranghetti, Tiziana Plati, Barbara Camisa, Chiara Brombin, Davide Cittaro, Andrea Annoni, Attilio Bondanza, Renato Ostuni, Bernhard Gentner & Luigi Naldini

An immune suppressive tumor microenvironment (TME) is a limitation for immunotherapy. Here the authors show that, in a B cell acute lymphoblastic leukemia mouse model, gene-based delivery of IFNα  reprograms the leukemia-induced immunosuppressive TME into immunostimulatory and enhances T-cell responses.

24 July 2018 | doi: 10.1038/s41467-018-05315-0
Cancer immunotherapy  Cancer microenvironment  Tumour immunology 

Rapid tremor migration and pore-pressure waves in subduction zones OPEN
Víctor M. Cruz-Atienza, Carlos Villafuerte & Harsha S. Bhat

Rapid tremor migration in subduction zones has been associated with aseismic, shear strain at the plate interface. Here, the authors develop a physical model that shows that pore-pressure waves at the plate interface are likely to generate secondary slip fronts triggering rapid tremor migrations with speeds and pathways similar to those observed in subduction zones.

24 July 2018 | doi: 10.1038/s41467-018-05150-3
Seismology  Tectonics 

In-orbit operation of an atomic clock based on laser-cooled 87Rb atoms OPEN
Liang Liu, De-Sheng Lü, Wei-Biao Chen, Tang Li, Qiu-Zhi Qu, Bin Wang, Lin Li, Wei Ren, Zuo-Ren Dong, Jian-Bo Zhao, Wen-Bing Xia, Xin Zhao, Jing-Wei Ji, Mei-Feng Ye, Yan-Guang Sun, Yuan-Yuan Yao, Dan Song, Zhao-Gang Liang, Shan-Jiang Hu, Dun-He Yu et al.

Cold atom clocks are among the most precise measuring devices and play key roles in everyday life and scientific explorations. Here the authors demonstrate the first in-orbit atomic clock using cold Rb atoms operating in microgravity and opening possibilities of space surveys and tests of fundamental physics.

24 July 2018 | doi: 10.1038/s41467-018-05219-z
Atomic and molecular interactions with photons  Quantum metrology  Quantum optics 

Excitatory synaptic dysfunction cell-autonomously decreases inhibitory inputs and disrupts structural and functional plasticity OPEN
Hai-yan He, Wanhua Shen, Lijun Zheng, Xia Guo & Hollis T. Cline

Both inhibitory and excitatory input development are shaped by activity, but one may be dependent on the other. Here, the authors examine plasticity of inhibitory inputs in vivo, as well as behavioral consequences in tadpoles where excitatory transmission has been impaired.

24 July 2018 | doi: 10.1038/s41467-018-05125-4
Cellular neuroscience  Synaptic plasticity 

NIR-II nanoprobes in-vivo assembly to improve image-guided surgery for metastatic ovarian cancer OPEN
Peiyuan Wang, Yong Fan, Lingfei Lu, Lu Liu, Lingling Fan, Mengyao Zhao, Yang Xie, Congjian Xu & Fan Zhang

Real-time fluorescence imaging in the NIR-II region offers non-invasive detection of ovarian metastatic tumors and their image-guided surgery. Here the authors describe NIR-II nanoprobes in vivo assembly for detection of disseminated ovarian cancer.

24 July 2018 | doi: 10.1038/s41467-018-05113-8
Cancer  Imaging  Nanobiotechnology  Nanoscience and technology 

A new Middle Jurassic diplodocoid suggests an earlier dispersal and diversification of sauropod dinosaurs OPEN
Xing Xu, Paul Upchurch, Philip D. Mannion, Paul M. Barrett, Omar R. Regalado-Fernandez, Jinyou Mo, Jinfu Ma & Hongan Liu

Diplodocoid dinosaurs are generally thought to have been excluded from East Asia due to the fragmentation of Pangaea. Here, Xu et al. describe the new diplodocoid Lingwulong shenqi from the Jurassic of East Asia, suggesting an earlier diversification and dispersal of diplodocoids and other sauropods.

24 July 2018 | doi: 10.1038/s41467-018-05128-1
Biogeography  Palaeoecology  Palaeontology 

Femtosecond formation dynamics of the spin Seebeck effect revealed by terahertz spectroscopy OPEN
Tom S. Seifert, Samridh Jaiswal, Joseph Barker, Sebastian T. Weber, Ilya Razdolski, Joel Cramer, Oliver Gueckstock, Sebastian F. Maehrlein, Lukas Nadvornik, Shun Watanabe, Chiara Ciccarelli, Alexey Melnikov, Gerhard Jakob, Markus Münzenberg, Sebastian T. B. Goennenwein, Georg Woltersdorf, Baerbel Rethfeld, Piet W. Brouwer, Martin Wolf, Mathias Kläui et al.

Probing spin-transfer in THz regime facilities new understanding of magnon control and applications. Here the authors show that spin Seebeck current arises as fast as metal electron thermalization by femtosecond laser pulse in YIG/Pt, which reveals its critical dependence on carrier dynamics after excitation.

24 July 2018 | doi: 10.1038/s41467-018-05135-2
Spintronics  Terahertz optics 

Introduction of pathogenic mutations into the mouse Psen1 gene by Base Editor and Target-AID OPEN
Hiroki Sasaguri, Kenichi Nagata, Misaki Sekiguchi, Ryo Fujioka, Yukio Matsuba, Shoko Hashimoto, Kaori Sato, Deepika Kurup, Takanori Yokota & Takaomi C. Saido

CRISPR-guided cytidine deaminases, including BE3 (Base Editor 3) and Target-AID (activation-induced cytidine deaminase), can covert C:G base pairs to T:A at target site. Here, the authors generate missense mutations of mouse Psen1 gene and find BE3 has higher editing efficiency than Target-AID.

24 July 2018 | doi: 10.1038/s41467-018-05262-w
Alzheimer's disease  CRISPR-Cas9 genome editing  Diseases  Neurochemistry 

Bottle-grade polyethylene furanoate from ring-opening polymerisation of cyclic oligomers OPEN
Jan-Georg Rosenboom, Diana Kay Hohl, Peter Fleckenstein, Giuseppe Storti & Massimo Morbidelli

The synthesis of polyethylene furanoate, a promising renewable resource-based bioplastic, still has challenges. Here the authors show that bottle-grade polyethylene furanoate can be obtained within minutes from ring-opening polymerisation of its cyclic oligomers, thereby avoiding degradation and discolouration.

