Nature Communications - 09 May 2018

Advertisement Nature Outline: Spinal-cord injury  There is currently no way to reverse damage to the spinal cord, nor restore the ability to move and feel that such an injury takes away. But regenerative therapies in early clinical testing are offering much-needed hope.  Access free online  Produced with support from  Translational Research Informatics Center (TRI)   Sapporo Medical University      Weekly Content Alert Nature Communications is fully open access. Read more. 09 May 2018  Latest content: Editorial Perspective Articles Author Corrections Publisher Corrections Advertisement   Advanced Imaging with Proven Optics Olympus is dedicated to your work, vision, and science. Through innovation and service, we seek to aide in your discoveries, advance your research, and inspire you to explore new possibilities. Our wide range of microscopes are built with the optical excellence and proven application expertise you can depend on. Your Science Matters™. > Learn more about Olympus microscopes Journal homepage Recommend to library Web feed   Advertisement The Enhanced Human: Risks and Opportunities  May 21, 2018 | 6:00 PM, NYC LIVESTREAM available This panel, featuring geneticist George Church, bioethicist Josephine Johnston, futurist Jamie Metzl, AI specialist Meredith Whittaker, and moderated by bioethicist Mildred Z. 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Visit our open access funding page or contact openaccess@nature.com to learn more about APC funding.       Latest Editorial       Epidemiology is a science of high importance OPEN 07 May 2018 | doi: 10.1038/s41467-018-04243-3     Latest Perspective       Tracing the origin of heterogeneity and symmetry breaking in the early mammalian embryo OPEN Qi Chen, Junchao Shi, Yi Tao & Magdalena Zernicka-Goetz What breaks symmetry in early mammalian embryonic development has been much questioned. Here, Magdalena Zernicka-Goetz and colleagues propose that compartmentalized intracellular reactions generate micro-scale inhomogeneity, which is amplified in the developing embryo, driving pattern formation. 08 May 2018 | doi: 10.1038/s41467-018-04155-2 Differentiation  Embryogenesis  Pattern formation      Latest Review View all Articles         Nature Communications JOBS of the week postdoctoral fellow Necker Institut Enfants Malades - The Laboratory of Normal and Pathological T-cell Differentiation Senior Development Officer World Wildlife Fund (WWF) Post Doctoral Associate - 30132 University of Massachusetts UK Employee Relations Manager AstraZeneca Postdoctoral Fellow, Greenblatt Lab Cornell University Postdoctoral Research Assistant University of Dundee Postdoctoral Position in Biochemistry Umeå University Laboratory Manager Albert Einstein College of Medicine of Yeshiva University (AECOM) Staff Editor, Physics American Physical Society (APS) Director Position Institute of Molecular Biology Academia Sinica, Taiwan More Science jobs from Nature Communications EVENT Cheltenham Science Festival 05.06.18 Cheltenham, UK More science events from     Latest Articles View all Articles     A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum OPEN Alison Roth , Steven P. Maher, Amy J. Conway, Ratawan Ubalee, Victor Chaumeau, Chiara Andolina, Stephen A. Kaba, Amélie Vantaux, Malina A. Bakowski, Richard Thomson Luque, Swamy Rakesh Adapa, Naresh Singh, Samantha J. Barnes, Caitlin A. Cooper, Mélanie Rouillier, Case W. McNamara, Sebastian A. Mikolajczak, Noah Sather, Benoît Witkowski, Brice Campo et al. Currently available platforms to study liver stage of Plasmodium species have limitations. Here, the authors show that primary human hepatocyte cultures in 384-well format support hypnozoite and other liver stage development and are suitable for drug and antibody screens. 09 May 2018 | doi: 10.1038/s41467-018-04221-9 Drug screening  High-throughput screening  Malaria  Vaccines  Breaking the limitation of mode building time in an optoelectronic oscillator OPEN Tengfei Hao, Qizhuang Cen, Yitang Dai, Jian Tang, Wei Li, Jianping Yao, Ninghua Zhu & Ming Li In optoelectronic oscillators used to produce chirps for radar or communications, low phase noise usually comes at a cost of slow tuning due to mode-building time. The authors use Fourier-domain mode locking to break this limitation and enable fast-tunable chirp production for microwave photonics. 09 May 2018 | doi: 10.1038/s41467-018-04240-6 Microwave photonics  Optoelectronic devices and components  Gravitational clustering of cosmic relic neutrinos in the Milky Way OPEN Jue Zhang & Xin Zhang In order to detect relic neutrinos in the vicinity of the Earth, quantitative knowledge of the gravitational clustering effects on cosmic relic neutrinos in the Milky Way is necessary. Here, the authors develop a computational method capable of yielding neutrino density profiles for different neutrino masses and phase space distributions in a single simulation. 09 May 2018 | doi: 10.1038/s41467-018-04264-y Astronomy and astrophysics  Particle physics  78,000-year-old record of Middle and Later stone age innovation in an East African tropical forest OPEN Ceri Shipton , Patrick Roberts, Will Archer, Simon J. Armitage, Caesar Bita, James Blinkhorn, Colin Courtney-Mustaphi, Alison Crowther, Richard Curtis, Francesco d’ Errico, Katerina Douka, Patrick Faulkner, Huw S. Groucutt, Richard Helm, Andy I. R Herries, Severinus Jembe, Nikos Kourampas, Julia Lee-Thorp, Rob Marchant, Julio Mercader et al. Most of the archaeological record of the Middle to Later Stone Age transition comes from southern Africa. Here, Shipton et al. describe the new site Panga ya Saidi on the coast of Kenya that covers the last 78,000 years and shows gradual cultural and technological change in the Late Pleistocene. 