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Nature Communications - 25 April 2018

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Nature Research Custom presents a webcast on: Ultra-sensitive detection of interferon alpha protein in human disease by digital ELISA

Date: Tuesday, May 15, 2018

Darragh Duffy, Institut Pasteur, will address how digital ELISA enables direct qualification of IFNa protein in human samples. This webcast has been produced on behalf of the sponsor who retains sole responsibility for content
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Nature Neuroscience: Poster on Cerebral Organoids

Emerging three-dimensional culture methods enable differentiated human stem cells to form into brain organoids or assembloids, which can be used to study evolution, development, and disease. 

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24 April 2018 | doi: 10.1038/s41467-018-04085-z
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Uncovering inherent cellular plasticity of multiciliated ependyma leading to ventricular wall transformation and hydrocephalus OPEN
Khadar Abdi, Chun-Hsiang Lai, Patricia Paez-Gonzalez, Mark Lay, Joon Pyun & Chay T. Kuo

Multiciliated ependymal cells (ECs) in the mammalian brain are glial cells facilitating cerebral spinal fluid movement. This study describes an inherent cellular plasticity of ECs as maintained by Foxj1 and IKK2 signaling, and shows resulting hydrocephalus when EC de-differentiation is triggered.

25 April 2018 | doi: 10.1038/s41467-018-03812-w
Adult neurogenesis  Ciliogenesis  Developmental disorders  Stem-cell niche 

Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry OPEN
Matthew M. Makowski, Cathrin Gräwe, Benjamin M. Foster, Nhuong V. Nguyen, Till Bartke & Michiel Vermeulen

Quantitative mass spectrometry enables the proteome-wide assessment of biomolecular binding affinities. While previous approaches mainly focused on protein–small molecule interactions, the authors here present a method to probe protein–DNA and protein–nucleosome binding affinities at proteome scale.

25 April 2018 | doi: 10.1038/s41467-018-04084-0
DNA-binding proteins  Mass spectrometry  Nucleosomes  Proteomics 

Aqueous rechargeable zinc/sodium vanadate batteries with enhanced performance from simultaneous insertion of dual carriers OPEN
Fang Wan, Linlin Zhang, Xi Dai, Xinyu Wang, Zhiqiang Niu & Jun Chen

Rechargeable zinc-ion batteries are promising energy storage devices but suffer from the limited choice of positive electrodes. Here Niu and co-workers show a design with sodium vanadate hydrate as cathode, allowing simultaneous proton and zinc-ion insertion/extraction and enhanced performance.

25 April 2018 | doi: 10.1038/s41467-018-04060-8

Cryo-EM reveals the structural basis of microtubule depolymerization by kinesin-13s OPEN
Matthieu P.M.H. Benoit, Ana B. Asenjo & Hernando Sosa

Kinesin-13s are microtubule depolymerases that lack motile activity. Here the authors present the cryo-EM structures of kinesin-13 microtubule complexes in different nucleotide bound states, which reveal how ATP hydrolysis is linked to conformational changes and propose a model for kinesin induced depolymerisation.

25 April 2018 | doi: 10.1038/s41467-018-04044-8
Electron microscopy  Motor protein structure  Motor proteins  Structural biology 

Crystalline polymer nanofibers with ultra-high strength and thermal conductivity OPEN
Ramesh Shrestha, Pengfei Li, Bikramjit Chatterjee, Teng Zheng, Xufei Wu, Zeyu Liu, Tengfei Luo, Sukwon Choi, Kedar Hippalgaonkar, Maarten P. de Boer & Sheng Shen

Polymers compared to structural materials usually have low strength and thermal conductivity. Here the authors show a fabrication method to form bio-compatible crystalline polyethylene nanofibers that exhibit ultra-high strength, thermal conductivity and electrical insulation.

25 April 2018 | doi: 10.1038/s41467-018-03978-3
Nanowires  Polymers 

Magnetically tunable bidirectional locomotion of a self-assembled nanorod-sphere propeller OPEN
José García-Torres, Carles Calero, Francesc Sagués, Ignacio Pagonabarraga & Pietro Tierno

Controlled transport at the micro and nanoscale is a challenge and strategies are needed for applications such as targeted drug delivery and soft microrobotics. Here the authors propose a hybrid nanorod and microsphere propeller which can be actuated and reconfigured by an oscillating magnetic field.

25 April 2018 | doi: 10.1038/s41467-018-04115-w
Colloids  Fluid dynamics  Nanoparticles 

Structural basis for GPR40 allosteric agonism and incretin stimulation OPEN
Joseph D. Ho , Betty Chau, Logan Rodgers, Frances Lu, Kelly L. Wilbur, Keith A. Otto, Yanyun Chen, Min Song, Jonathan P. Riley, Hsiu-Chiung Yang, Nichole A. Reynolds, Steven D. Kahl, Anjana Patel Lewis, Christopher Groshong, Russell E. Madsen, Kris Conners, Jayana P. Lineswala, Tarun Gheyi, Melbert-Brian Decipulo Saflor, Matthew R. Lee et al.

GPR40 is a G-protein coupled receptor that binds to free fatty acids, mediating insulin and incretin secretion. Here, the authors present the crystal structure of human GPR40 with an agonist bound to an allosteric site located near the lipid-rich region that suggests a mechanism for biased agonism.

25 April 2018 | doi: 10.1038/s41467-017-01240-w
Receptor pharmacology  Type 2 diabetes  X-ray crystallography 

The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression OPEN
Mina Ali, Ram Ajore, Anna-Karin Wihlborg, Abhishek Niroula, Bhairavi Swaminathan, Ellinor Johnsson, Owen W Stephens, Gareth Morgan, Tobias Meissner, Ingemar Turesson, Hartmut Goldschmidt, Ulf-Henrik Mellqvist, Urban Gullberg, Markus Hansson, Kari Hemminki, Hareth Nahi, Anders Waage, Niels Weinhold & Björn Nilsson

ELL2 was recently discovered as a susceptibility gene for multiple myeloma (MM). Here, they show that the MM risk allele lowers ELL2 expression in plasma cells, that it also upregulates gene sets related to ribosome biogenesis, and that one of the linked variants reduces binding of MAFF/G/K family transcription factors.

25 April 2018 | doi: 10.1038/s41467-018-04082-2
Cancer genetics  Clinical genetics  Myeloma  Risk factors 

Obesity exacerbates colitis-associated cancer via IL-6-regulated macrophage polarisation and CCL-20/CCR-6-mediated lymphocyte recruitment OPEN
Claudia M. Wunderlich, P. Justus Ackermann, Anna Lena Ostermann, Petra Adams-Quack, Merly C. Vogt, My-Ly Tran, Alexei Nikolajev, Ari Waisman, Christoph Garbers, Sebastian Theurich, Jan Mauer, Nadine Hövelmeyer & F. Thomas Wunderlich

Inflammation can be induced by obesity, and has been linked with onset of colorectal cancer (CAC). Here the authors show in mouse models that obesity-induced interleukin-6 alters macrophage function to enhance CCL-20/CCR-6-mediated recruitment of B cells and γδ T cells, thereby promoting gut inflammation and CAC progression.

25 April 2018 | doi: 10.1038/s41467-018-03773-0
Cancer microenvironment  Chemokines  Interleukins  Tumour immunology 

Strain-engineered inverse charge-funnelling in layered semiconductors OPEN
Adolfo De Sanctis, Iddo Amit, Steven P. Hepplestone, Monica F. Craciun & Saverio Russo

The application of strain to semiconducting materials can be used to engineer electric fields through a varying energy gap. Here, the authors observe an inverse charge-funnel effect in atomically thin HfS2, enabled by strain-induced electric fields.

25 April 2018 | doi: 10.1038/s41467-018-04099-7
Devices for energy harvesting  Electronic devices  Electronic properties and materials  Two-dimensional materials 

Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies OPEN
Mette Boyd , Malte Thodberg, Morana Vitezic, Jette Bornholdt, Kristoffer Vitting-Seerup, Yun Chen, Mehmet Coskun, Yuan Li, Bobby Zhao Sheng Lo, Pia Klausen, Pawel Jan Schweiger, Anders Gorm Pedersen, Nicolas Rapin, Kerstin Skovgaard, Katja Dahlgaard, Robin Andersson, Thilde Bagger Terkelsen, Berit Lilje, Jesper Thorvald Troelsen, Andreas Munk Petersen et al.

Many SNPs associated with inflammatory bowel disease are located in non-coding genomic regions. Here, the authors perform CAGE-sequencing on descending colon biopsies of Crohn’s disease and ulcerative colitis patients to map transcription start sites and enhancer activity for analysis of regulatory regions.