24 July 2018 | doi: 10.1038/s41467-018-05147-y
Chemical engineering  Polymer synthesis  Polymers  Sustainability 

Prioritizing phylogenetic diversity captures functional diversity unreliably OPEN
Florent Mazel, Matthew W. Pennell, Marc W. Cadotte, Sandra Diaz, Giulio Valentino Dalla Riva, Richard Grenyer, Fabien Leprieur, Arne O. Mooers, David Mouillot, Caroline M. Tucker & William D. Pearse

An ongoing conservation question is if we can maintain functional diversity by optimizing for preservation of phylogenetic diversity. Here, Mazel et al. show that functional diversity increases with phylogenetic diversity in some clades but not others, and thus could be a risky conservation strategy.

23 July 2018 | doi: 10.1038/s41467-018-05126-3
Biodiversity  Conservation biology 

Discovery of a silicate rock-boring organism and macrobioerosion in fresh water OPEN
Ivan N. Bolotov, Olga V. Aksenova, Torkild Bakken, Christopher J. Glasby, Mikhail Yu. Gofarov, Alexander V. Kondakov, Ekaterina S. Konopleva, Manuel Lopes-Lima, Artyom A. Lyubas, Yu Wang, Andrey Yu. Bychkov, Agniya M. Sokolova, Kitti Tanmuangpak, Sakboworn Tumpeesuwan, Ilya V. Vikhrev, J. Bruce H. Shyu, Than Win & Oleg S. Pokrovsky

Macrobioerosion, the boring of rock and other hard substrates by living organisms, is used as a marker of marine paleo-environments. Here, Bolotov et al. describe a rock-boring mussel and its associated community from freshwater in Myanmar, demonstrating that macrobioerosion is a wider phenomenon.

23 July 2018 | doi: 10.1038/s41467-018-05133-4
Biodiversity  Biogeography  Freshwater ecology  Palaeoecology 

Single olfactory receptors set odor detection thresholds OPEN
Adam Dewan, Annika Cichy, Jingji Zhang, Kayla Miguel, Paul Feinstein, Dmitry Rinberg & Thomas Bozza

Odorous chemicals broadly activate subsets of olfactory receptors in the nose, but how individual receptors contribute to behavioral sensitivity is not clear. Here, the authors demonstrate that detection thresholds in mice are set solely by the highest affinity receptor for a given odorant.

23 July 2018 | doi: 10.1038/s41467-018-05129-0
Olfactory receptors  Olfactory system  Sensory processing 

Room-temperature pyro-catalytic hydrogen generation of 2D few-layer black phosphorene under cold-hot alternation OPEN
Huilin You, Yanmin Jia, Zheng Wu, Feifei Wang, Haitao Huang & Yu Wang

2D elemental materials, with their atomic-scale dimensions, present exciting opportunities for energy conversion applications. Here, the authors use few-layer black phosphorene to perform pyro-catalysis, in which thermal cycling the material induces hydrogen gas production and dye degradation.

23 July 2018 | doi: 10.1038/s41467-018-05343-w
Heterogeneous catalysis  Materials for energy and catalysis  Two-dimensional materials 

Microbial biogeography of 925 geothermal springs in New Zealand OPEN
Jean F. Power, Carlo R. Carere, Charles K. Lee, Georgia L. J. Wakerley, David W. Evans, Mathew Button, Duncan White, Melissa D. Climo, Annika M. Hinze, Xochitl C. Morgan, Ian R. McDonald, S. Craig Cary & Matthew B. Stott

Power et al. catalogue the microbial biodiversity and physicochemistry of around 1000 hotsprings across New Zealand, providing insights into the ecological conditions that drive community assembly in these ecosystems.

23 July 2018 | doi: 10.1038/s41467-018-05020-y
Biogeography  Environmental microbiology  Microbial ecology 

Lithography for robust and editable atomic-scale silicon devices and memories OPEN
Roshan Achal, Mohammad Rashidi, Jeremiah Croshaw, David Churchill, Marco Taucer, Taleana Huff, Martin Cloutier, Jason Pitters & Robert A. Wolkow

Manipulation at the atomic scale comes with a trade-off between simplicity and thermal stability. Here, Achal et al. demonstrate improved automated hydrogen lithography and repassivation, enabling error-corrected atomic writing of large-scale structures/memories that are stable at room temperature.

23 July 2018 | doi: 10.1038/s41467-018-05171-y
Electronics, photonics and device physics  Semiconductors  Surface patterning 

Non-integumentary melanosomes can bias reconstructions of the colours of fossil vertebrates OPEN
Maria E. McNamara, Jonathan S. Kaye, Michael J. Benton, Patrick J. Orr, Valentina Rossi, Shosuke Ito & Kazumasa Wakamatsu

The colour of extinct animals has been inferred from fossilized melanosomes – organelles rich in melanin. Here, the authors show that internal melanosomes that do not contribute to colour are abundant in some extant vertebrates and may redistribute during fossilization, necessitating caution in interpreting fossil colour.

23 July 2018 | doi: 10.1038/s41467-018-05148-x

A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer OPEN
Tomoko Saito, Atsushi Niida, Ryutaro Uchi, Hidenari Hirata, Hisateru Komatsu, Shotaro Sakimura, Shuto Hayashi, Sho Nambara, Yosuke Kuroda, Shuhei Ito, Hidetoshi Eguchi, Takaaki Masuda, Keishi Sugimachi, Taro Tobo, Haruto Nishida, Tsutomu Daa, Kenichi Chiba, Yuichi Shiraishi, Tetsuichi Yoshizato, Masaaki Kodama et al.

Advanced colorectal cancers are characterised by intra-tumour heterogeneity dictated by neutral evolution. Here the authors analyse early colorectal tumours by whole-exome sequencing and find that Darwinian evolution determines the fate of early lesions in colorectal adenoma and carcinoma in situ.

23 July 2018 | doi: 10.1038/s41467-018-05226-0
Colorectal cancer  Tumour heterogeneity 

The conformational wave in capsaicin activation of transient receptor potential vanilloid 1 ion channel OPEN
Fan Yang, Xian Xiao, Bo Hyun Lee, Simon Vu, Wei Yang, Vladimir Yarov-Yarovoy & Jie Zheng

The capsaicin receptor TRPV1 has been structurally characterized, but the capsaicin activation dynamics remain elusive. Here authors use fluorescent unnatural amino acid incorporation, computational modeling and Φ-analysis to derive the capsaicin-bound open state model and reveal the capsaicin induced conformational changes.

23 July 2018 | doi: 10.1038/s41467-018-05339-6
Permeation and transport  Receptor pharmacology  Transient receptor potential channels 

Atomic-level insight into super-efficient electrocatalytic oxygen evolution on iron and vanadium co-doped nickel (oxy)hydroxide OPEN
Jian Jiang, Fanfei Sun, Si Zhou, Wei Hu, Hao Zhang, Jinchao Dong, Zheng Jiang, Jijun Zhao, Jianfeng Li, Wensheng Yan & Mei Wang

While splitting water could provide a renewable way to produce fuel, highly active catalysts are needed to overcome water oxidation’s sluggish kinetics. Here, authors gain atomic-level insight on metal ion synergetic interactions that boost water oxidation performances in co-doped nickel hydroxide.