09 May 2018 | doi: 10.1038/s41467-018-04057-3 Archaeology  Palaeoecology  Small GTPases and BAR domain proteins regulate branched actin polymerisation for clathrin and dynamin-independent endocytosis OPEN Mugdha Sathe, Gayatri Muthukrishnan, James Rae, Andrea Disanza, Mukund Thattai, Giorgio Scita, Robert G. Parton & Satyajit Mayor Several endocytic pathways operate simultaneously at the cell surface, including the clathrin and dynamin-independent CLIC/GEEC (CG) pathway. Here the authors show that small GTPases and BAR domain proteins regulate branched actin to make clathrin and dynamin-independent endocytic vesicles. 09 May 2018 | doi: 10.1038/s41467-018-03955-w Endocytosis  Membrane curvature  Small GTPases  NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence OPEN Aled J. Parry, Matthew Hoare, Dóra Bihary, Robert Hänsel-Hertsch, Stephen Smith, Kosuke Tomimatsu, Elizabeth Mannion, Amy Smith, Paula D’Santos, I. Alasdair Russell, Shankar Balasubramanian, Hiroshi Kimura, Shamith A. Samarajiwa & Masashi Narita Notch can drive senescence in a cell contact dependent manner. Here the authors show that NOTCH signalling can modulate chromatin structure autonomously and non-autonomously via the JAG1-NOTCH-HMGA1 interplay during senescence. 09 May 2018 | doi: 10.1038/s41467-018-04283-9 Cancer genomics  Cell signalling  Chromatin structure  Epigenetics  Senescence  Biosynthetic pathway for furanosteroid demethoxyviridin and identification of an unusual pregnane side-chain cleavage OPEN Gao-Qian Wang, Guo-Dong Chen, Sheng-Ying Qin, Dan Hu, Takayoshi Awakawa, Shao-Yang Li, Jian-Ming Lv, Chuan-Xi Wang, Xin-Sheng Yao, Ikuro Abe & Hao Gao Demethoxyviridin is a fungal steroid that inhibits a phosphatidylinositol 3-kinase, an enzyme contributing to tumor progression. Here, the authors elucidate the biosynthetic route that leads to the formation of demethoxyviridin in fungi. 09 May 2018 | doi: 10.1038/s41467-018-04298-2 Biocatalysis  Biosynthesis  Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene OPEN Carolin Seuring , Kartik Ayyer, Eleftheria Filippaki, Miriam Barthelmess, Jean-Nicolas Longchamp, Philippe Ringler, Tommaso Pardini, David H. Wojtas, Matthew A. Coleman, Katerina Dörner, Silje Fuglerud, Greger Hammarin, Birgit Habenstein, Annette E. Langkilde, Antoine Loquet, Alke Meents, Roland Riek, Henning Stahlberg, Sébastien Boutet, Mark S. Hunter et al. The structures of amyloid fibres are currently primarily studied through solid state NMR and cryo-EM. Here the authors present a free-standing graphene support device that allows diffraction imaging of non-crystalline amyloid fibrils with single X-ray pulses from an X-ray free-electron laser. 09 May 2018 | doi: 10.1038/s41467-018-04116-9 Biological physics  Imaging techniques  Peptide hormones  Protein aggregation  Structural biology  Sema7A/PlxnCl signaling triggers activity-dependent olfactory synapse formation OPEN Nobuko Inoue, Hirofumi Nishizumi, Hiromi Naritsuka, Hiroshi Kiyonari & Hitoshi Sakano The molecular mechanisms underlying synapse formation in the olfactory bulb are not fully understood. Here the authors demonstrate that semaphorin 7A on olfactory sensory neurons, and its receptor plexin C1 expressed on mitral and tufted cells, is required for correct synapse formation. 09 May 2018 | doi: 10.1038/s41467-018-04239-z Axon and dendritic guidance  Olfactory bulb  Designer cells programming quorum-sensing interference with microbes OPEN Ferdinand Sedlmayer, Dennis Hell, Marius Müller, David Ausländer & Martin Fussenegger Bacterial populations communicate with AI-2 signaling molecules, helping to coordinate biofilm development and other group behaviors. Here the authors design a genetic circuit for mammalian cells that allows them to sense bacterial populations and interfere with quorum communication. 08 May 2018 | doi: 10.1038/s41467-018-04223-7 Bacterial secretion  Synthetic biology  Networks of genetic similarity reveal non-neutral processes shape strain structure in Plasmodium falciparum OPEN Qixin He, Shai Pilosof, Kathryn E. Tiedje, Shazia Ruybal-Pesántez, Yael Artzy-Randrup, Edward B. Baskerville, Karen P. Day & Mercedes Pascual Plasmodium has evolved high genetic diversity in var genes, which encode for the major blood-stage antigen. Here, He et al. show how immune selection shapes the var gene repertoire in both simulated systems and a population in Ghana, by using neutral models and genetic similarity networks. 08 May 2018 | doi: 10.1038/s41467-018-04219-3 Computational models  Ecological epidemiology  Malaria  Supramolecular Kandinsky circles with high antibacterial activity OPEN Heng Wang, Xiaomin Qian, Kun Wang, Ma Su, Wei-Wei Haoyang, Xin Jiang, Robert Brzozowski, Ming Wang, Xiang Gao, Yiming Li, Bingqian Xu, Prahathees Eswara, Xin-Qi Hao, Weitao Gong, Jun-Li Hou, Jianfeng Cai & Xiaopeng Li Nested structures are common throughout nature and art, yet remain challenging synthetic targets in supramolecular chemistry. Here, the authors design multitopic terpyridine ligands that coordinate into nested concentric hexagons, and show that these discrete supramolecules display potent antimicrobial activity. 