25 April 2018 | doi: 10.1038/s41467-018-03766-z
Disease genetics  Inflammatory bowel disease  Transcriptional regulatory elements  Transcriptomics 

Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity OPEN
Tanguy Le Marchand, Matteo de Rosa, Nicola Salvi, Benedetta Maria Sala, Loren B. Andreas, Emeline Barbet-Massin, Pietro Sormanni, Alberto Barbiroli, Riccardo Porcari, Cristiano Sousa Mota, Daniele de Sanctis, Martino Bolognesi, Lyndon Emsley, Vittorio Bellotti, Martin Blackledge, Carlo Camilloni, Guido Pintacuda & Stefano Ricagno

The aggregation prone D76N beta-2 microglobulin mutant causes systemic amyloidosis. Here the authors combine crystallography, solid-state NMR, and computational studies and show that the D76N mutation increases protein dynamics and destabilizes the outer strands, which leads to an exposure of amyloidogenic parts explaining its aggregation propensity.

25 April 2018 | doi: 10.1038/s41467-018-04078-y
Molecular modelling  NMR spectroscopy  Protein aggregation  X-ray crystallography 

Correlation of the Dzyaloshinskii–Moriya interaction with Heisenberg exchange and orbital asphericity OPEN
Sanghoon Kim, Kohei Ueda, Gyungchoon Go, Peong-Hwa Jang, Kyung-Jin Lee, Abderrezak Belabbes, Aurelien Manchon, Motohiro Suzuki, Yoshinori Kotani, Tetsuya Nakamura, Kohji Nakamura, Tomohiro Koyama, Daichi Chiba, Kihiro. T. Yamada, Duck-Ho Kim, Takahiro Moriyama, Kab-Jin Kim & Teruo Ono

Dzyaloshinskii–Moriya interaction (DMI) is one of the key factors to control the chiral spin textures in spintronic applications. Here the authors demonstrate the correlation of the DMI with the anisotropy of the orbital magnetic moment and magnetic dipole moment in Pt/Co/MgO ultrathin trilayers.

25 April 2018 | doi: 10.1038/s41467-018-04017-x
Ferromagnetism  Spintronics 

Exercise induces new cardiomyocyte generation in the adult mammalian heart OPEN
Ana Vujic, Carolin Lerchenmüller, Ting-Di Wu, Christelle Guillermier, Charles P. Rabolli, Emilia Gonzalez, Samuel E. Senyo, Xiaojun Liu, Jean-Luc Guerquin-Kern, Matthew L. Steinhauser, Richard T. Lee & Anthony Rosenzweig

The adult mammalian heart has a limited cardiomyogenic capacity. Here the authors show that intensive exercise leads to a 4.6-fold increase in murine cardiomyocyte proliferation requiring the expression of miR-222, and that exercise induces an extended cardiomyogenic response in the murine heart after infarction.

25 April 2018 | doi: 10.1038/s41467-018-04083-1
Cardiac regeneration  Cell division 

Regulation of Yki/Yap subcellular localization and Hpo signaling by a nuclear kinase PRP4K OPEN
Yong suk Cho, Jian Zhu, Shuangxi Li, Bing Wang, Yuhong Han & Jin Jiang

The Hippo signaling pathway controls tissue growth by regulating the subcellular localization of Yorkie /Yap. Here the authors show that PRP4K, a kinase involved in mRNA splicing, phosphorylates Yki/Yap in the nucleus, which prevents its nuclear accumulation and inhibits Hippo signaling.

25 April 2018 | doi: 10.1038/s41467-018-04090-2
Cell growth  Developmental biology 

Gold-catalyzed stereoselective cycloisomerization of allenoic acids for two types of common natural γ-butyrolactones OPEN
Jing Zhou, Chunling Fu & Shengming Ma

Gamma-butyrolactones are widespread in Nature, however direct catalytic methods to access them are limited. Here, the authors report a gold-catalyzed cycloisomerization of allenoic acids to acces γ-butyrolactones and apply it to the asymmetric synthesis of xestospongienes E, F, G, and H and other naturally occurring lactones.

25 April 2018 | doi: 10.1038/s41467-018-03894-6
Homogeneous catalysis  Natural product synthesis  Chemical synthesis 

Chemical diversity in a metal–organic framework revealed by fluorescence lifetime imaging OPEN
Waldemar Schrimpf, Juncong Jiang, Zhe Ji, Patrick Hirschle, Don C. Lamb, Omar M. Yaghi & Stefan Wuttke

Metal-organic frameworks are typically characterized by a variety of techniques, but most only provide information on properties as an average of a bulk sample. Here, Wuttke and colleagues demonstrate that fluorescence imaging and lifetime analysis allows access to local information on defects and functional groups.

25 April 2018 | doi: 10.1038/s41467-018-04050-w
Imaging techniques  Metal–organic frameworks  Photochemistry  Porous materials 

Blackbody radiation shift assessment for a lutetium ion clock OPEN
K. J. Arnold, R. Kaewuam, A. Roy, T. R. Tan & M. D. Barrett

There is a continuous effort to improve the accuracy of atomic clocks. Here the authors measure the static differential scalar polarizability of Lutetium ion resonant transitions and its lower light shift from blackbody radiation makes it a promising candidate for ion-based atomic clocks.

25 April 2018 | doi: 10.1038/s41467-018-04079-x
Atomic and molecular physics  Optical physics 

A phase transformable ultrastable titanium-carboxylate framework for photoconduction OPEN
Sujing Wang, Takashi Kitao, Nathalie Guillou, Mohammad Wahiduzzaman, Charlotte Martineau-Corcos, Farid Nouar, Antoine Tissot, Laurent Binet, Naseem Ramsahye, Sabine Devautour-Vinot, Susumu Kitagawa, Shu Seki, Yusuke Tsutsui, Valérie Briois, Nathalie Steunou, Guillaume Maurin, Takashi Uemura & Christian Serre

Porous TiO2 materials are attractive for energy-related applications owing to their accessible active sites, but suffer from poor stability. Here the authors synthesize a highly stable and porous metal–organic framework containing polymeric 1D Ti–O subunits, which displays a high condensation degree and high photoconductivity.

25 April 2018 | doi: 10.1038/s41467-018-04034-w
Electronic devices  Metal–organic frameworks  Nanowires  Porous materials 

Demographic causes of adult sex ratio variation and their consequences for parental cooperation OPEN
Luke J. Eberhart-Phillips, Clemens Küpper, María Cristina Carmona-Isunza, Orsolya Vincze, Sama Zefania, Medardo Cruz-López, András Kosztolányi, Tom E. X. Miller, Zoltán Barta, Innes C. Cuthill, Terry Burke, Tamás Székely, Joseph I. Hoffman & Oliver Krüger

Biases in adult sex ratio (ASR) are common, yet their causes and consequences are not well understood. Here, the authors analyse data from >6000 individuals of five shorebird species, showing that sex differences in juvenile survival drive ASR variation and biased ASR is associated with uniparental care.

25 April 2018 | doi: 10.1038/s41467-018-03833-5
Behavioural ecology  Population dynamics  Sexual selection 

A SUMO-dependent feedback loop senses and controls the biogenesis of nuclear pore subunits OPEN
Jérôme O. Rouvière, Manuel Bulfoni, Alex Tuck, Bertrand Cosson, Frédéric Devaux & Benoit Palancade

The nuclear pore complex is crucial for mediating nucleocytoplasmic exchanges. Here the authors use budding yeast to reveal a mechanism responsible of maintaining nucleoporin homeostasis by sensing changes in the complex integrity and further altering the metabolism of the corresponding mRNAs.

25 April 2018 | doi: 10.1038/s41467-018-03673-3
Nuclear pore complex  Post-translational modifications  RNA metabolism 

Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin OPEN
Evgenia Ntini, Annita Louloupi, Julia Liz, Jose M. Muino, Annalisa Marsico & Ulf Andersson Vang Ørom

The functional role of dissociation of long ncRNAs from chromatin is poorly understood. Here, the authors provide evidence that release of the long ncRNA AROD from chromatin enhances DKK1 transcription, and suggest that this regulatory mechanism of transcription applies to a subset of long ncRNAs.

24 April 2018 | doi: 10.1038/s41467-018-04100-3
Chromatin  Long non-coding RNAs 

Mineral dissolution and reprecipitation mediated by an amorphous phase OPEN
Matthias Konrad-Schmolke, Ralf Halama, Richard Wirth, Aurélien Thomen, Nico Klitscher, Luiz Morales, Anja Schreiber & Franziska D. H. Wilke

Fluid-mediated mineral dissolution is a key mechanism for mineral reactions in the Earth. Here, the authors show that element transport during mineral dissolution and reprecipitation reactions can be mediated by an amorphous phase, which can contain significant amounts of metals.