23 July 2018 | doi: 10.1038/s41467-018-05341-y
Characterization and analytical techniques  Electrocatalysis  Solid-state chemistry 

Programmed loading and rapid purification of engineered bacterial microcompartment shells OPEN
Andrew Hagen, Markus Sutter, Nancy Sloan & Cheryl A. Kerfeld

Bacterial microcompartments are protein-bound organelles encapsulating segments of metabolic pathways. Here the authors functionalise shell proteins to facilitate facile purification and enable cargo encapsulation via covalent linkage.

23 July 2018 | doi: 10.1038/s41467-018-05162-z
Metabolic engineering  Microbiology techniques  Protein design 

The ubiquitin ligase UBR5 suppresses proteostasis collapse in pluripotent stem cells from Huntington’s disease patients OPEN
Seda Koyuncu, Isabel Saez, Hyun Ju Lee, Ricardo Gutierrez-Garcia, Wojciech Pokrzywa, Azra Fatima, Thorsten Hoppe & David Vilchez

Induced pluripotent stem cells (iPSCs) suppress the aggregation of Huntington’s disease (HD) polyQ-expanded huntingtin (HTT). Here the authors show that proteasome activity determines the levels of mutant HTT in HD-iPSCs and find that UBR5 is a modulator of super-vigilant proteostasis of iPSCs.

23 July 2018 | doi: 10.1038/s41467-018-05320-3
Huntington's disease  Mechanisms of disease  Proteasome  Protein quality control  Ubiquitin ligases 

Cryopreservation of infectious Cryptosporidium parvum oocysts OPEN
Justyna J. Jaskiewicz, Rebecca D. Sandlin, Anisa A. Swei, Giovanni Widmer, Mehmet Toner & Saul Tzipori

Research on Cryptosporidium parasites, a major cause of acute infant diarrhea, is hampered by the short shelf life of oocysts, thus requiring routine propagation in laboratory animals. Here, the authors report a method to cryopreserve viable and infectious Cryptosporidium oocysts by ultra-fast cooling.

23 July 2018 | doi: 10.1038/s41467-018-05240-2
Biological techniques  Diseases  Microbiology  Parasitology 

Unraveling substituent effects on the glass transition temperatures of biorenewable polyesters OPEN
Xiaopeng Yu, Junteng Jia, Shu Xu, Ka Un Lao, Maria J. Sanford, Ramesh K. Ramakrishnan, Sergei I. Nazarenko, Thomas R. Hoye, Geoffrey W. Coates & Robert A. DiStasio Jr.

Biorenewable feedstocks allow the design of polymers with targeted properties and functionalities. Here the authors report a series of high glass transition temperature sugar-based polyesters and investigate how substituents affect their thermal properties.

23 July 2018 | doi: 10.1038/s41467-018-05269-3
Homogeneous catalysis  Polymer characterization  Polymer synthesis  Sustainability 

Signatures of transient Wannier-Stark localization in bulk gallium arsenide OPEN
C. Schmidt, J. Bühler, A.-C. Heinrich, J. Allerbeck, R. Podzimski, D. Berghoff, T. Meier, W. G. Schmidt, C. Reichl, W. Wegscheider, D. Brida & A. Leitenstorfer

In strong enough electric fields the non-linear response of electrons in crystals is expected to lead to spatial localization but so far this has only been seen in artificial structures. Schmidt et al. present evidence of this Wannier-Stark localization effect in bulk GaAs driven by intense mid-infrared pulses.

23 July 2018 | doi: 10.1038/s41467-018-05229-x
Electronic properties and materials  Semiconductors  Terahertz optics 

In situ topographical chemical and electrical imaging of carboxyl graphene oxide at the nanoscale OPEN
Weitao Su, Naresh Kumar, Andrey Krayev & Marc Chaigneau

Mapping the distribution of functional groups on 2D materials with high resolution remains challenging. Here, the authors combine tip-enhanced Raman spectroscopy and Kelvin probe force microscopy to simultaneously examine the topography, chemical composition and electronic nature of graphene oxide surfaces with nanoscale spatial resolution.

23 July 2018 | doi: 10.1038/s41467-018-05307-0
Nanoscale materials  Optical properties and devices  Raman spectroscopy 

Middle Eocene greenhouse warming facilitated by diminished weathering feedback OPEN
Robin van der Ploeg, David Selby, Margot J. Cramwinckel, Yang Li, Steven M. Bohaty, Jack J. Middelburg & Appy Sluijs

Silicate rock weathering represents a negative feedback mechanism that regulates atmospheric CO2 levels on geological timescales. Here, the authors show that a diminished silicate weathering feedback may have set the stage for greenhouse warming and ocean acidification during the Middle Eocene, ~40 million years ago.

23 July 2018 | doi: 10.1038/s41467-018-05104-9
Carbon cycle  Climate and Earth system modelling  Element cycles  Palaeoceanography  Palaeoclimate 

Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease OPEN
Xu Zhang, Shelley A. Deeke, Zhibin Ning, Amanda E. Starr, James Butcher, Jennifer Li, Janice Mayne, Kai Cheng, Bo Liao, Leyuan Li, Ruth Singleton, David Mack, Alain Stintzi & Daniel Figeys

Gut microbial dysbiosis has been implicated in the pathogenesis of inflammatory bowel disease. Here, the authors examine host-microbiota protein interactions that occur in inflammatory bowel disease; they show an upregulation in proteins related to antimicrobial activities, and alterations in intestinal extracellular vesicles that are associated with aberrant microbiota-interactions.

20 July 2018 | doi: 10.1038/s41467-018-05357-4
Gastrointestinal diseases  Microbiome  Paediatric research  Proteomics 

A coastal coccolithophore maintains pH homeostasis and switches carbon sources in response to ocean acidification OPEN
Yi-Wei Liu, Robert A. Eagle, Sarah M. Aciego, Rosaleen E. Gilmore & Justin B. Ries

Calcifying species have diverse responses to ocean acidification, but the underlying mechanisms are not well-constrained. Here, Liu et al. show that O. neapolitana maintains its calcification site pH and utilizes more CO2 compared to HCO3 to support its growth under high-CO2 conditions.

20 July 2018 | doi: 10.1038/s41467-018-04463-7
Biogeochemistry  Climate-change impacts 

Non-collinear spin states in bottom-up fabricated atomic chains OPEN
Manuel Steinbrecher, Roman Rausch, Khai Ton That, Jan Hermenau, Alexander A. Khajetoorians, Michael Potthoff, Roland Wiesendanger & Jens Wiebe

Scanning tunnelling microscopes can be used to accurately position atoms and measure emergent behaviour arising from interatomic couplings. Here, the authors fabricate a model spin chain and show the formation of a tunable spiral state due to competing Heisenberg and Dzyaloshinskii-Moriya interactions

20 July 2018 | doi: 10.1038/s41467-018-05364-5
Magnetic properties and materials  Spintronics 

Simplified ChIP-exo assays OPEN
Matthew J. Rossi, William K. M. Lai & B. Franklin Pugh

While ChIP-exo is low noise and highly informative regarding genome-wide binding proteins, libraries are difficult to construct. Here the authors present a simplified ChIP-exo method for high-resolution detection of interactions.