08 May 2018 | doi: 10.1038/s41467-018-04247-z Antimicrobials  Biomedical materials  Supramolecular chemistry  In situ coherent diffractive imaging OPEN Yuan Hung Lo, Lingrong Zhao, Marcus Gallagher-Jones, Arjun Rana, Jared J. Lodico, Weikun Xiao, B. C. Regan & Jianwei Miao Coherent diffractive imaging (CDI) allows for high resolution imaging without lenses. Here, Lo et al. develop in situ CDI with real-time imaging and a corresponding low-dose requirement, with expected applications in the physical and life sciences. 08 May 2018 | doi: 10.1038/s41467-018-04259-9 Imaging techniques  Microscopy  X-rays  Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition OPEN Marios G. Koliopoulos, Mathilde Lethier, Annemarthe G. van der Veen, Kevin Haubrich, Janosch Hennig, Eva Kowalinski, Rebecca V. Stevens, Stephen R. Martin, Caetano Reis e Sousa, Stephen Cusack & Katrin Rittinger NS1 of influenza A virus inhibits TRIM25 activity, which is an E3 ligase important for induction of the interferon response. Here, Koliopoulos et al. present structures of TRIM25 and NS1 and show how NS1 binding interferes with substrate recognition of TRIM25. 08 May 2018 | doi: 10.1038/s41467-018-04214-8 Influenza virus  Ubiquitylation  Virus–host interactions  X-ray crystallography  NOTCH signaling specifies arterial-type definitive hemogenic endothelium from human pluripotent stem cells OPEN Gene I. Uenishi, Ho Sun Jung, Akhilesh Kumar, Mi Ae Park, Brandon K. Hadland, Ethan McLeod, Matthew Raymond, Oleg Moskvin, Catherine E. Zimmerman, Derek J. Theisen, Scott Swanson, Owen J. Tamplin, Leonard I. Zon, James A. Thomson, Irwin D. Bernstein & Igor I. Slukvin It is unclear whether arterial specification is required for hematopoietic stem cell formation. Here, the authors use a chemically defined human pluripotent stem cell (hPSC) differentiation system to show the role of NOTCH signaling in forming arterial-type hemogenic endothelial cells. 08 May 2018 | doi: 10.1038/s41467-018-04134-7 Embryonic stem cells  Lymphopoiesis  Supersonic propagation of lattice energy by phasons in fresnoite OPEN M. E. Manley, P. J. Stonaha, D. L. Abernathy, S. Chi, R. Sahul, R. P. Hermann & J. D. Budai Fresnoite has an incommensurate structure that can be described as a nonlinear soliton lattice. Manley et al. show that the additional phason degrees of freedom associated with the solitonic structure can travel faster than more conventional phonon excitations, enabling supersonic energy transport. 08 May 2018 | doi: 10.1038/s41467-018-04229-1 Ferroelectrics and multiferroics  Nonlinear phenomena  Structure of solids and liquids  Inversion symmetry and bulk Rashba effect in methylammonium lead iodide perovskite single crystals OPEN Kyle Frohna, Tejas Deshpande, John Harter, Wei Peng, Bradford A. Barker, Jeffrey B. Neaton, Steven G. Louie, Osman M. Bakr, David Hsieh & Marco Bernardi The high performance of hybrid perovskite solar cells has attracted significant attention but the nature of the underlying mechanisms remains unclear. Frohna et al. show methylammonium lead iodide perovskite is centrosymmetric, invalidating previous predictions of a large bulk Rashba effect. 08 May 2018 | doi: 10.1038/s41467-018-04212-w Electronic properties and materials  Electronic structure  Solar cells  Reprocessable thermosets for sustainable three-dimensional printing OPEN Biao Zhang, Kavin Kowsari, Ahmad Serjouei, Martin L. Dunn & Qi Ge Thermosetting polymers are widely used in 3D printing owing to their superior mechanical stability, but once they are printed, the highly crosslinked polmyers cannot be reprocessed or repaired. Here the authors demonstrate a two-step polymerization strategy toward 3D printing of reprocessable thermosets. 08 May 2018 | doi: 10.1038/s41467-018-04292-8 Mechanical engineering  Mechanical properties  Giant energy density and high efficiency achieved in bismuth ferrite-based film capacitors via domain engineering OPEN Hao Pan, Jing Ma, Ji Ma, Qinghua Zhang, Xiaozhi Liu, Bo Guan, Lin Gu, Xin Zhang, Yu-Jun Zhang, Liangliang Li, Yang Shen, Yuan-Hua Lin & Ce-Wen Nan Dielectrics with high capacitive energy storage density are essential for modern electrical devices and pulsed power systems. Here, the authors realised superior energy storage performance in lead-free bismuth ferrite-based relaxor ferroelectric films through domain engineering. 08 May 2018 | doi: 10.1038/s41467-018-04189-6 Energy storage  Ferroelectrics and multiferroics  Surfaces, interfaces and thin films  Recurrent hotspot mutations in HRAS Q61 and PI3K-AKT pathway genes as drivers of breast adenomyoepitheliomas OPEN Felipe C. Geyer , Anqi Li, Anastasios D. Papanastasiou, Alison Smith, Pier Selenica, Kathleen A. Burke, Marcia Edelweiss, Huei-Chi Wen, Salvatore Piscuoglio, Anne M. Schultheis, Luciano G. Martelotto, Fresia Pareja, Rahul Kumar, Alissa Brandes, Dan Fan, Thais Basili, Arnaud Da Cruz Paula, John R. Lozada, Pedro Blecua, Simone Muenst et al. Adenomyoepithelioma is a rare tumor of the breast with an unknown genetic basis. Here the authors perform a genomic analysis of adenomyoepitheliomas revealing that their repertoire of somatic mutations vary according to the estrogen receptor (ER) status, and that ER-negative tumors harbor recurrent mutations in HRAS and PI3K pathway genes. 