24 April 2018 | doi: 10.1038/s41467-018-03944-z
Geochemistry  Mineralogy 

Dissociation of two-dimensional excitons in monolayer WSe2 OPEN
Mathieu Massicotte, Fabien Vialla, Peter Schmidt, Mark B. Lundeberg, Simone Latini, Sten Haastrup, Mark Danovich, Diana Davydovskaya, Kenji Watanabe, Takashi Taniguchi, Vladimir I. Fal’ko, Kristian S. Thygesen, Thomas G. Pedersen & Frank H. L. Koppens

In two-dimensional semiconductors excitons are strongly bound, suppressing the creation of free carriers. Here, the authors investigate the main exciton dissociation pathway in p-n junctions of monolayer WSe2 by means of time and spectrally resolved photocurrent measurements.

24 April 2018 | doi: 10.1038/s41467-018-03864-y
Optical properties and devices  Two-dimensional materials 

De novo main-chain modeling for EM maps using MAINMAST OPEN
Genki Terashi & Daisuke Kihara

Main-chain tracing remains a time-consuming task for medium resolution cryo-EM maps. Here the authors describe MAINMAST, a computational approach for building main-chain structure models of proteins from EM maps of 4-5 Å resolution that builds main-chain models of the protein by tracing local dense points in the density distribution.

24 April 2018 | doi: 10.1038/s41467-018-04053-7
Computational biophysics  Computational models  Cryoelectron microscopy 

Snord116-dependent diurnal rhythm of DNA methylation in mouse cortex OPEN
Rochelle L. Coulson, Dag H. Yasui, Keith W. Dunaway, Benjamin I. Laufer, Annie Vogel Ciernia, Yihui Zhu, Charles E. Mordaunt, Theresa S. Totah & Janine M. LaSalle

Many genes have oscillating gene expression pattern in circadian centers of the brain. This study shows cortical diurnal DNA methylation oscillation in a mouse model of Prader-Willi syndrome, and describes corresponding changes in gene expression and chromatin compaction.

24 April 2018 | doi: 10.1038/s41467-018-03676-0
Circadian regulation  Epigenomics  Experimental models of disease  Molecular medicine 

Control of mechanical pain hypersensitivity in mice through ligand-targeted photoablation of TrkB-positive sensory neurons OPEN
Rahul Dhandapani, Cynthia Mary Arokiaraj, Francisco J. Taberner, Paola Pacifico, Sruthi Raja, Linda Nocchi, Carla Portulano, Federica Franciosa, Mariano Maffei, Ahmad Fawzi Hussain, Fernanda de Castro Reis, Luc Reymond, Emerald Perlas, Simone Garcovich, Stefan Barth, Kai Johnsson, Stefan G. Lechner & Paul A. Heppenstall

There are several classes of sensory neuron that contribute to pain states. Here, the authors demonstrate that TrkB+ sensory neurons detect light touch under normal conditions in mice but contribute to hypersensitivity in models of chronic pain, and that ligand-guided laser ablation of TrkB+ sensory neurons in the mouse skin attenuates this hypersensitivity.

24 April 2018 | doi: 10.1038/s41467-018-04049-3
Chronic pain  Sensory processing 

Invasive alien pests threaten the carbon stored in Europe’s forests OPEN
Rupert Seidl, Günther Klonner, Werner Rammer, Franz Essl, Adam Moreno, Mathias Neumann & Stefan Dullinger

Invasive alien pests can cause large-scale forest mortality and release carbon stored in forests. Here the authors show that climate change increases the potential range of alien pests and that their impact on the carbon cycle could be as severe as the current natural disturbance regime in Europe’s forests.

24 April 2018 | doi: 10.1038/s41467-018-04096-w
Carbon cycle  Climate-change ecology  Ecosystem ecology  Forest ecology 

Analysis of predicted loss-of-function variants in UK Biobank identifies variants protective for disease OPEN
Connor A. Emdin , Amit V. Khera, Mark Chaffin, Derek Klarin, Pradeep Natarajan, Krishna Aragam, Mary Haas, Alexander Bick, Seyedeh M. Zekavat, Akihiro Nomura, Diego Ardissino, James G. Wilson, Heribert Schunkert, Ruth McPherson, Hugh Watkins, Roberto Elosua, Matthew J. Bown, Nilesh J. Samani, Usman Baber, Jeanette Erdmann et al.

Examination of predicted loss-of-function (pLOF) genetic variants allows direct identification of genes with therapeutic potential. Here, Emdin et al. perform association analysis for 3759 pLOF variants with 24 traits and highlight protective variants against cardiometabolic and immune phenotypes.

24 April 2018 | doi: 10.1038/s41467-018-03911-8
Genetic association study  Genetic predisposition to disease  Medical genomics  Rare variants 

Fine manipulation of sound via lossy metamaterials with independent and arbitrary reflection amplitude and phase OPEN
Yifan Zhu, Jie Hu, Xudong Fan, Jing Yang, Bin Liang, Xuefeng Zhu & Jianchun Cheng

The formation of true holograms requires control of both amplitude and phase; however, acoustic metamaterials are generally limited to phase control only. Here, Zhu et al. tailor lossy metamaterials to independently control the amplitude and phase of acoustic wavefronts.

24 April 2018 | doi: 10.1038/s41467-018-04103-0
Acoustics  Physics 

A serum microRNA signature predicts trastuzumab benefit in HER2-positive metastatic breast cancer patients OPEN
Huiping Li, Jiang Liu, Jianing Chen, Huiyun Wang, Linbin Yang, Fei Chen, Siting Fan, Jing Wang, Bin Shao, Dong Yin, Musheng Zeng, Mengfeng Li, Jun Li, Fengxi Su, Qiang Liu, Herui Yao, Shicheng Su & Erwei Song

Resistance to therapy is a significant issue for patients with metastatic breast cancer (MBC). Here the authors analyze total miRNA from serum samples of 386 MBC patients before treatment with a follow up of 31 months and define a four miRNA signature that predicts the therapeutic benefit of trastuzumab.

24 April 2018 | doi: 10.1038/s41467-018-03537-w
Breast cancer  Cancer therapeutic resistance  Tumour biomarkers 

Bio-inspired nano-traps for uranium extraction from seawater and recovery from nuclear waste OPEN
Qi Sun, Briana Aguila, Jason Perman, Aleksandr S. Ivanov, Vyacheslav S. Bryantsev, Lyndsey D. Earl, Carter W. Abney, Lukasz Wojtas & Shengqian Ma

Uranium extraction is important for both uranium recovery and nuclear waste management. Here, inspired by the high sensitivity of proteins towards specific metal ions, Ma and colleagues demonstrate that introducing secondary coordination spheres into amidoxime-functionalized porous polymers can enhance their uranyl chelating abilities.

24 April 2018 | doi: 10.1038/s41467-018-04032-y
Nuclear fuel  Nuclear waste  Polymers  Porous materials 

Fetal demise and failed antibody therapy during Zika virus infection of pregnant macaques OPEN
Diogo M. Magnani , Thomas F. Rogers, Nicholas J. Maness, Nathan D. Grubaugh, Nathan Beutler, Varian K. Bailey, Lucas Gonzalez-Nieto, Martin J. Gutman, Núria Pedreño-Lopez, Jaclyn M. Kwal, Michael J. Ricciardi, Tereance A. Myers, Justin G. Julander, Rudolf P. Bohm, Margaret H. Gilbert, Faith Schiro, Pyone P. Aye, Robert V. Blair, Mauricio A. Martins, Kathrine P. Falkenstein et al.

Zika virus (ZIKV) infection in pregnant women has been associated with fetal developmental defects. Here, the authors show that a Brazilian ZIKV isolate causes fetal demise in non-human primates and that antibody treatment at time of peak viremia is insufficient to clear ZIKV replication from amniotic fluid.

24 April 2018 | doi: 10.1038/s41467-018-04056-4
Antibody therapy  Viral infection  Viral pathogenesis 

Epigenetic landscape influences the liver cancer genome architecture OPEN
Natsuko Hama, Yasushi Totoki, Fumihito Miura, Kenji Tatsuno, Mihoko Saito-Adachi, Hiromi Nakamura, Yasuhito Arai, Fumie Hosoda, Tomoko Urushidate, Shoko Ohashi, Wakako Mukai, Nobuyoshi Hiraoka, Hiroyuki Aburatani, Takashi Ito & Tatsuhiro Shibata

Genomic aberrations contribute to the development of cancer; however, their interdependence remains poorly understood. Here the authors analyze liver cancer samples to find correlation between epigenetic features and genetic aberrations including somatic substitutions, mutation signatures, and HBV integration sites.