20 July 2018 | doi: 10.1038/s41467-018-05265-7
DNA  Genomics 

Differential temporal salience of earning and saving OPEN
Kesong Hu, Eve De Rosa & Adam K. Anderson

Economists have observed that many people seem unwilling to save for the future. Here, the authors show that earning and saving are subject to a basic asymmetry in attentional choice, such that cues that are associated with saving are perceived as occurring later than cues associated with earning.

20 July 2018 | doi: 10.1038/s41467-018-05201-9
Human behaviour  Perception 

Direct reprogramming of fibroblasts into neural stem cells by single non-neural progenitor transcription factor Ptf1a OPEN
Dongchang Xiao, Xiaoning Liu, Min Zhang, Min Zou, Qinqin Deng, Dayu Sun, Xuting Bian, Yulong Cai, Yanan Guo, Shuting Liu, Shengguo Li, Evelyn Shiang, Hongyu Zhong, Lin Cheng, Haiwei Xu, Kangxin Jin & Mengqing Xiang

Fibroblasts can be reprogrammed into induced neural stem cells (iNSCs) using transcription factors expressed in neural progenitors. Here the authors show that Ptf1a, which is normally expressed in postmitotic neurons, can reprogram fibroblasts to iNSCs through Notch independent interaction with Rbpj.

20 July 2018 | doi: 10.1038/s41467-018-05209-1
Alzheimer's disease  Neural stem cells 

The Medusae Fossae Formation as the single largest source of dust on Mars OPEN
Lujendra Ojha, Kevin Lewis, Suniti Karunatillake & Mariek Schmidt

Martian dust is globally enriched in S and Cl and has a distinct mean S:Cl ratio. Here the authors identify that the largest potential source region for Martian dust based on analysis of elemental abundance data may be the Medusae Fossae Formation.

20 July 2018 | doi: 10.1038/s41467-018-05291-5
Geochemistry  Mineralogy  Planetary science 

Collective magnetism in an artificial 2D XY spin system OPEN
Naëmi Leo, Stefan Holenstein, Dominik Schildknecht, Oles Sendetskyi, Hubertus Luetkens, Peter M. Derlet, Valerio Scagnoli, Diane Lançon, José R. L. Mardegan, Thomas Prokscha, Andreas Suter, Zaher Salman, Stephen Lee & Laura J. Heyderman

Magnetic metamaterials can be designed to provide models of frustrated systems that allow theoretical predictions to be experimentally tested. Here the authors realise a 2D XY model with dipolar interactions and find behaviour consistent with predictions of a low-temperature ordered state.

20 July 2018 | doi: 10.1038/s41467-018-05216-2
Magnetic properties and materials  Phase transitions and critical phenomena  Statistical physics, thermodynamics and nonlinear dynamics 

Co-transmission of acetylcholine and GABA regulates hippocampal states OPEN
Virág T. Takács, Csaba Cserép, Dániel Schlingloff, Balázs Pósfai, András Szőnyi, Katalin E. Sos, Zsuzsanna Környei, Ádám Dénes, Attila I. Gulyás, Tamás F. Freund & Gábor Nyiri

Acetylcholine (ACh) release in the central nervous system is thought to be unitary and mediated non-synaptically in volume transmission. Here, Takács and colleagues show cholinergic terminals juxtapose GABAergic synapses anatomically and functionally, and GABA and ACh molecules are co-transmitted.

20 July 2018 | doi: 10.1038/s41467-018-05136-1
Cellular neuroscience  Neurotransmitters 

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism OPEN
Amir Zarrinpar, Amandine Chaix, Zhenjiang Z. Xu, Max W. Chang, Clarisse A. Marotz, Alan Saghatelian, Rob Knight & Satchidananda Panda

Antibiotic-induced microbiome depletion is one of the most common approaches to modulate the gut microbiome. Here the authors demonstrate that it affects gut homeostasis and glucose metabolism by decreasing luminal short chain fatty acids and leading to a shift of energy utilization by colonocytes.

20 July 2018 | doi: 10.1038/s41467-018-05336-9
Homeostasis  Metabolomics  Microbiome 

Dissecting myosin-5B mechanosensitivity and calcium regulation at the single molecule level OPEN
Lucia Gardini, Sarah M. Heissler, Claudia Arbore, Yi Yang, James R. Sellers, Francesco S. Pavone & Marco Capitanio

Myosin-5B is an actin-based motor important for endosome recycling, but the molecular mechanism underlying its motility remains unknown. Here authors use single molecule imaging and high-speed laser tweezers to dissect the mechanoenzymatic properties of myosin-5B, which shows processive motility with peculiar mechanosensitivity.

20 July 2018 | doi: 10.1038/s41467-018-05251-z
Intracellular movement  Motor protein function  Optical tweezers  Single-molecule biophysics 

Abnormal RNA stability in amyotrophic lateral sclerosis OPEN
E. M. Tank, C. Figueroa-Romero, L. M. Hinder, K. Bedi, H. C. Archbold, X. Li, K. Weskamp, N. Safren, X. Paez-Colasante, C. Pacut, S. Thumma, M. T. Paulsen, K. Guo, J. Hur, M. Ljungman, E. L. Feldman & S. J. Barmada

RNA instability may be a contributing factor in amyotrophic lateral sclerosis (ALS). Here the authors carry out genome-wide assessment of RNA synthesis and stability in cells derived from patients with C9orf72 ALS, sporadic ALS and healthy controls.

20 July 2018 | doi: 10.1038/s41467-018-05049-z
Amyotrophic lateral sclerosis  RNA 

Highly fractionated chromium isotopes in Mesoproterozoic-aged shales and atmospheric oxygen OPEN
Donald E. Canfield, Shuichang Zhang, Anja B. Frank, Xiaomei Wang, Huajian Wang, Jin Su, Yuntao Ye & Robert Frei

There is a long standing debate whether low atmospheric oxygen levels during the Mesoproterozoic Era hindered the evolution of crown-group animals. Here, the authors show with shale-hosted chromium isotopes that sufficient atmospheric oxygen for crown-group animals likely predated their evolution by over 400 million years.