08 May 2018 | doi: 10.1038/s41467-018-04128-5 Breast cancer  Cancer genetics  Cancer genomics  Mimicking the surface and prebiotic chemistry of early Earth using flow chemistry OPEN Dougal J. Ritson, Claudio Battilocchio, Steven V. Ley & John D. Sutherland There is still much debate on early Earth geochemical conditions affecting the chemistry of simple synthons that originated life. Here, the authors report an uninterrupted multistep synthetic route to 2-aminooxazole by means of flow chemistry equipment, mimicking a plausible early Earth (geo)chemical scenario. 08 May 2018 | doi: 10.1038/s41467-018-04147-2 Geochemistry  Organic chemistry  Chemical origin of life  Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics OPEN Alvaro N. Barbeira, Scott P. Dickinson, Rodrigo Bonazzola, Jiamao Zheng, Heather E. Wheeler, Jason M. Torres, Eric S. Torstenson, Kaanan P. Shah, Tzintzuni Garcia, Todd L. Edwards, Eli A. Stahl, Laura M. Huckins, Dan L. Nicolae, Nancy J. Cox & Hae Kyung Im Phenotypic variation and diseases are influenced by factors such as genetic variants and gene expression. Here, Barbeira et al. develop S-PrediXcan to compute PrediXcan results using summary data, and investigate the effects of gene expression variation on human phenotypes in 44 GTEx tissues and >100 phenotypes. 08 May 2018 | doi: 10.1038/s41467-018-03621-1 Data integration  Genome-wide association studies  Single quantum dot tracking reveals the impact of nanoparticle surface on intracellular state OPEN Mohammad U. Zahid, Liang Ma, Sung Jun Lim & Andrew M. Smith Quantum dots (QDs) mimic delivery agents for drugs and analytic compounds, but which route do they take inside cells? Here, the authors developed a technique to follow QDs, and they show that zwitterionic nanoparticle surface coatings make for the best delivery vehicle. 08 May 2018 | doi: 10.1038/s41467-018-04185-w Cell delivery  Nanobiotechnology  Nanoparticles  Quantum dots  Single-molecule biophysics  Genome-wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure OPEN Alessia Visconti , David L. Duffy, Fan Liu, Gu Zhu, Wenting Wu, Yan Chen, Pirro G. Hysi, Changqing Zeng, Marianna Sanna, Mark M. Iles, Peter A. Kanetsky, Florence Demenais, Merel A. Hamer, Andre G. Uitterlinden, M. Arfan Ikram, Tamar Nijsten, Nicholas G. Martin, Manfred Kayser, Tim D. Spector, Jiali Han et al. The skin’s tanning response to sun exposure shows great interindividual variability. Here, Visconti et al. perform a genome-wide association study for ease of skin tanning and identify 20 genetic loci, ten of which had not previously been associated with pigmentation-related traits. 08 May 2018 | doi: 10.1038/s41467-018-04086-y Cancer genomics  Genome-wide association studies  Enhanced electrocaloric efficiency via energy recovery OPEN E. Defay, R. Faye, G. Despesse, H. Strozyk, D. Sette, S. Crossley, X. Moya & N. D. Mathur Electrocaloric materials can be electrically driven to pump heat and hold promise for use in efficient solid-state refrigeration. Here, the authors demonstrate an approach to recycle recoverable energy from electrocaloric cycles, offering a method to enhance performance in electrocaloric refrigeration systems. 08 May 2018 | doi: 10.1038/s41467-018-04027-9 Energy harvesting  Ferroelectrics and multiferroics  Thermodynamics  Enhanced pupillary light reflex in infancy is associated with autism diagnosis in toddlerhood OPEN Pär Nyström, Teodora Gliga, Elisabeth Nilsson Jobs, Gustaf Gredebäck, Tony Charman, Mark H. Johnson, Sven Bölte & Terje Falck-Ytter Previous studies showed that children with autism spectrum disorder (ASD) have atypicalities in the pupillary light reflex (PLR). This study uses longitudinal monitoring of infants at risk for ASD to show that PLR magnitude at 10 months of age is associated with later ASD diagnosis and symptom severity. 07 May 2018 | doi: 10.1038/s41467-018-03985-4 Autism spectrum disorders  Biomarkers  Development of the nervous system  Defining a conformational ensemble that directs activation of PPARγ OPEN Ian M. Chrisman, Michelle D. Nemetchek, Ian Mitchelle S. de Vera, Jinsai Shang, Zahra Heidari, Yanan Long, Hermes Reyes-Caballero, Rodrigo Galindo-Murillo, Thomas E. Cheatham III, Anne-Laure Blayo, Youseung Shin, Jakob Fuhrmann, Patrick R. Griffin, Theodore M. Kamenecka, Douglas J. Kojetin & Travis S. Hughes Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor. Here the authors provide insights into PPARγ activation by combining fluorine (19F) NMR and molecular dynamics simulations to characterize the nuclear receptor conformational ensemble in solution and the response of this ensemble to ligand and coregulatory peptide binding. 04 May 2018 | doi: 10.1038/s41467-018-04176-x Biophysical chemistry  Mechanism of action  Molecular conformation  Nuclear receptors  Receptor pharmacology  Transparent and attachable ionic communicators based on self-cleanable triboelectric nanogenerators OPEN Younghoon Lee, Seung Hee Cha, Yong-Woo Kim, Dukhyun Choi & Jeong-Yun Sun Flexible, transparent wearable electronics harvesting energy from human motion are nearing reality, but stable adhesion while staying clean remains a problem. Here the authors solve both issues with a functionalized organic polymer/hydrogel-based device capable of wireless communication via finger gestures. 04 May 2018 | doi: 10.1038/s41467-018-03954-x Devices for energy harvesting  Electrical and electronic engineering  Sensors and biosensors  Ediacara biota flourished in oligotrophic and bacterially dominated marine environments across Baltica OPEN Kelden Pehr, Gordon D. Love, Anton Kuznetsov, Victor Podkovyrov, Christopher K. Junium, Leonid Shumlyanskyy, Tetyana Sokur & Andrey Bekker The environments and food sources that sustained Ediacara biota 575-541 million years ago remain unclear. Here, the authors perform lipid biomarker and isotopic analyses on biota fossil-containing Ediacaran strata from Baltica and propose the presence of a microbial loop bolstered by bacteria. 