24 April 2018 | doi: 10.1038/s41467-018-03999-y
Cancer genomics  Hepatocellular carcinoma 

Universality in volume-law entanglement of scrambled pure quantum states OPEN
Yuya O. Nakagawa, Masataka Watanabe, Hiroyuki Fujita & Sho Sugiura

The entanglement in a quantum system between a small region and the surrounding environment contains details about the whole state. Nakagawa et al. find a formula for the entanglement entropy of a class of thermal-like states and show that it can be applied more broadly to identify equilibrating states.

24 April 2018 | doi: 10.1038/s41467-018-03883-9
Statistical physics  Theoretical physics 

Galectin-3 deficiency drives lupus-like disease by promoting spontaneous germinal centers formation via IFN-γ OPEN
Cristian Gabriel Beccaria, María Carolina Amezcua Vesely, Facundo Fiocca Vernengo, Ricardo Carlos Gehrau, María Cecilia Ramello, Jimena Tosello Boari, Melisa Gorosito Serrán, Juan Mucci, Eliane Piaggio, Oscar Campetella, Eva Virginia Acosta Rodríguez, Carolina Lucía Montes & Adriana Gruppi

Germinal center (GC) is where B cells interact with other immune cells for optimal induction of antibody responses. Here the authors show that galectin-3 regulates GC development by modulating interferon-γ and B cell-intrinsic signaling, such that galectin-3 deficiency mice exhibit lupus-like autoimmune symptoms.

24 April 2018 | doi: 10.1038/s41467-018-04063-5
Autoimmunity  Follicular B cells  Germinal centres  Interferons 

Non-invasive detection of human cardiomyocyte death using methylation patterns of circulating DNA OPEN
Hai Zemmour, David Planer, Judith Magenheim, Joshua Moss, Daniel Neiman, Dan Gilon, Amit Korach, Benjamin Glaser, Ruth Shemer, Giora Landesberg & Yuval Dor

The detection of cardiomyocyte death is a critical aspect in the diagnosis and monitoring of heart diseases. Here the authors show that cardiomyocyte-specific methylation patterns of circulating cell-free DNA may serve as a biomarker of cardiac cell death in infarcted and septic patients.

24 April 2018 | doi: 10.1038/s41467-018-03961-y
Cardiology  Cell death  Diagnostic markers  Methylation analysis 

Causes and implications of the unforeseen 2016 extreme yield loss in the breadbasket of France OPEN
Tamara Ben-Ari, Julien Boé, Philippe Ciais, Remi Lecerf, Marijn Van der Velde & David Makowski

In France, the 2016 winter wheat harvest was at its lowest since over 50 years. Here, Ben-Ari et al. show the role of seasonal temperature and precipitation extremes in this loss, and accounting for both of these variables explains large, historical yield loss events.

24 April 2018 | doi: 10.1038/s41467-018-04087-x
Agroecology  Environmental impact 

Precisely printable and biocompatible silk fibroin bioink for digital light processing 3D printing OPEN
Soon Hee Kim, Yeung Kyu Yeon, Jung Min Lee, Janet Ren Chao, Young Jin Lee, Ye Been Seo, Md. Tipu Sultan, Ok Joo Lee, Ji Seung Lee, Sung-il Yoon, In-Sun Hong, Gilson Khang, Sang Jin Lee, James J. Yoo & Chan Hum Park

Although 3D bioprinting technology has gained much attention in the field of tissue engineering, there are still several significant challenges that need to be overcome. Here, the authors present silk fibroin bioink with printability and biocompatibility suited for digital light processing 3D printing.

24 April 2018 | doi: 10.1038/s41467-018-03759-y
Biomaterials – cells  Tissue engineering 

Molecular doping enabled scalable blading of efficient hole-transport-layer-free perovskite solar cells OPEN
Wu-Qiang Wu, Qi Wang, Yanjun Fang, Yuchuan Shao, Shi Tang, Yehao Deng, Haidong Lu, Ye Liu, Tao Li, Zhibin Yang, Alexei Gruverman & Jinsong Huang

The existing hole-transporting materials cause problems in the cost and scalability of the perovskite solar cells. Here Wu et al. fabricate high efficiency cells by molecularly doping the perovskite layer without using hole-transporting layers, thus simplify the device architecture and processing steps.

24 April 2018 | doi: 10.1038/s41467-018-04028-8
Devices for energy harvesting  Electrical and electronic engineering  Electronic devices 

Layer-specific morphological and molecular differences in neocortical astrocytes and their dependence on neuronal layers OPEN
Darin Lanjakornsiripan, Baek-Jun Pior, Daichi Kawaguchi, Shohei Furutachi, Tomoaki Tahara, Yu Katsuyama, Yutaka Suzuki, Yugo Fukazawa & Yukiko Gotoh

Several studies have suggested that astrocytes in the neocortex are more diverse than previously thought. Here, the authors describe layer-specific differences in morphology and molecular characteristics of astrocytes that depend on the neurons within those layers.

24 April 2018 | doi: 10.1038/s41467-018-03940-3
Astrocyte  Cortex 

Repeated evolution of self-compatibility for reproductive assurance OPEN
Bart P. S. Nieuwenhuis, Sergio Tusso, Pernilla Bjerling, Josefine Stångberg, Jochen B. W. Wolf & Simone Immler

Mating-type switching enables self-compatible reproduction in fungi, but switching ability is variable even within species. Here, the authors find de novo evolution of switching genotypes in experimentally evolved fission yeast populations and show a trade-off between mating success and growth.

24 April 2018 | doi: 10.1038/s41467-018-04054-6
Experimental evolution  Genetic variation  Genomics 

Arctic sea ice is an important temporal sink and means of transport for microplastic OPEN
Ilka Peeken, Sebastian Primpke, Birte Beyer, Julia Gütermann, Christian Katlein, Thomas Krumpen, Melanie Bergmann, Laura Hehemann & Gunnar Gerdts

Microplastic (MP) pollution in polar regions is a growing environmental concern, yet little is known regarding the role of sea-ice as a sink and transport vector of MPs. Here, the authors show that MPs in sea-ice have no uniform polymer composition and observe unique MP patterns in different sea-ice horizons.

24 April 2018 | doi: 10.1038/s41467-018-03825-5
Cryospheric science  Environmental impact 

Structural basis for the activation of acid ceramidase OPEN
Ahmad Gebai, Alexei Gorelik, Zixian Li, Katalin Illes & Bhushan Nagar

Acid ceramidase (aCDase) hydrolyzes lysosomal membrane ceramide into sphingosine and its dysfunction leads to a variety of disease phenotypes. Here, the authors present structures of aCDase in its proenzyme and autocleaved forms, which provides insight into its mechanism of action.

24 April 2018 | doi: 10.1038/s41467-018-03844-2
Hydrolases  Metabolic disorders  X-ray crystallography 

Mesopores induced zero thermal expansion in single-crystal ferroelectrics OPEN
Zhaohui Ren, Ruoyu Zhao, Xing Chen, Ming Li, Xiang Li, He Tian, Ze Zhang & Gaorong Han

Zero thermal expansion materials—often composites of negative and positive coefficient materials—are needed for applications that see large temperature changes. Here, the authors demonstrate that polarization around pores in single-phase mesoporous lead titanate can be used to tune thermal expansion to near zero.

24 April 2018 | doi: 10.1038/s41467-018-04113-y
Materials science  Nanoscale materials 

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese OPEN
Yukinori Okada, Yukihide Momozawa, Saori Sakaue, Masahiro Kanai, Kazuyoshi Ishigaki, Masato Akiyama, Toshihiro Kishikawa, Yasumichi Arai, Takashi Sasaki, Kenjiro Kosaki, Makoto Suematsu, Koichi Matsuda, Kazuhiko Yamamoto, Michiaki Kubo, Nobuyoshi Hirose & Yoichiro Kamatani

Recent natural selection left signals in human genomes. Here, Okada et al. generate high-depth whole-genome sequence (WGS) data (25.9×) from 2,234 Japanese people of the BioBank Japan Project (BBJ), and identify signals of recent natural selection which overlap variants associated with human traits.

24 April 2018 | doi: 10.1038/s41467-018-03274-0
Evolutionary biology  Next-generation sequencing  Population genetics 

Methylated DNMT1 and E2F1 are targeted for proteolysis by L3MBTL3 and CRL4DCAF5 ubiquitin ligase OPEN
Feng Leng, Jiekai Yu, Chunxiao Zhang, Salvador Alejo, Nam Hoang, Hong Sun, Fei Lu & Hui Zhang

Lysine methylation is increasingly being implicated in the modification of non-histone proteins. Here the authors find that the methylation of DNMT1 and E2F1 are recognized by the protein L3MBTL3 and the ubiquitin E3 ligase CRL4DCAF5, which cooperatively target these methylated proteins for ubiquitin-dependent proteolysis.