20 July 2018 | doi: 10.1038/s41467-018-05263-9
Element cycles  Palaeontology 

An autophagy assay reveals the ESCRT-III component CHMP2A as a regulator of phagophore closure OPEN
Yoshinori Takahashi, Haiyan He, Zhenyuan Tang, Tatsuya Hattori, Ying Liu, Megan M. Young, Jacob M. Serfass, Longgui Chen, Melat Gebru, Chong Chen, Carson A. Wills, Jennifer M. Atkinson, Han Chen, Thomas Abraham & Hong-Gang Wang

During autophagy, phagophores elongate to form double-membrane vesicles but the mechanism behind their closure is unknown. Here, the authors develop an autophagy assay and find a role for the endosomal sorting complexes required for transport component CHMP2A as a phagophore closure regulator.

20 July 2018 | doi: 10.1038/s41467-018-05254-w
ESCRT  Macroautophagy  Molecular biology 

Spin inversion in graphene spin valves by gate-tunable magnetic proximity effect at one-dimensional contacts OPEN
Jinsong Xu, Simranjeet Singh, Jyoti Katoch, Guanzhong Wu, Tiancong Zhu, Igor Žutić & Roland K. Kawakami

Owing to its long spin diffusion length, graphene shows promise for spintronics applications, especially when encapsulated within hexagonal boron nitride. Here, the authors demonstrate gate-tunable spin transport in encapsulated graphene-based spin valves with one-dimensional ferromagnetic edge contacts via magnetic proximity effect.

20 July 2018 | doi: 10.1038/s41467-018-05358-3
Electronic properties and devices  Spintronics 

Arc-like magmas generated by mélange-peridotite interaction in the mantle wedge OPEN
E. A. Codillo, V. Le Roux & H. R. Marschall

Mélange rocks are predicted to form at the slab-mantle interface in most subduction zones, but their role in arc magmatism is still debated. Here, the authors show that melting of peridotite hybridized by mélange rocks produces melts that carry the major and trace element abundances of natural arc magmas.

20 July 2018 | doi: 10.1038/s41467-018-05313-2
Geochemistry  Petrology  Solid Earth sciences 

TIGIT+ iTregs elicited by human regulatory macrophages control T cell immunity OPEN
Paloma Riquelme, Jan Haarer, Anja Kammler, Lisa Walter, Stefan Tomiuk, Norbert Ahrens, Anja K. Wege, Ivan Goecze, Daniel Zecher, Bernhard Banas, Rainer Spang, Fred Fändrich, Manfred B. Lutz, Birgit Sawitzki, Hans J. Schlitt, Jordi Ochando, Edward K. Geissler & James A. Hutchinson

Regulatory macrophages (Mreg) can directly suppress T effector cell responses. Here the authors show that human Mreg also elicit TIGIT+ regulatory T cells by integrating multiple differentiation signals, and that donor Mreg-induced recipient Tregs may promote kidney transplant acceptance in patients.

20 July 2018 | doi: 10.1038/s41467-018-05167-8
Allotransplantation  Immunosuppression  Monocytes and macrophages  Regulatory T cells 

Concerted pulsatile and graded neural dynamics enables efficient chemotaxis in C. elegans OPEN
Eyal Itskovits, Rotem Ruach & Alon Zaslaver

Finding one’s way to a food source along a complex gradient is central to survival for many animals. Here, the authors report that in C. elegans, the distinct response dynamics of two sensory neurons to odor gradients can support a navigation model more efficient than the biased-random walk.

20 July 2018 | doi: 10.1038/s41467-018-05151-2
Sensory processing  Systems analysis 

Accelerated microfluidic native chemical ligation at difficult amino acids toward cyclic peptides OPEN
Nathalie Ollivier, Thomas Toupy, Ruben C. Hartkoorn, Rémi Desmet, Jean-Christophe M. Monbaliu & Oleg Melnyk

Flow-based peptide synthesis is a well-established method, yet difficult to combine with native chemical ligation (NCL), the go-to method for peptide cyclization. Here, the authors developed a microfluidic procedure for peptide cyclization within minutes, using NCL and an SEA alkylthioester peptide.

20 July 2018 | doi: 10.1038/s41467-018-05264-8
Automation  Flow chemistry  Synthetic chemistry methodology 

Recurrent homozygous deletion of DROSHA and microduplication of PDE4DIP in pineoblastoma OPEN
Matija Snuderl, Kasthuri Kannan, Elke Pfaff, Shiyang Wang, James M. Stafford, Jonathan Serrano, Adriana Heguy, Karina Ray, Arline Faustin, Olga Aminova, Igor Dolgalev, Stacie L. Stapleton, David Zagzag, Luis Chiriboga, Sharon L. Gardner, Jeffrey H. Wisoff, John G. Golfinos, David Capper, Volker Hovestadt, Marc K. Rosenblum et al.

Pineoblastoma is a highly aggressive and rare childhood brain cancer, and the genetic drivers of sporadic pineoblastoma are unknown. Here, the authors genomically interrogated pediatric and adult pineoblastomas and found novel variants including recurrent homozygous deletions of DROSHA.

20 July 2018 | doi: 10.1038/s41467-018-05029-3
Cancer epigenetics  Cancer genomics  CNS cancer  Paediatric cancer 

High-throughput discovery of organic cages and catenanes using computational screening fused with robotic synthesis OPEN
R. L. Greenaway, V. Santolini, M. J. Bennison, B. M. Alston, C. J. Pugh, M. A. Little, M. Miklitz, E. G. B. Eden-Rump, R. Clowes, A. Shakil, H. J. Cuthbertson, H. Armstrong, M. E. Briggs, K. E. Jelfs & A. I. Cooper

Supramolecular assemblies remain of great importance to a variety of fields, yet their targeted design and synthesis remains highly challenging. Here, Cooper and colleagues combine computational screening with high-throughput robotic synthesis and discover 33 new organic cage molecules that form cleanly in one-pot syntheses.

20 July 2018 | doi: 10.1038/s41467-018-05271-9
Computational chemistry  Interlocked molecules  Molecular capsules  Self-assembly 

Abrupt high-latitude climate events and decoupled seasonal trends during the Eemian OPEN
J. Sakari Salonen, Karin F. Helmens, Jo Brendryen, Niina Kuosmanen, Minna Väliranta, Simon Goring, Mikko Korpela, Malin Kylander, Annemarie Philip, Anna Plikk, Hans Renssen & Miska Luoto

The Eemian period (120 ka) is considered a past analogue for future climatic warming, yet data from the high latitudes remains sparse. Here, the authors show that in Northern Europe, the Eemian saw dramatic climatic shifts, linked to changes in Earth’s orbit and North Atlantic oceanic circulation.

20 July 2018 | doi: 10.1038/s41467-018-05314-1
Climate change  Palaeoclimate  Palaeoecology 

Spatial frequency sensitivity in macaque midbrain OPEN
Chih-Yang Chen, Lukas Sonnenberg, Simone Weller, Thede Witschel & Ziad M. Hafed

In primates, the superior colliculus (SC) contributes to rapid visual exploration with saccades. Here the authors show that the superior colliculus preferentially represents low spatial frequencies, which are the most prevalent in natural scenes.