04 May 2018 | doi: 10.1038/s41467-018-04195-8 Element cycles  Evolution  Generation of App knock-in mice reveals deletion mutations protective against Alzheimer’s disease-like pathology OPEN Kenichi Nagata, Mika Takahashi, Yukio Matsuba, Fumi Okuyama-Uchimura, Kaori Sato, Shoko Hashimoto, Takashi Saito & Takaomi C. Saido To date, only one mutation in the gene for amyloid-beta precursor protein APP has been suggested to be protective against Alzheimer’s disease. Here, authors found using gene editing of a mutant App knock-in mouse line that deletion of the 3’UTR region is protective against amyloid-β accumulation in vivo, and subsequently identify a 52-bp element in the 3’UTR region that is responsible for this effect. 04 May 2018 | doi: 10.1038/s41467-018-04238-0 Alzheimer's disease  CRISPR-Cas9 genome editing  Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB OPEN Bastian Bräuning, Eva Bertosin, Florian Praetorius, Christian Ihling, Alexandra Schatt, Agnes Adler, Klaus Richter, Andrea Sinz, Hendrik Dietz & Michael Groll The Yersinia YaxAB system is a pore-forming toxin of so far unknown structure. Here authors present X-ray and cryo-EM to structures of individual subunits and of the YaxAB pore complex, and find that YaxA binds to membranes first and recruits YaxB for subsequent oligomerization. 04 May 2018 | doi: 10.1038/s41467-018-04139-2 Electron microscopy  Pathogens  X-ray crystallography  Optical circulation in a multimode optomechanical resonator OPEN Freek Ruesink, John P. Mathew, Mohammad-Ali Miri, Andrea Alù & Ewold Verhagen Nonreciprocal optical elements mostly rely on magnetic fields to break time-reversal symmetry, an approach that is difficult to integrate on-chip. Here, Ruesink et al. describe and demonstrate 4-port circulation at telecom wavelengths using a magnetic-field-free optomechanical resonator. 04 May 2018 | doi: 10.1038/s41467-018-04202-y Applied optics  Microresonators  Optomechanics  Depletion of Nsd2-mediated histone H3K36 methylation impairs adipose tissue development and function OPEN Lenan Zhuang, Younghoon Jang, Young-Kwon Park, Ji-Eun Lee, Shalini Jain, Eugene Froimchuk, Aaron Broun, Chengyu Liu, Oksana Gavrilova & Kai Ge The epigenetic mechanisms regulating adipose tissue development are poorly understood. Here the authors show that reduction of H3K36 methylation in preadipocytes, both by H3.3K36M expression and depletion of H3K36 methyltransferase Nsd2, impairs adipogenesis by increasing H3K27me3. 04 May 2018 | doi: 10.1038/s41467-018-04127-6 Differentiation  Fat metabolism  Histone post-translational modifications  Integrated molecular subtyping defines a curable oligometastatic state in colorectal liver metastasis OPEN Sean P. Pitroda , Nikolai N. Khodarev, Lei Huang, Abhineet Uppal, Sean C. Wightman, Sabha Ganai, Nora Joseph, Jason Pitt, Miguel Brown, Martin Forde, Kathy Mangold, Lai Xue, Christopher Weber, Jeremy P. Segal, Sabah Kadri, Melinda E. Stack, Sajid Khan, Philip Paty, Karen Kaul, Jorge Andrade et al. The oligometastasis hypothesis suggests certain metastases are limited in extent and curable with focal therapies. Here they identify three integrated molecular subtypes of colorectal cancer liver metastasis, which complement clinical risk stratification to distinguish the subset of oligometastatic patients. 04 May 2018 | doi: 10.1038/s41467-018-04278-6 Cancer  Metastasis  Oncology  Flutter to tumble transition of buoyant spheres triggered by rotational inertia changes OPEN Varghese Mathai, Xiaojue Zhu, Chao Sun & Detlef Lohse Spiral trajectories of falling leaves represent the phase instabilities that are commonly observed for objects move through fluids, but the precise conditions that trigger instabilities remains unclear. Mathai et al. show the MoI governs the rotational dynamics of rising spherical particles. 04 May 2018 | doi: 10.1038/s41467-018-04177-w Fluid dynamics  Mechanical engineering  Climate-driven shifts in sediment chemistry enhance methane production in northern lakes OPEN E. J. S. Emilson, M. A. Carson, K. M. Yakimovich, H. Osterholz, T. Dittmar, J. M. Gunn, N. C. S. Mykytczuk, N. Basiliko & A. J. Tanentzap Methane emissions from lakes vary by orders of magnitude, leaving large uncertainty in regional and global carbon budgets. Here the authors show that phenols from forest litter act as a latch to suppress microbial activity and produce over 400-times less methane than the decomposition of aquatic plant litter. 04 May 2018 | doi: 10.1038/s41467-018-04236-2 Biogeochemistry  Climate-change impacts  Limnology  Heterochromatin protein 1a functions for piRNA biogenesis predominantly from pericentric and telomeric regions in Drosophila OPEN Ryan Yee Wei Teo, Amit Anand, Vishweshwaren Sridhar, Katsutomo Okamura & Toshie Kai Heterochromatin protein 1a (HP1a) is thought to function downstream of transposon repression in the Drosophila female germline. Here the authors show that HP1a also functions upstream of piRNA processing by repressing splicing of piRNA precursors, predominantly at telomeric and centromeric regions. 