24 April 2018 | doi: 10.1038/s41467-018-04019-9
DNA methylation  Ubiquitin ligases 

Gender inequity in speaking opportunities at the American Geophysical Union Fall Meeting OPEN
Heather L. Ford, Cameron Brick, Karine Blaufuss & Petra S. Dekens

Speaking at a scientific conference helps spread scientific results and is also fundamental for career advancement. Here the authors show that at the American Geophysical Union Fall Meeting, the largest Earth and space science conference, women are offered speaking opportunities less often than men overall.

24 April 2018 | doi: 10.1038/s41467-018-03809-5
Careers  Psychology and behaviour 

A biochemical framework for anaerobic oxidation of methane driven by Fe(III)-dependent respiration OPEN
Zhen Yan, Prachi Joshi, Christopher A. Gorski & James G. Ferry

The unavailability of pure cultures has prevented a mechanistic understanding of anaerobic methanotrophy. Here the authors report a biochemical investigation of Methanosarcina acetivorans that supports a pathway anchored by Fe(III)-dependent mechanisms for energy conservation and driving endergonic reactions.

24 April 2018 | doi: 10.1038/s41467-018-04097-9
Carbon cycle  Element cycles  Water microbiology 

The basic helix-loop-helix transcription factor SHARP1 is an oncogenic driver in MLL-AF6 acute myelogenous leukemia OPEN
Akihiko Numata, Hui Si Kwok, Akira Kawasaki, Jia Li, Qi-Ling Zhou, Jon Kerry, Touati Benoukraf, Deepak Bararia, Feng Li, Erica Ballabio, Marta Tapia, Aniruddha J. Deshpande, Robert S. Welner, Ruud Delwel, Henry Yang, Thomas A. Milne, Reshma Taneja & Daniel G. Tenen

Gene fusions involving MLL and different partner genes define unique subgroups of acute myelogenous leukemia, but the mechanisms underlying specific subgroups are not fully clear. Here the authors elucidate the mechanisms of MLL-AF6 induced transformation, providing a distinct pathway that involves SHARP1 as a critical target.

24 April 2018 | doi: 10.1038/s41467-018-03854-0
Acute myeloid leukaemia  Cancer stem cells 

Barium bioaccumulation by bacterial biofilms and implications for Ba cycling and use of Ba proxies OPEN
Francisca Martinez-Ruiz, Fadwa Jroundi, Adina Paytan, Isabel Guerra-Tschuschke, María del Mar Abad & María Teresa González-Muñoz

Despite the broad use of barium as a proxy for past ocean export production, the underlying mechanisms of barite precipitation remain unknown. Here, the authors show, under experimental conditions, that barium bioaccumulation on bacterially produced biofilms is the crucial step for barite formation.

24 April 2018 | doi: 10.1038/s41467-018-04069-z
Biogeochemistry  Element cycles  Marine chemistry  Palaeoceanography 

Warm summers during the Younger Dryas cold reversal OPEN
Frederik Schenk, Minna Väliranta, Francesco Muschitiello, Lev Tarasov, Maija Heikkilä, Svante Björck, Jenny Brandefelt, Arne V. Johansson, Jens-Ove Näslund & Barbara Wohlfarth

Mechanisms causing the Younger Dryas cold reversal have been questioned by inconsistencies between proxy and modelling results. Here, the authors show that the concept of a strong North Atlantic Ocean cooling event as major driver is consistent with warm European summers caused by intensified atmospheric blocking.

24 April 2018 | doi: 10.1038/s41467-018-04071-5
Palaeoceanography  Palaeoclimate 

Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study OPEN
Christopher DeBoever, Yosuke Tanigawa, Malene E. Lindholm, Greg McInnes, Adam Lavertu, Erik Ingelsson, Chris Chang, Euan A. Ashley, Carlos D. Bustamante, Mark J. Daly & Manuel A. Rivas

Protein-truncating variants (PTVs) are predicted to significantly affect a gene’s function and, thus, human traits. Here, DeBoever et al. systematically analyze PTVs in more than 300,000 individuals across 135 phenotypes and identify 27 associations between PTVs and medical conditions.

24 April 2018 | doi: 10.1038/s41467-018-03910-9
Genetic predisposition to disease  Genome-wide association studies  Medical genomics  Rare variants 

Capping protein-controlled actin polymerization shapes lipid membranes OPEN
Katharina Dürre, Felix C. Keber, Philip Bleicher, Fridtjof Brauns, Christian J. Cyron, Jan Faix & Andreas R. Bausch

Cell membrane protrusions and invaginations are both driven by actin assembly but the mechanism leading to different membrane shapes is unknown. Using a minimal system and modelling the authors reconstitute the deformation modes and identify capping protein as a regulator of both deformation types.

24 April 2018 | doi: 10.1038/s41467-018-03918-1
Actin  Biological physics  Membrane biophysics  Molecular biophysics 

Feed-forward alpha particle radiotherapy ablates androgen receptor-addicted prostate cancer OPEN
Michael R. McDevitt, Daniel L. J. Thorek, Takeshi Hashimoto, Tatsuo Gondo, Darren R. Veach, Sai Kiran Sharma, Teja Muralidhar Kalidindi, Diane S. Abou, Philip A. Watson, Bradley J. Beattie, Oskar Vilhemsson Timmermand, Sven-Erik Strand, Jason S. Lewis, Peter T. Scardino, Howard I. Scher, Hans Lilja, Steven M. Larson & David Ulmert

Radionuclides that emit alpha particles (charged helium nuclei) are currently used clinically to treat cancers including prostate cancer. Here, the authors combine a humanized antibody to an alpha particle emitter, specifically to target a downstream effector of the androgen receptor and create a feed forward loop that increases the therapeutic efficacy.

24 April 2018 | doi: 10.1038/s41467-018-04107-w
Cancer  Prostate cancer  Radiotherapy  Targeted therapies 

Motor imagery involves predicting the sensory consequences of the imagined movement OPEN
Konstantina Kilteni, Benjamin Jan Andersson, Christian Houborg & H. Henrik Ehrsson

Forward models predict and attenuate the sensory feedback of voluntary movement yet their involvement in motor imagery has only been theorized. Here the authors show that motor imagery recruits forward models to elicit sensory attenuation to the same extent as real movements.

24 April 2018 | doi: 10.1038/s41467-018-03989-0
Human behaviour  Motor control  Somatosensory system 

The Gastrodia elata genome provides insights into plant adaptation to heterotrophy OPEN
Yuan Yuan , Xiaohua Jin, Juan Liu, Xing Zhao, Junhui Zhou, Xin Wang, Deyi Wang, Changjiangsheng Lai, Wei Xu, Jingwen Huang, Liangping Zha, Dahui Liu, Xiao Ma, Li Wang, Menyan Zhou, Zhi Jiang, Hubiao Meng, Huasheng Peng, Yuting Liang, Ruiqiang Li et al.

Gastrodia elata is an obligate mycoheterotrophic plant with highly reduced leaves and bracts in scape. Here, Yuan et al sequence and analyze its 1.06 Gb genome which provides insights in adaptation to a lifestyle of heterotrophy.

24 April 2018 | doi: 10.1038/s41467-018-03423-5
Genome  Genomic analysis  Plant symbiosis 

Relativistic magnetic reconnection driven by a laser interacting with a micro-scale plasma slab OPEN
Longqing Yi, Baifei Shen, Alexander Pukhov & Tünde Fülöp

Plasma releases magnetic energy by magnetic reconnection but the clear evidence of this phenomenon in relativistic regime is still lacking. Here the authors present a scheme for laboratory observation of the relativistic magnetic reconnection driven by laser-produced energetic electrons in the plasma.

23 April 2018 | doi: 10.1038/s41467-018-04065-3
Laser-produced plasmas  Plasma-based accelerators 

Placental miR-340 mediates vulnerability to activity based anorexia in mice OPEN
Mariana Schroeder, Mira Jakovcevski, Tamar Polacheck, Yonat Drori, Alessia Luoni, Simone Röh, Jonas Zaugg, Shifra Ben-Dor, Christiane Albrecht & Alon Chen

Anorexia nervosa is characterised by self-starvation but its etiology is not completely understood. Here the authors describe how prenatal stress can induce activity-based anorexia in the offspring during early adulthood by upregulating miR-340 expression in the placenta that affects expression of nutrient transporters.