20 July 2018 | doi: 10.1038/s41467-018-05302-5
Brainstem  Pattern vision  Saccades  Superior colliculus 

Microscopic mechanism of biphasic interface relaxation in lithium iron phosphate after delithiation OPEN
Shunsuke Kobayashi, Akihide Kuwabara, Craig A. J. Fisher, Yoshio Ukyo & Yuichi Ikuhara

Improving the performance of Li-ion batteries relies on understanding charging/discharging mechanisms. Here the authors visualize the interfacial structure and composition of a partially delithiated lithium iron phosphate single crystal as a function of time, revealing a mechanism of relaxation.

20 July 2018 | doi: 10.1038/s41467-018-05241-1
Batteries  Imaging techniques  Transmission electron microscopy 

How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins OPEN
Matthieu Chavent, Anna L. Duncan, Patrice Rassam, Oliver Birkholz, Jean Hélie, Tyler Reddy, Dmitry Beliaev, Ben Hambly, Jacob Piehler, Colin Kleanthous & Mark S. P. Sansom

In Escherichia coli, outer membrane protein (OMP) cluster and form islands, but the origin and behaviour of those clusters remains poorly understood. Here authors use coarse grained molecular dynamics simulation and show that their mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs.

20 July 2018 | doi: 10.1038/s41467-018-05255-9
Biophysical chemistry  Computational biophysics 

Drug capture materials based on genomic DNA-functionalized magnetic nanoparticles OPEN
Carl M. Blumenfeld, Michael D. Schulz, Mariam S. Aboian, Mark W. Wilson, Terilynn Moore, Steven W. Hetts & Robert H. Grubbs

Chemotherapy agents are prone to producing severe side-effects, and their sequestration prior to their entering of the circulatory system is thus highly desirable. Here, the authors functionalize iron oxide nanoparticles with genomic DNA and achieve sequestration of doxorubicin, cisplatin, and epirubicin from biological solutions.

20 July 2018 | doi: 10.1038/s41467-018-05305-2
Biomedical materials  Chemotherapy  Magnetic materials 

Hollow-core conjoined-tube negative-curvature fibre with ultralow loss OPEN
Shou-fei Gao, Ying-ying Wang, Wei Ding, Dong-liang Jiang, Shuai Gu, Xin Zhang & Pu Wang

Countering the optical network ‘capacity crunch’ requires developments in optical fibres. Here, the authors report a hollow-core fibre with conjoined tubes in the cladding and a negative-curvature core shape. It exhibits a transmission loss of 2 dB/km at 1512 nm and less than 16 dB/km bandwidth in the 1302–1637 nm range.

19 July 2018 | doi: 10.1038/s41467-018-05225-1
Fibre optics and optical communications  Photonic devices 

CTC1-STN1 terminates telomerase while STN1-TEN1 enables C-strand synthesis during telomere replication in colon cancer cells OPEN
Xuyang Feng, Shih-Jui Hsu, Anukana Bhattacharjee, Yongyao Wang, Jiajie Diao & Carolyn M. Price

The human CST complex (CTC1-STN1-TEN1) is essential for telomere homeostasis. Here the authors dissect the roles of individual CST subunits in telomere length maintenance through regulation of telomerase-mediated G-strand synthesis and DNA polymerase-mediated C-strand synthesis in colon cancer cells.

19 July 2018 | doi: 10.1038/s41467-018-05154-z
DNA  Telomeres 

FoxM1 repression during human aging leads to mitotic decline and aneuploidy-driven full senescence OPEN
Joana Catarina Macedo, Sara Vaz, Bjorn Bakker, Rui Ribeiro, Petra Lammigje Bakker, Jose Miguel Escandell, Miguel Godinho Ferreira, René Medema, Floris Foijer & Elsa Logarinho

Evidence for mitotic decline in aged cells and for aneuploidy-driven progression into full senescence is limited. Here, the authors find that in aged cells, mitotic gene repression leads to increased chromosome mis-segregation and aneuploidy that triggers permanent cell cycle arrest and full senescence.

19 July 2018 | doi: 10.1038/s41467-018-05258-6
Aneuploidy  Chromosome segregation  Mechanisms of disease  Senescence 

HIV-1 targets L-selectin for adhesion and induces its shedding for viral release OPEN
Joseph Kononchik, Joanna Ireland, Zhongcheng Zou, Jason Segura, Genevieve Holzapfel, Ashley Chastain, Ruipeng Wang, Matthew Spencer, Biao He, Nicole Stutzman, Daiji Kano, James Arthos, Elizabeth Fischer, Tae-Wook Chun, Susan Moir & Peter Sun

HIV binding is mediated via CD4 and chemokine co-receptors, but this does not explain the preferential infection of central memory CD4+ T cells. Here the authors show HIV targets L-selectin, induces shedding from the infected cell, and inhibition of L-selectin reduces HIV infection and release.

19 July 2018 | doi: 10.1038/s41467-018-05197-2
HIV infections 

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota OPEN
Zheng-Shuang Hua, Yan-Ni Qu, Qiyun Zhu, En-Min Zhou, Yan-Ling Qi, Yi-Rui Yin, Yang-Zhi Rao, Ye Tian, Yu-Xian Li, Lan Liu, Cindy J. Castelle, Brian P. Hedlund, Wen-Sheng Shu, Rob Knight & Wen-Jun Li

The phylum of archaea Aigarchaeota is poorly characterized due to limited genomic sampling. Here, Hua and colleagues use genome-resolved metagenome sequencing to reconstruct six hot spring strains of Aigarchaeota and then infer their metabolism and evolutionary history.

19 July 2018 | doi: 10.1038/s41467-018-05284-4
Archaeal genomics  Archaeal physiology  Metagenomics  Molecular evolution 

Probing the coordination and function of Fe4S4 modules in nitrogenase assembly protein NifB OPEN
Lee A. Rettberg, Jarett Wilcoxen, Chi Chung Lee, Martin T. Stiebritz, Kazuki Tanifuji, R. David Britt & Yilin Hu

NifB is a key enzyme in the biosynthesis pathway of the nitrogenase FeMo cofactor. Here, the authors investigate the maturation of its iron-sulfur clusters by EPR and biochemical analyses, showing how individual precursor clusters participate in the formation of the final iron-sulfur cluster.

19 July 2018 | doi: 10.1038/s41467-018-05272-8
Biosynthesis  Metalloproteins 

Iridium-catalyzed reductive Ugi-type reactions of tertiary amides OPEN
Lan-Gui Xie & Darren J. Dixon

Chemical transformation of amides is normally occurring under harsh conditions. Here, the authors report a mild iridium-catalyzed reductive Ugi-type coupling of tertiary amides, isocyanides and (thio)acetic acid or trimethylsilyl azide to give homologous, bioactive amine products.