04 May 2018 | doi: 10.1038/s41467-018-03908-3 Piwi RNAs  RNAi  Air separation with graphene mediated by nanowindow-rim concerted motion OPEN Fernando Vallejos-Burgos, François-Xavier Coudert & Katsumi Kaneko Graphene with nanowindows can have 1000 times higher permeability and four times the selectivity for air separation than conventional membranes, Vallejos-Burgos et al. reveal by molecular simulation, due to flexibility at the nanoscale and thermal vibrations of the nanowindows' functional groups. 04 May 2018 | doi: 10.1038/s41467-018-04224-6 Chemical physics  Nanofluidics  Two-dimensional materials  Defect-enriched iron fluoride-oxide nanoporous thin films bifunctional catalyst for water splitting OPEN Xiujun Fan, Yuanyue Liu, Shuai Chen, Jianjian Shi, Juanjuan Wang, Ailing Fan, Wenyan Zan, Sidian Li, William A. Goddard III & Xian-Ming Zhang While iron-containing materials are excellent water electrolysis electrocatalysts, their poor conductivity requires them to be incorporated into conductive matrices. Here, the authors prepare highly conductive iron fluoride-oxide mixed phase substrates with strong water electrolysis performances. 04 May 2018 | doi: 10.1038/s41467-018-04248-y Electrocatalysis  Synthesis and processing  A self-destructive nanosweeper that captures and clears amyloid β-peptides OPEN Qiang Luo, Yao-Xin Lin, Pei-Pei Yang, Yi Wang, Guo-Bin Qi, Zeng-Ying Qiao, Bing-Nan Li, Kuo Zhang, Jing-Ping Zhang, Lei Wang & Hao Wang Cerebral amyloid β-peptide accumulation is a causative factor in Alzheimer’s Disease. Here the authors design a 'nanosweeper' that binds amyloid β-peptide and induces autophagy to clear the accumulated plagues. 04 May 2018 | doi: 10.1038/s41467-018-04255-z Biomaterials  Drug delivery  Unconventional slowing down of electronic recovery in photoexcited charge-ordered La1/3Sr2/3FeO3 OPEN Yi Zhu, Jason Hoffman, Clare E. Rowland, Hyowon Park, Donald A. Walko, John W. Freeland, Philip J. Ryan, Richard D. Schaller, Anand Bhattacharya & Haidan Wen Unusual electronic behavior can emerge in complex oxides due to strong coupling between charge, magnetic and lattice degrees of freedom. Zhu et al. observe separation of electronic and lattice equilibration times in La1/3Sr2/3FeO3 as magnetic interactions make the recovery of charge order much slower than lattice relaxation. 04 May 2018 | doi: 10.1038/s41467-018-04199-4 Electronic properties and materials  Magnetic properties and materials  Phase transitions and critical phenomena  Reconfigurable optomechanical circulator and directional amplifier OPEN Zhen Shen, Yan-Lei Zhang, Yuan Chen, Fang-Wen Sun, Xu-Bo Zou, Guang-Can Guo, Chang-Ling Zou & Chun-Hua Dong Upconversion nanoparticles, which convert lower-energy light into higher-energy light, have many potential applications including sensing and imaging. Here, Wen et al. review recent advances that have addressed concentration quenching and enabled increasingly bright nanoparticles, opening up their full potential. 04 May 2018 | doi: 10.1038/s41467-018-04187-8 Applied optics  Microresonators  Optomechanics  Bayesian model selection for complex dynamic systems OPEN Christoph Mark, Claus Metzner, Lena Lautscham, Pamela L. Strissel, Reiner Strick & Ben Fabry Systematic changes in stock market prices or in the migration behaviour of cancer cells may be hidden behind random fluctuations. Here, Mark et al. describe an empirical approach to identify when and how such real-world systems undergo systematic changes. 04 May 2018 | doi: 10.1038/s41467-018-04241-5 Cellular motility  Projection and prediction  Scientific data  Statistics  Chemically triggered drug release from an antibody-drug conjugate leads to potent antitumour activity in mice OPEN Raffaella Rossin, Ron M. Versteegen, Jeremy Wu, Alisher Khasanov, Hans J. Wessels, Erik J. Steenbergen, Wolter ten Hoeve, Henk M. Janssen, Arthur H. A. M. van Onzen, Peter J. Hudson & Marc S. Robillard Current antibody-drug conjugates (ADCs) target internalising receptors on cancer cells. Here, the authors report the development and in vivo validation of a non-internalising ADC with the capacity to target cancer cells and release its therapeutic cargo extracellularly via a chemical trigger. 04 May 2018 | doi: 10.1038/s41467-018-03880-y Cancer imaging  Drug delivery  Molecular medicine  Proteins  Targeted therapies  Rechargeable lithium-ion cell state of charge and defect detection by in-situ inside-out magnetic resonance imaging OPEN Andrew J. Ilott, Mohaddese Mohammadi, Christopher M. Schauerman, Matthew J. Ganter & Alexej Jerschow The development of noninvasive methodology plays an important role in advancing lithium ion battery technology. Here the authors utilize the measurement of tiny magnetic field changes within a cell to assess the lithiation state of the active material, and detect defects. 03 May 2018 | doi: 10.1038/s41467-018-04192-x Batteries  Energy  NMR spectroscopy  Chemokines cooperate with TNF to provide protective anti-viral immunity and to enhance inflammation OPEN Alí Alejo, M. Begoña Ruiz-Argüello, Sergio M. Pontejo, María del Mar Fernández de Marco, Margarida Saraiva, Bruno Hernáez & Antonio Alcamí Cytokines play critical roles in the anti-viral response but their contribution in vivo remains unclear. Here the authors show that viral CrmD is a major virulence determinant and requires the SECRET and TNF binding domains to counter both the chemokine and cytokine driven inflammatory defenses. 