23 April 2018 | doi: 10.1038/s41467-018-03836-2
Epigenetics and behaviour  Stress and resilience 

Chromatin conformation regulates the coordination between DNA replication and transcription OPEN
Ricardo Almeida, José Miguel Fernández-Justel, Cristina Santa-María, Jean-Charles Cadoret, Laura Cano-Aroca, Rodrigo Lombraña, Gonzalo Herranz, Alessandra Agresti & María Gómez

The maintenance of chromatin integrity during replication is critical for cell viability. Here the authors study how dividing cells respond to alterations in chromatin structure and find that these elicit a range of responses in the dynamics of DNA replication and consequences on replicative stress.

23 April 2018 | doi: 10.1038/s41467-018-03539-8
Chromatin structure  Replisome  Stalled forks  Transcription 

Cross-coupling polycondensation via C–O or C–N bond cleavage OPEN
Ze-Kun Yang, Ning-Xin Xu, Ryo Takita, Atsuya Muranaka, Chao Wang & Masanobu Uchiyama

π-Conjugated polymers are useful commodities as they are used in the fabrication of organic photovoltaic devices, light-emitting diodes and field effect transistors. Here the authors describe the polycondensation of bifunctional aryl ethers or aryl ammonium salts with aromatic dimetallic compounds through cleavage of inert C–O/C–N bonds.

23 April 2018 | doi: 10.1038/s41467-018-03928-z
Synthetic chemistry methodology  Polymer synthesis 

Vibrio vulnificus quorum-sensing molecule cyclo(Phe-Pro) inhibits RIG-I-mediated antiviral innate immunity OPEN
Wooseong Lee, Seung-Hoon Lee, Minwoo Kim, Jae-Su Moon, Geon-Woo Kim, Hae-Gwang Jung, In Hwang Kim, Ji Eun Oh, Hi Eun Jung, Heung Kyu Lee, Keun Bon Ku, Dae-Gyun Ahn, Seong-Jun Kim, Kun-Soo Kim & Jong-Won Oh

Quorum sensing signaling molecules are known to be critical determinants in bacterial pathogenesis. Here the authors show the quorum sensing molecule cFP from Vibrio vulnificus inhibits the RIG-I mediated antiviral interferon response and enhances susceptibility to viral infection.

23 April 2018 | doi: 10.1038/s41467-018-04075-1
Bacterial host response  Hepatitis C virus  Molecular medicine  Viral host response 

Anthropogenic combustion iron as a complex climate forcer OPEN
Hitoshi Matsui, Natalie M. Mahowald, Nobuhiro Moteki, Douglas S. Hamilton, Sho Ohata, Atsushi Yoshida, Makoto Koike, Rachel A. Scanza & Mark G. Flanner

As a source of soluble iron, anthropogenic combustion iron is considered less important than natural sources. Here, the authors combine new measurements with a global aerosol model and show the atmospheric burden of anthropogenic combustion iron to be 8 times greater than previous estimates.

23 April 2018 | doi: 10.1038/s41467-018-03997-0
Atmospheric chemistry  Atmospheric science  Climate and Earth system modelling  Climate change  Climate sciences 

Evolution of high-level resistance during low-level antibiotic exposure OPEN
Erik Wistrand-Yuen, Michael Knopp, Karin Hjort, Sanna Koskiniemi, Otto G. Berg & Dan I. Andersson

Mutational antibiotic resistance can emerge under either high or low antibiotic levels. Here, the authors show several small-effect resistance mutations are combined to confer high-level resistance in Salmonella enterica exposed to sub-MIC levels of streptomycin.

23 April 2018 | doi: 10.1038/s41467-018-04059-1
Antimicrobial resistance  Evolution  Experimental evolution  Microbiology 

The IL-33-PIN1-IRAK-M axis is critical for type 2 immunity in IL-33-induced allergic airway inflammation OPEN
Morris Nechama, Jeahoo Kwon, Shuo Wei, Adrian Tun Kyi, Robert S. Welner, Iddo Z. Ben-Dov, Mohamed S. Arredouani, John M. Asara, Chun-Hau Chen, Cheng-Yu Tsai, Kyle F. Nelson, Koichi S Kobayashi, Elliot Israel, Xiao Zhen Zhou, Linda K. Nicholson & Kun Ping Lu

IL-33 orchestrates type 2 immunity in allergic asthma. Here the authors show, using biochemical, structural and patient data, that upon IL-33 or allergic challenge, the isomerase Pin1 modifies IRAK-M to control the production of pro-inflammatory cytokines in the setting of airway inflammation.

23 April 2018 | doi: 10.1038/s41467-018-03886-6
Antibodies  Chronic inflammation  Inflammatory diseases  Interleukins 

A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development OPEN
Mingtang Xie, Hongyu Chen, Ling Huang, Ryan C. O’Neil, Maxim N. Shokhirev & Joseph R. Ecker

Cytokinin regulates gene expression by activation of ARR transcription factors. Here, the authors use ChIP-seq to show how three type B-ARRs mediate cytokinin response in Arabidopsis and provide evidence that cytokinin regulates meristem development by promoting B-ARR binding to WUSCHEL.

23 April 2018 | doi: 10.1038/s41467-018-03921-6
Cytokinin  Shoot apical meristem 

Effect of interstitial palladium on plasmon-driven charge transfer in nanoparticle dimers OPEN
Sarah Lerch & Björn M. Reinhard

Plasmon coupling between nanoparticles may depend not only on interparticle gap distance, but also on gap conductance. Here, the authors modify the gap conductance—and thus the plasmon response—between gold nanoparticle dimers by growing varying amounts of palladium nanoparticles in the gap.

23 April 2018 | doi: 10.1038/s41467-018-04066-2
Electron transfer  Nanoparticles  Nanophotonics and plasmonics  Optical spectroscopy 

Multi-faceted immunomodulatory and tissue-tropic clinical bacterial isolate potentiates prostate cancer immunotherapy OPEN
Jonathan F. Anker, Anum F. Naseem, Hanlin Mok, Anthony J. Schaeffer, Sarki A. Abdulkadir & Praveen Thumbikat

CP1 is an uropathogenic Escherichia coli previously shown to promote inflammation and progression to prostate cancer. Here the authors show that in the context of a fully developed prostate cancer, CP1 promotes T cell infiltration into the tumour and increases the efficacy of anti-PD1 immunotherapy.

23 April 2018 | doi: 10.1038/s41467-018-03900-x
Cancer immunotherapy  Cancer microenvironment  Prostate cancer  Tumour immunology 

High spectral resolution of gamma-rays at room temperature by perovskite CsPbBr3 single crystals OPEN
Yihui He, Liviu Matei, Hee Joon Jung, Kyle M. McCall, Michelle Chen, Constantinos C. Stoumpos, Zhifu Liu, John A. Peters, Duck Young Chung, Bruce W. Wessels, Michael R. Wasielewski, Vinayak P. Dravid, Arnold Burger & Mercouri G. Kanatzidis

Detection and spectroscopic measurements of gamma-ray used to rely on expensive materials such as CdZnTe crystals. Here He et al. develop a melt method to grow large size CsPbBr3 perovskite crystals and the devices achieve low cost, high energy resolving capabilities and stability.

23 April 2018 | doi: 10.1038/s41467-018-04073-3
Engineering  Materials science  Optics and photonics 

Gauging force by tapping tendons OPEN
Jack A. Martin, Scott C. E. Brandon, Emily M. Keuler, James R. Hermus, Alexander C. Ehlers, Daniel J. Segalman, Matthew S. Allen & Darryl G. Thelen

Mechanical forces exerted on tendons during locomotion cannot be readily measured without invasive methods. Here, the authors develop a non-invasive wearable device to track tendon loads by measuring shear wave propagation speed, and demonstrate its use during dynamic human movements.

23 April 2018 | doi: 10.1038/s41467-018-03797-6
Biomedical engineering  Mechanical engineering  Tendons 

Quantum spin liquid in the semiclassical regime OPEN
Ioannis Rousochatzakis, Yuriy Sizyuk & Natalia B. Perkins

Strongly correlated quantum spin liquid phases form when quantum fluctuations prevent magnetic ordering, which normally requires low spin systems that cannot be analyzed semiclassically. Here, the authors show that a large-spin Kitaev model supports a spin liquid phase in the semiclassical limit.

23 April 2018 | doi: 10.1038/s41467-018-03934-1
Magnetic properties and materials  Theoretical physics  Topological matter 

A mobile endocytic network connects clathrin-independent receptor endocytosis to recycling and promotes T cell activation OPEN
Ewoud B. Compeer, Felix Kraus, Manuela Ecker, Gregory Redpath, Mayan Amiezer, Nils Rother, Philip R. Nicovich, Natasha Kapoor-Kaushik, Qiji Deng, Guerric P. B. Samson, Zhengmin Yang, Jieqiong Lou, Michael Carnell, Haig Vartoukian, Katharina Gaus & Jérémie Rossy

Endocytosis of T cell receptors (TCR) and their polarized recycling back to the plasma membrane is crucial for T cell activation; however, the underlying mechanisms remain unclear. Here the authors follow TCR and show that a mobile endocytic network connects clathrin-independent receptor endocytosis to recycling which is required for T cell activation.