19 July 2018 | doi: 10.1038/s41467-018-05192-7
Combinatorial libraries  Homogeneous catalysis  Synthetic chemistry methodology 

Microglia permit climbing fiber elimination by promoting GABAergic inhibition in the developing cerebellum OPEN
Hisako Nakayama, Manabu Abe, Chie Morimoto, Tadatsune Iida, Shigeo Okabe, Kenji Sakimura & Kouichi Hashimoto

In the mammalian cerebellum, surplus synapses between climbing fibers (CF) and Purkinje cells (PC) are developmentally pruned. Here, Nakayama and colleagues show that ablation of microglia impairs pruning of CF-PC synapses because of dysfunction of GABAergic inhibition prerequisite for pruning.

19 July 2018 | doi: 10.1038/s41467-018-05100-z
Cellular neuroscience  Microglia  Neuronal physiology  Synaptic development 

Hyperuniformity with no fine tuning in sheared sedimenting suspensions OPEN
Jikai Wang, J. M. Schwarz & Joseph D. Paulsen

Suspensions appear in a wide range of industrial settings, and dispersing particles in a uniform manner throughout a fluid remains challenging for applications. Wang et al. obtain hyperuniform mixtures without fine tuning by harnessing self-organized criticality due to slow sedimentation and shear.

19 July 2018 | doi: 10.1038/s41467-018-05195-4
Colloids  Condensed-matter physics  Self-assembly  Soft materials  Statistical physics, thermodynamics and nonlinear dynamics 

Quantifying the spatial spread of dengue in a non-endemic Brazilian metropolis via transmission chain reconstruction OPEN
Giorgio Guzzetta, Cecilia A. Marques-Toledo, Roberto Rosà, Mauro Teixeira & Stefano Merler

There is increasing urgency to understand the spatiotemporal dynamics of dengue in non-endemic regions. Here, the authors reconstruct likely dengue transmission chains in the city of Porto Alegre based on geo-located cases only, and find that most transmission events occur over short-distances.

19 July 2018 | doi: 10.1038/s41467-018-05230-4
Epidemiology  Infectious diseases  Statistical methods 

Gate-controlled quantum dots and superconductivity in planar germanium OPEN
N. W. Hendrickx, D. P. Franke, A. Sammak, M. Kouwenhoven, D. Sabbagh, L. Yeoh, R. Li, M. L. V. Tagliaferri, M. Virgilio, G. Capellini, G. Scappucci & M. Veldhorst

Superconductor–semiconductor hybrid systems can bring together physical properties that are promising for fast and coherent quantum technology. Here, Hendrickx et al. realize such a system in planar germanium heterostructures demonstrating excellent quantum dots and tunable Josephson supercurrents.

19 July 2018 | doi: 10.1038/s41467-018-05299-x
Quantum dots  Superconducting devices  Superconducting properties and materials 

Mapping the sensing spots of aerolysin for single oligonucleotides analysis OPEN
Chan Cao, Meng-Yin Li, Nuria Cirauqui, Ya-Qian Wang, Matteo Dal Peraro, He Tian & Yi-Tao Long

Nanopores are an emerging powerful single-molecule method of DNA sequencing. Here the authors map the structure of aerolysin for use as a nanopore and show detection of modified and unmodified nucleobases.

19 July 2018 | doi: 10.1038/s41467-018-05108-5
DNA  Nanopores 

Designing a norepinephrine optical tracer for imaging individual noradrenergic synapses and their activity in vivo OPEN
Matthew Dunn, Adam Henke, Samuel Clark, Yekaterina Kovalyova, Kimberly A. Kempadoo, Richard J. Karpowicz Jr., Eric R. Kandel, David Sulzer & Dalibor Sames

The noradrenergic system plays numerous physiological roles but tools to study it are scarce. Here the authors develop a fluorescent analogue of norepinephrine that can be used to label noradrenergic neurons and the synaptic vesicles, and use it to measure single synaptic vesicle release sites in living mice.

19 July 2018 | doi: 10.1038/s41467-018-05075-x
Imaging and sensing  Synaptic transmission  Transporters 

Identification of dynamic undifferentiated cell states within the male germline OPEN
Hue M. La, Juho-Antti Mäkelä, Ai-Leen Chan, Fernando J. Rossello, Christian M. Nefzger, Julien M. D. Legrand, Mia De Seram, Jose M. Polo & Robin M. Hobbs

Sustained spermatogenesis depends on stem cell activity which is contained within a population of undifferentiated spermatogonia. Here, the authors identify a new population of undifferentiated spermatogonia in adult testis that expresses the transcription factor PDX1 and has stem cell capacity.

19 July 2018 | doi: 10.1038/s41467-018-04827-z
Adult stem cells  Regeneration  Stem-cell niche 

Impaired recruitment of dopamine neurons during working memory in mice with striatal D2 receptor overexpression OPEN
Sevil Duvarci, Eleanor H. Simpson, Gaby Schneider, Eric R. Kandel, Jochen Roeper & Torfi Sigurdsson

Disrupted dopamine neuron firing is thought to contribute to cognitive dysfunction in psychiatric disorders. Here the authors show that mice overexpressing D2R in the striatum, commonly seen in schizophrenia, are also impaired in recruitment of dopamine neurons during working memory performance.

19 July 2018 | doi: 10.1038/s41467-018-05214-4
Neural circuits  Schizophrenia  Working memory 

Enzymatic one-step ring contraction for quinolone biosynthesis OPEN
Shinji Kishimoto, Kodai Hara, Hiroshi Hashimoto, Yuichiro Hirayama, Pier Alexandre Champagne, Kendall N. Houk, Yi Tang & Kenji Watanabe

Viridicatin is a fungal alkaloid. Here, the authors identify and characterize the cyclopenase that catalyzes the last step of its biosynthesis in Aspergillus nidulans, the conversion of cyclopenin to viridicatin, and find that the reaction proceeds via an unusual elimination mechanism.

19 July 2018 | doi: 10.1038/s41467-018-05221-5
Biocatalysis  Biosynthesis  Enzyme mechanisms 

Assessment of the impact of shared brain imaging data on the scientific literature OPEN
Michael P. Milham, R. Cameron Craddock, Jake J. Son, Michael Fleischmann, Jon Clucas, Helen Xu, Bonhwang Koo, Anirudh Krishnakumar, Bharat B. Biswal, F. Xavier Castellanos, Stan Colcombe, Adriana Di Martino, Xi-Nian Zuo & Arno Klein

Data sharing is recognized as a way to promote scientific collaboration and reproducibility, but some are concerned over whether research based on shared data can achieve high impact. Here, the authors show that neuroimaging papers using shared data are no less likely to appear in top-ranked journals.