03 May 2018 | doi: 10.1038/s41467-018-04098-8 Chemokines  Immune evasion  Viral infection  Viral pathogenesis  Gut microbiomes of wild great apes fluctuate seasonally in response to diet OPEN Allison L. Hicks, Kerry Jo Lee, Mara Couto-Rodriguez, Juber Patel, Rohini Sinha, Cheng Guo, Sarah H. Olson, Anton Seimon, Tracie A. Seimon, Alain U. Ondzie, William B. Karesh, Patricia Reed, Kenneth N. Cameron, W. Ian Lipkin & Brent L. Williams Microbiota composition fluctuates in response to changes in environmental and lifestyle factors. Here, Hicks et al. show that the faecal microbiota of wild gorillas and chimpanzees is temporally dynamic, with shifts that correlate with seasonal rainfall patterns and periods of high and low frugivory. 03 May 2018 | doi: 10.1038/s41467-018-04204-w Conservation biology  Metagenomics  Microbial ecology  Microbiome  Reconfigurable engineered motile semiconductor microparticles OPEN Ugonna Ohiri, C. Wyatt Shields IV, Koohee Han, Talmage Tyler, Orlin D. Velev & Nan Jokerst Active particles that demonstrate life-like behavior may find use in bio-inspired technologies, but achieving on-demand reconfiguration remains challenging. Here, the authors demonstrate controllable, collective behavior in silicon microparticles, which are fabricated via conventional semiconductor methods. 03 May 2018 | doi: 10.1038/s41467-018-04183-y Chemical engineering  Electrical and electronic engineering  Electronic devices  Materials for devices  A retinoic acid-dependent stroma-leukemia crosstalk promotes chronic lymphocytic leukemia progression OPEN Diego Farinello , Monika Wozińska, Elisa Lenti, Luca Genovese, Silvia Bianchessi, Edoardo Migliori, Nicolò Sacchetti, Alessia di Lillo, Maria Teresa Sabrina Bertilaccio, Claudia de Lalla, Roberta Valsecchi, Sabrina Bascones Gleave, David Lligé, Cristina Scielzo, Laura Mauri, Maria Grazia Ciampa, Lydia Scarfò, Rosa Bernardi, Dejan Lazarevic, Blanca Gonzalez-Farre et al. The stromal microenvironment plays a key role in the expansion of chronic lymphocytic leukemia. Here, the authors use the Eµ-TCL1 mouse model to show that leukemic B-cells induce the activation of retinoic acid synthesis in stromal cells of the lymphoid microenvironment, and that impacting on retinoic acid signalling via diet or chemical inhibition prolonged survival by preventing leukemia dissemination and accumulation in lymphoid tissues. 03 May 2018 | doi: 10.1038/s41467-018-04150-7 Cancer microenvironment  Chronic lymphocytic leukaemia  Nanoscale origins of creep in calcium silicate hydrates OPEN A. Morshedifard, S. Masoumi & M. J. Abdolhosseini Qomi The nanoscale mechanisms behind the creep of calcium-silicate-hydrates remain difficult to model over long periods of time. Here, the authors use a three-staged incremental stress-marching technique to tie atomistic simulations and nanomechanical experimental measurements together. 03 May 2018 | doi: 10.1038/s41467-018-04174-z Atomistic models  Computational methods  Mechanical properties  Clinical and genomic landscape of gastric cancer with a mesenchymal phenotype OPEN Sang Cheul Oh , Bo Hwa Sohn, Jae-Ho Cheong, Sang-Bae Kim, Jae Eun Lee, Ki Cheong Park, Sang Ho Lee, Jong-Lyul Park, Yun-Yong Park, Hyun-Sung Lee, Hee-Jin Jang, Eun Sung Park, Sang-Cheol Kim, Jeonghoon Heo, In-Sun Chu, You-Jin Jang, Young-Jae Mok, WonKyung Jung, Baek-Hui Kim, Aeree Kim et al. The prognosis and treatment of gastric cancer is complicated by heterogeneity. Here, the authors reveal two molecular subtypes, the mesenchymal subtype associated with poor survival and chemoresistance, and the epithelial phenotype associated with better survival and sensitivity to chemotherapy. 03 May 2018 | doi: 10.1038/s41467-018-04179-8 Cancer genomics  Gastrointestinal cancer  Transcriptomics  Nuclear fate of yeast snoRNA is determined by co-transcriptional Rnt1 cleavage OPEN Pawel Grzechnik, Sylwia A. Szczepaniak, Somdutta Dhir, Anna Pastucha, Hannah Parslow, Zaneta Matuszek, Hannah E. Mischo, Joanna Kufel & Nicholas J. Proudfoot Small nucleolar ribonucleoprotein complexes (snoRNP) are fundamental for ribosome biogenesis. Here the authors provide insight into the 5ʹend processing of S. cerevisiae snoRNA and its important role in downstream nuclear events. 03 May 2018 | doi: 10.1038/s41467-018-04094-y RNA  RNA metabolism  The southern ocean meridional overturning in the sea-ice sector is driven by freshwater fluxes OPEN Violaine Pellichero, Jean-Baptiste Sallée, Christopher C. Chapman & Stephanie M. Downes The Southern Ocean is key in sustaining the world’s ocean global circulation, yet the influence of its freshwater cycle remains unconstrained. Here, the authors use a detailed oceanographic database to evaluate surface buoyancy fluxes and reveal central roles for both precipitation and sea-ice formation and melt. 03 May 2018 | doi: 10.1038/s41467-018-04101-2 Cryospheric science  Physical oceanography  C/EBPβ regulates delta-secretase expression and mediates pathogenesis in mouse models of Alzheimer’s disease OPEN Zhi-Hao Wang, Ke Gong, Xia Liu, Zhentao Zhang, Xiaoou Sun, Zheng Zachory Wei, Shan Ping Yu, Fredric P. Manfredsson, Ivette M. Sandoval, Peter F. Johnson, Jianping Jia, Jian-Zhi Wang & Keqiang Ye Delta-secretase cleaves both APP and Tau, and contributes to Alzheimer’s disease-like pathology. Here the authors show that C/EBPβ, a regulator of inflammation, also regulates transcription of delta-secretase in an age-dependent manner and contributes to Alzheimer’s disease-like pathology in mouse models. 