23 April 2018 | doi: 10.1038/s41467-018-04088-w
Cell signalling  Endosomes  Imaging the immune system 

Evidence for prevalent Z=6 magic number in neutron-rich carbon isotopes OPEN
D. T. Tran , H. J. Ong, G. Hagen, T. D. Morris, N. Aoi, T. Suzuki, Y. Kanada-En’yo, L. S. Geng, S. Terashima, I. Tanihata, T. T. Nguyen, Y. Ayyad, P. Y. Chan, M. Fukuda, H. Geissel, M. N. Harakeh, T. Hashimoto, T. H. Hoang, E. Ideguchi, A. Inoue et al.

Magic numbers are associated with the stability of atomic nuclei. Here, the authors analyse the proton radii, binding energies and electric quadrupole transition rates of neutron-rich carbon isotopes at proton number six and use nuclear structure models to support the magic number Z = 6.

23 April 2018 | doi: 10.1038/s41467-018-04024-y
Experimental nuclear physics  Theoretical nuclear physics 

Perovskite seeding growth of formamidinium-lead-iodide-based perovskites for efficient and stable solar cells OPEN
Yicheng Zhao, Hairen Tan, Haifeng Yuan, Zhenyu Yang, James Z. Fan, Junghwan Kim, Oleksandr Voznyy, Xiwen Gong, Li Na Quan, Chih Shan Tan, Johan Hofkens, Dapeng Yu, Qing Zhao & Edward H. Sargent

Formamidinium-lead-iodide-based perovskites have a preferred bandgap below 1.55 eV for solar cell applications but suffer from operational instability. Here, Zhao et al. improve the film quality using cesium-containing seeded growth to show high stabilized efficiency and more than 100 h lifetime under simulated sunlight.

23 April 2018 | doi: 10.1038/s41467-018-04029-7
Energy  Solar cells 

Targeting GLP-1 receptor trafficking to improve agonist efficacy OPEN
Ben Jones , Teresa Buenaventura, Nisha Kanda, Pauline Chabosseau, Bryn M. Owen, Rebecca Scott, Robert Goldin, Napat Angkathunyakul, Ivan R. Corrêa Jr, Domenico Bosco, Paul R. Johnson, Lorenzo Piemonti, Piero Marchetti, A. M. James Shapiro, Blake J. Cochran, Aylin C. Hanyaloglu, Asuka Inoue, Tricia Tan, Guy A. Rutter, Alejandra Tomas et al.

Glucagon-like peptide-1 receptor (GLP-1R) promotes insulin secretion from pancreatic beta cells and undergoes agonist-mediated endocytosis. Here, authors study GLP-1R endocytosis caused by different agonists and show that a longer plasma membrane retention time of GLP-1R results in greater long-term insulin release.

23 April 2018 | doi: 10.1038/s41467-018-03941-2
Membrane trafficking  Receptor pharmacology 

Heterogeneous Fe3 single-cluster catalyst for ammonia synthesis via an associative mechanism OPEN
Jin-Cheng Liu, Xue-Lu Ma, Yong Li, Yang-Gang Wang, Hai Xiao & Jun Li

The current industrial ammonia synthesis relies on the Haber-Bosch process that is limited by the Brønsted–Evans–Polanyi relation. Here, the authors propose a new strategy that an anchored Fe3 on θ-Al2O3(010) surface serves as a heterogeneous single cluster catalyst for ammonia synthesis from first-principles calculations and microkinetic analysis.

23 April 2018 | doi: 10.1038/s41467-018-03795-8
Catalytic mechanisms  Heterogeneous catalysis  Reaction mechanisms 

Quantifying absolute addressability in DNA origami with molecular resolution OPEN
Maximilian T. Strauss, Florian Schueder, Daniel Haas, Philipp C. Nickels & Ralf Jungmann

Self-assembled DNA nanostructures hold potential as nanomachines or platforms for organized chemical synthesis, but methods for assembly quality control are lacking. Here the authors use DNA-PAINT to quantify the incorporation and accessibility of individual strands in a DNA origami platform with molecular resolution.

23 April 2018 | doi: 10.1038/s41467-018-04031-z
DNA nanostructures  Super-resolution microscopy 

Identity prediction errors in the human midbrain update reward-identity expectations in the orbitofrontal cortex OPEN
James D. Howard & Thorsten Kahnt

Responses in the dopaminergic midbrain are known to signal prediction errors for reward value. Here, the authors show that the human midbrain also encodes errors in predicted reward identity, and that these signals update expectations of reward identity in the orbitofrontal cortex.

23 April 2018 | doi: 10.1038/s41467-018-04055-5
Decision  Reward 

True equilibrium measurement of transcription factor-DNA binding affinities using automated polarization microscopy OPEN
Christophe Jung, Peter Bandilla, Marc von Reutern, Max Schnepf, Susanne Rieder, Ulrich Unnerstall & Ulrike Gaul

Methods to measure selective transcription factor-DNA binding often lack sensitivity and are not performed in solution. Here the authors develop a method to perform fluorescence anisotropy measurements of transcription factor-DNA binding energies with high sensitivity and throughput.

23 April 2018 | doi: 10.1038/s41467-018-03977-4
Biophysical methods  Embryogenesis  Polarization microscopy 

Cold adaptation recorded in tree rings highlights risks associated with climate change and assisted migration OPEN
David Montwé, Miriam Isaac-Renton, Andreas Hamann & Heinrich Spiecker

Assisted migration has been proposed to aid trees in altering their ranges under climate change. Here, Montwé et al. use common garden experiments to show that lodgepole pine populations vary in their cold susceptibility, suggesting seed transfer may increase the risk of frost damage.

23 April 2018 | doi: 10.1038/s41467-018-04039-5
Climate-change impacts  Ecological genetics  Forest ecology  Forestry 

Tamoxifen-resistant breast cancer cells are resistant to DNA-damaging chemotherapy because of upregulated BARD1 and BRCA1 OPEN
Yinghua Zhu, Yujie Liu, Chao Zhang, Junjun Chu, Yanqing Wu, Yudong Li, Jieqiong Liu, Qian Li, Shunying Li, Qianfeng Shi, Liang Jin, Jianli Zhao, Dong Yin, Sol Efroni, Fengxi Su, Herui Yao, Erwei Song & Qiang Liu

Most breast cancer patients are estrogen receptor positive and thus benefit from treatments that inhibit estrogen production; however, one third of tamoxifen-treated patients develops resistance and relapse. Here the authors show that tamoxifen resistant cells are resistant to chemotherapy because of BARD1 and BRCA1 upregulation.

23 April 2018 | doi: 10.1038/s41467-018-03951-0
Biological sciences  Breast cancer  Cancer therapeutic resistance 

High-order coherent communications using mode-locked dark-pulse Kerr combs from microresonators OPEN
Attila Fülöp, Mikael Mazur, Abel Lorences-Riesgo, Óskar B. Helgason, Pei-Hsun Wang, Yi Xuan, Dan E. Leaird, Minghao Qi, Peter A. Andrekson, Andrew M. Weiner & Victor Torres-Company

Dark-pulse combs may be useful for coherent communications since they display high power conversion efficiency. Here, the authors report the first demonstration of coherent wavelength division multiplexing using dark pulse microresonator combs high signal-to-noise while maintaining a low on-chip pump power.

23 April 2018 | doi: 10.1038/s41467-018-04046-6
Fibre optics and optical communications  Frequency combs  Microresonators  Nonlinear optics 

Quantitative diffusion measurements using the open-source software PyFRAP OPEN
Alexander Bläßle, Gary Soh, Theresa Braun, David Mörsdorf, Hannes Preiß, Ben M. Jordan & Patrick Müller

FRAP analysis often relies on simplified assumptions that can affect measurement accuracy. Here the authors present a Python-based FRAP analysis software using simulations instead of simplified theoretical models to fit the data, which accounts for complex sample geometries and bleach conditions.

20 April 2018 | doi: 10.1038/s41467-018-03975-6
Biophysical methods  Computational biology and bioinformatics  Developmental biology 

Biological recognition of graphene nanoflakes OPEN
V. Castagnola, W. Zhao, L. Boselli, M. C. Lo Giudice, F. Meder, E. Polo, K. R. Paton, C. Backes, J. N. Coleman & K. A. Dawson

The production of graphene nanoflakes for biological studies is usually done in a controlled chemical environment. Here, the authors develop a method to produce graphene nanoflakes in biofluids and find that their protein coats are different from that of other materials.