19 July 2018 | doi: 10.1038/s41467-018-04976-1
Cognitive neuroscience  Databases  Policy 

Synchronized mesenchymal cell polarization and differentiation shape the formation of the murine trachea and esophagus OPEN
Keishi Kishimoto, Masaru Tamura, Michiru Nishita, Yasuhiro Minami, Akira Yamaoka, Takaya Abe, Mayo Shigeta & Mitsuru Morimoto

Tracheal development arises due to tube morphogenesis but how this is regulated is unclear. Here, the authors identify polarization of smooth muscle progenitors as controlling murine tracheal development, activating noncanonical Wnt signaling followed by subepithelial morphogenesis and ring cartilage development.

19 July 2018 | doi: 10.1038/s41467-018-05189-2
Cell polarity  Embryonic induction  Organogenesis 

Abrupt events and population synchrony in the dynamics of Bovine Tuberculosis OPEN
Aristides Moustakas, Matthew R. Evans, Ioannis N. Daliakopoulos & Yannis Markonis

The disease dynamics of bovine tuberculosis have been of interest given the pathogen’s effect on wild animal and livestock health. Here, the authors show that a brief cessation of testing for bovine tuberculosis in 2001 altered the population synchrony of the disease dynamics across regions of Great Britain.

19 July 2018 | doi: 10.1038/s41467-018-04915-0
Ecological epidemiology  Ecological modelling  Population dynamics 

Non-covalent control of spin-state in metal-organic complex by positioning on N-doped graphene OPEN
Bruno de la Torre, Martin Švec, Prokop Hapala, Jesus Redondo, Ondřej Krejčí, Rabindranath Lo, Debashree Manna, Amrit Sarmah, Dana Nachtigallová, Jiří Tuček, Piotr Błoński, Michal Otyepka, Radek Zbořil, Pavel Hobza & Pavel Jelínek

Molecules can change their electronic properties when they are adsorbed on substrates, which can be useful for sensing and catalysis. Here, the authors use atomic force microscopy to show that the spin state of an iron complex can be changed upon displacing the molecule to different sites of a nitrogen-doped graphene

19 July 2018 | doi: 10.1038/s41467-018-05163-y
Magnetic properties and materials  Molecular electronics  Scanning probe microscopy  Two-dimensional materials 

PRMT5-mediated regulation of developmental myelination OPEN
Antonella Scaglione, Julia Patzig, Jialiang Liang, Rebecca Frawley, Jabez Bok, Angeliki Mela, Camila Yattah, Jingxian Zhang, Shun Xie Teo, Ting Zhou, Shuibing Chen, Emily Bernstein, Peter Canoll, Ernesto Guccione & Patrizia Casaccia

Myelin-forming cells derive from oligodendrocyte progenitors. Here the authors identify histone arginine methyl-transferase PRMT5 as critical for developmental myelination by modulating the cross-talk between histone arginine methylation and lysine acetylation, to favor differentiation.

19 July 2018 | doi: 10.1038/s41467-018-04863-9
Epigenetics  Epigenetics in the nervous system  Glial biology  Histone post-translational modifications 

Armadillo repeat containing 12 promotes neuroblastoma progression through interaction with retinoblastoma binding protein 4 OPEN
Dan Li, Huajie Song, Hong Mei, Erhu Fang, Xiaojing Wang, Feng Yang, Huanhuan Li, Yajun Chen, Kai Huang, Liduan Zheng & Qiangsong Tong

Armadillo (ARM) family proteins can act as oncogenes or tumor suppressors. Here, the authors show that a new ARM protein (ARMC12) is upregulated in neuroblastoma, binds the PRC2 component RBBP4, and inhibits transcription of tumor suppressive genes.

19 July 2018 | doi: 10.1038/s41467-018-05286-2
Oncogenes  Paediatric cancer 

SIRT7 has a critical role in bone formation by regulating lysine acylation of SP7/Osterix OPEN
Masatoshi Fukuda, Tatsuya Yoshizawa, Md. Fazlul Karim, Shihab U. Sobuz, Wataru Korogi, Daiki Kobayasi, Hiroki Okanishi, Masayoshi Tasaki, Katsuhiko Ono, Tomohiro Sawa, Yoshifumi Sato, Mami Chirifu, Takeshi Masuda, Teruya Nakamura, Hironori Tanoue, Kazuhisa Nakashima, Yoshihiro Kobashigawa, Hiroshi Morioka, Eva Bober, Sumio Ohtsuki et al.

SP7/Osterix is a transcription factor involved in osteoblast differentiation. Here, the authors show that Sirtuin 7 activates Osterix posttranslationally by regulating its lysine acylation, and that mice lacking Sirtuin 7 in osteoblasts show reduced bone formation.

19 July 2018 | doi: 10.1038/s41467-018-05187-4
Bone remodelling  Post-translational modifications 

The potassium channel KCNJ13 is essential for smooth muscle cytoskeletal organization during mouse tracheal tubulogenesis OPEN
Wenguang Yin, Hyun-Taek Kim, ShengPeng Wang, Felix Gunawan, Lei Wang, Keishi Kishimoto, Hua Zhong, Dany Roman, Jens Preussner, Stefan Guenther, Viola Graef, Carmen Buettner, Beate Grohmann, Mario Looso, Mitsuru Morimoto, Graeme Mardon, Stefan Offermanns & Didier Y. R. Stainier

Tubulogenesis is required for the formation of many internal structures including the trachea. Here, the authors show that the potassium channel KCNJ13 regulates tracheal tube formation, with shorter tracheas forming in mutant mice due in part to changes in actin organization in tracheal smooth muscle cells.

19 July 2018 | doi: 10.1038/s41467-018-05043-5
Cytoskeleton  Morphogenesis 
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Trace N-glycans including sulphated species may originate from various plasma glycoproteins and not necessarily IgG OPEN
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25 July 2018 | doi: 10.1038/s41467-018-05173-w
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Reply to ‘Trace N-glycans including sulphated species may originate from various plasma glycoproteins and not necessarily IgG’ OPEN
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25 July 2018 | doi: 10.1038/s41467-018-05082-y
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No substantial long-term bias in the Cenozoic benthic foraminifera oxygen-isotope record OPEN
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Reply to 'No substantial long-term bias in the Cenozoic benthic foraminifera oxygen-isotope record' OPEN
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23 July 2018 | doi: 10.1038/s41467-018-05304-3
Geochemistry  Mineralogy  Palaeoceanography  Palaeoclimate 
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Thomas W Winkler, Felix Günther, Simon Höllerer, Martina Zimmermann, Ruth JF Loos, Zoltán Kutalik & Iris M Heid
20 July 2018 | doi: 10.1038/s41467-018-05088-6
Genome-wide association studies  Metabolic diseases  Quantitative trait 
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Publisher Correction: Bcl11b is essential for licensing Th2 differentiation during helminth infection and allergic asthma OPEN
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Epigenetics in immune cells  Transcriptional regulatory elements 

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19 July 2018 | doi: 10.1038/s41467-018-05212-6
Chemistry  Energy science and technology  Materials science 

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