03 May 2018 | doi: 10.1038/s41467-018-04120-z Alzheimer's disease  Transcription  CCDC102B confers risk of low vision and blindness in high myopia OPEN Myopic maculopathy is a complication of myopia that often progresses to blindness. Here, in a genome-wide association study, Hosoda et al. find that rs11873439 intronic to CCDC102B is associated with myopic maculopathy, but not with myopia, thus representing a risk factor independent of myopia. 03 May 2018 | doi: 10.1038/s41467-018-03649-3 Genetics research  Genome-wide association studies  Refractive errors  Retinal diseases  Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation OPEN Ron Geller, Sebastian Pechmann, Ashley Acevedo, Raul Andino & Judith Frydman It remains poorly understood whether and how chaperones control protein evolution. Here the authors show how the chaperone Hsp90 shapes the sequence space of its client, poliovirus protein P1, at the polypeptide and RNA level to balance the evolutionary trade-offs between protein stability, aggregation and translation rate. 03 May 2018 | doi: 10.1038/s41467-018-04203-x Biochemistry  Computational biology and bioinformatics  Virology  A distributive peptide cyclase processes multiple microviridin core peptides within a single polypeptide substrate OPEN Yi Zhang, Kunhua Li, Guang Yang, Joshua L. McBride, Steven D. Bruner & Yousong Ding Microviridins belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, the authors discover a microviridin-synthesizing enzyme in a cyanobacterium that modifies multiple core peptides from a single substrate in a distributive and unstrictly directional manner, an unusual biosynthetic logic for RiPPs. 03 May 2018 | doi: 10.1038/s41467-018-04154-3 Biosynthesis  WASP-mediated regulation of anti-inflammatory macrophages is IL-10 dependent and is critical for intestinal homeostasis OPEN Amlan Biswas, Dror S. Shouval, Alexandra Griffith, Jeremy A. Goettel, Michael Field, Yu Hui Kang, Liza Konnikova, Erin Janssen, Naresh Singh Redhu, Adrian J. Thrasher, Talal Chatila, Vijay K. Kuchroo, Raif S Geha, Luigi D. Notarangelo, Sung-Yun Pai, Bruce H. Horwitz & Scott B. Snapper Deficiency in Wiskott-Aldrich syndrome protein (WASP) has been associated with autoimmune colitis, but the underlying mechanism is still unclear. Here the authors show that WASP deficiency is associated with defective WASP/DOCK8 complex formation, altered IL-10 signalling, and impaired anti-inflammatory macrophage functions. 03 May 2018 | doi: 10.1038/s41467-018-03670-6 Inflammation  Interleukins  Monocytes and macrophages  Mucosal immunology  Population coding of conditional probability distributions in dorsal premotor cortex OPEN Joshua I. Glaser, Matthew G. Perich, Pavan Ramkumar, Lee E. Miller & Konrad P. Kording Movements are continually constrained by the current body position and its relation to the surroundings. Here the authors report that the population activity of monkey dorsal premotor cortex neurons dynamically represents the probability distribution of possible reach directions. 03 May 2018 | doi: 10.1038/s41467-018-04062-6 Motor cortex  Neural decoding  Neural encoding  Premotor cortex  Macroecology and macroevolution of the latitudinal diversity gradient in ants OPEN Evan P. Economo, Nitish Narula, Nicholas R. Friedman, Michael D. Weiser & Benoit Guénard Multiple hypotheses have been proposed for the declining biodiversity gradient between the tropics and poles. Here, the authors compile and analyze geographic data for all ant species and large-scale phylogenies, suggesting that diversification time drives the latitudinal diversity gradient in ants. 03 May 2018 | doi: 10.1038/s41467-018-04218-4 Biodiversity  Biogeography  Macroecology  Phylogenetics      Latest Author Corrections       Author Correction: A proteomic landscape of diffuse-type gastric cancer OPEN Sai Ge , Xia Xia, Chen Ding, Bei Zhen, Quan Zhou, Jinwen Feng, Jiajia Yuan, Rui Chen, Yumei Li, Zhongqi Ge, Jiafu Ji, Lianhai Zhang, Jiayuan Wang, Zhongwu Li, Yumei Lai, Ying Hu, Yanyan Li, Yilin Li, Jing Gao, Lin Chen et al. 08 May 2018 | doi: 10.1038/s41467-018-04166-z Gastric cancer  Proteomics  Author Correction: Floats with bio-optical sensors reveal what processes trigger the North Atlantic bloom OPEN A. Mignot, R. Ferrari & H. Claustre 04 May 2018 | doi: 10.1038/s41467-018-04181-0 Biooceanography  Marine biology  Population dynamics      Latest Publisher Corrections       Publisher Correction: Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow OPEN Yafeng Zhu, Lukas M. Orre, Henrik J. Johansson, Mikael Huss, Jorrit Boekel, Mattias Vesterlund, Alejandro Fernandez-Woodbridge, Rui M. M. Branca & Janne Lehtiö 08 May 2018 | doi: 10.1038/s41467-018-04279-5 Genome  Mass spectrometry  Proteome informatics  Proteomics  Publisher Correction: RING tetramerization is required for nuclear body biogenesis and PML sumoylation OPEN Pengran Wang, Shirine Benhenda, Haiyan Wu, Valérie Lallemand-Breitenbach, Tao Zhen, Florence Jollivet, Laurent Peres, Yuwen Li, Sai-Juan Chen, Zhu Chen, Hugues de Thé & Guoyu Meng 04 May 2018 | doi: 10.1038/s41467-018-04347-w Acute myeloid leukaemia  Sumoylation      Advertisement nature.com webcasts Nature Research Custom presents a webcast on: MicroRNAs in CSF as prodromal biomarkers for Huntington's disease Date: Tuesday, May 29, 2018 Join our webcast to learn about the fundamental characteristics of microRNAs and why Huntington's disease may serve as a disease model for the assessment of biomarkers. 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