20 April 2018 | doi: 10.1038/s41467-018-04009-x
Biomaterials – proteins  Nanoparticles 

Self-replication of DNA by its encoded proteins in liposome-based synthetic cells OPEN
Pauline van Nies, Ilja Westerlaken, Duco Blanken, Margarita Salas, Mario Mencía & Christophe Danelon

Replicating DNA and converting genetic information to protein is a feature of cellular life. Here the authors implement a coupled DNA replication and gene expression system inside vesicles.

20 April 2018 | doi: 10.1038/s41467-018-03926-1
DNA  DNA replication  Synthetic biology 

Nucleus accumbens controls wakefulness by a subpopulation of neurons expressing dopamine D1 receptors OPEN
Yan-Jia Luo, Ya-Dong Li, Lu Wang, Su-Rong Yang, Xiang-Shan Yuan, Juan Wang, Yoan Cherasse, Michael Lazarus, Jiang-Fan Chen, Wei-Min Qu & Zhi-Li Huang

The nucleus accumbens regulates many behaviours that depend on arousal. Here the authors show that dopamine D1 receptor neurons in the nucleus accumbens can directly regulate wakefulness.

20 April 2018 | doi: 10.1038/s41467-018-03889-3
Neural circuits  Wakefulness 

Mechanically interlocked functionalization of monoclonal antibodies OPEN
Krzysztof P. Bzymek, James W. Puckett, Cindy Zer, Jun Xie, Yuelong Ma, Jeremy D. King, Leah H. Goodstein, Kendra N. Avery, David Colcher, Gagandeep Singh, David A. Horne & John C. Williams

Meditope-Fab is a peptide-antibody complex potentially useful for drug delivery and diagnostic, but a short half-life prevents its use in vivo. Here the authors engineer the complex to improve its stability, create functionalized antibodies by click chemistry and use them for in vivo tumor imaging.

20 April 2018 | doi: 10.1038/s41467-018-03976-5
Biotechnology  Chemical biology 

Late Miocene climate cooling and intensification of southeast Asian winter monsoon OPEN
Ann E. Holbourn, Wolfgang Kuhnt, Steven C. Clemens, Karlos G. D. Kochhann, Janika Jöhnck, Julia Lübbers & Nils Andersen

The late Miocene period allows investigation of climate-carbon cycle dynamics on a warmer-than-modern Earth. Here, the authors show that changes in the global carbon cycle drove climate cooling, culminating in ephemeral Northern Hemisphere glaciations and intensification of the Asian winter monsoon from 7 to 5.5 Ma.

20 April 2018 | doi: 10.1038/s41467-018-03950-1
Palaeoceanography  Palaeoclimate 

The effect of crystallite size on pressure amplification in switchable porous solids OPEN
Simon Krause, Volodymyr Bon, Irena Senkovska, Daniel M. Többens, Dirk Wallacher, Renjith S. Pillai, Guillaume Maurin & Stefan Kaskel

Pressure amplification phenomena have recently been observed in ordered mesoporous solids, but little is understood about this counter-intuitive behaviour. Here, Kaskel and colleagues demonstrate that crystal size can play an important role in modulating pressure amplification in metal-organic frameworks.

20 April 2018 | doi: 10.1038/s41467-018-03979-2
Metal–organic frameworks  Porous materials  Solid-phase synthesis 

Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis OPEN
Jack P. Wang , Megan L. Matthews, Cranos M. Williams, Rui Shi, Chenmin Yang, Sermsawat Tunlaya-Anukit, Hsi-Chuan Chen, Quanzi Li, Jie Liu, Chien-Yuan Lin, Punith Naik, Ying-Hsuan Sun, Philip L. Loziuk, Ting-Feng Yeh, Hoon Kim, Erica Gjersing, Todd Shollenberger, Christopher M. Shuford, Jina Song, Zachary Miller et al.

A systematic analysis of lignin biosynthetic genes to quantitatively understand their effect on wood properties is still lacking. Here, the authors integrate transcriptomic, proteomic, fluxomic and phenomic data to quantify the impact of perturbations of transcript abundance on lignin biosynthesis and wood properties.

20 April 2018 | doi: 10.1038/s41467-018-03863-z
Genetic engineering  Molecular engineering in plants  Secondary metabolism 

The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage OPEN
Han N. Ho, Antoine M. van Oijen & Harshad Ghodke

The bacterial transcription-repair coupling factor Mfd displaces stalled RNA polymerase (RNAP) by promoting transcription termination at sites of DNA lesions. Here the authors find—using single molecule imaging in live Escherichia coli—that RNAP stalls frequently during transcription, and needs to be rescued by Mfd during normal growth.

20 April 2018 | doi: 10.1038/s41467-018-03790-z
Bacterial transcription  DNA  Enzyme mechanisms  Single-cell imaging  Single-molecule biophysics 

Proteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress OPEN
Jiska van der Reest, Sergio Lilla, Liang Zheng, Sara Zanivan & Eyal Gottlieb

Reactive oxygen species can modify cysteine residues on proteins to control cellular signalling. Here, the authors develop a proteomics approach to assess cysteine oxidation dynamics in cells and primary tissues, monitoring oxidative stress-induced metabolic adaptations and oxidation states of biofluid proteins.

20 April 2018 | doi: 10.1038/s41467-018-04003-3
Energy metabolism  Metabolomics  Post-translational modifications  Proteomics 

The mechanisms of crystal growth inhibition by organic and inorganic inhibitors OPEN
S. Dobberschütz, M. R. Nielsen, K. K. Sand, R. Civioc, N. Bovet, S. L. S. Stipp & M. P. Andersson

Although trace compounds are known to inhibit crystal growth, the mechanisms by which they do so are unclear. Here, the authors use a microkinetic model to study the mechanisms of several inhibitors of calcite growth, finding that the processes are quite different for inorganic and organic inhibitors.

20 April 2018 | doi: 10.1038/s41467-018-04022-0
Atomistic models  Geochemistry  Surface assembly 

Inducing skyrmions in ultrathin Fe films by hydrogen exposure OPEN
Pin-Jui Hsu, Levente Rózsa, Aurore Finco, Lorenz Schmidt, Krisztián Palotás, Elena Vedmedenko, László Udvardi, László Szunyogh, André Kubetzka, Kirsten von Bergmann & Roland Wiesendanger

Stabilization of skyrmions is one of the key issues in skyrmion-based spintronics. Here the authors demonstrate that hydrogenation can induce the formation of skyrmions in iron thin films, which provides an alternative way to tailor skyrmion states in low-dimensional magnetic materials.

20 April 2018 | doi: 10.1038/s41467-018-04015-z
Materials science  Nanoscience and technology  Physics 

The LINC01138 drives malignancies via activating arginine methyltransferase 5 in hepatocellular carcinoma OPEN
Zhe Li, Jiwei Zhang, Xinyang Liu, Shengli Li, Qifeng Wang, Di Chen, Zhixiang Hu, Tao Yu, Jie Ding, Jinjun Li, Ming Yao, Jia Fan, Shenglin Huang, Qiang Gao, Yingjun Zhao & Xianghuo He

Long intergenic non-coding RNAs have been linked to cancer development. Here the authors, using RNA-seq and genomic amplification data, identify lincRNAs deregulated in hepatocellular carcinoma and propose that Linc01138 is stabilized by IGF2BP1/3 in the cytoplasm, and binds and stabilizes the methyltransferase PRMT5 by preventing the association of PRMT5 to the E3 ubiquitin ligase CHIP.

20 April 2018 | doi: 10.1038/s41467-018-04006-0
Oncogenes  Tumour biomarkers 

Pathogen-derived extracellular vesicles mediate virulence in the fatal human pathogen Cryptococcus gattii OPEN
Ewa Bielska, Marta Arch Sisquella, Maha Aldeieg, Charlotte Birch, Eloise J. O’Donoghue & Robin C. May

Highly virulent cells of the fungal pathogen Cryptococcus gattiigrow rapidly within phagocytes by stimulating the growth of neighbouring fungal cells. Here, Bielska et al. show that this effect is mediated by the release of fungal extracellular vesicles that can be taken up by infected macrophages.

19 April 2018 | doi: 10.1038/s41467-018-03991-6
Fungal pathogenesis  Pathogens 

Hard magnetic properties in nanoflake van der Waals Fe3GeTe2 OPEN
Cheng Tan, Jinhwan Lee, Soon-Gil Jung, Tuson Park, Sultan Albarakati, James Partridge, Matthew R. Field, Dougal G. McCulloch, Lan Wang & Changgu Lee

Exploring the magnetism in the van der Waals materials facilitates two dimensional spintronic devices. Here the authors demonstrate the evolution of magnetic behavior, strong perpendicular magnetic anisotropy and existence of magnetic coupling between atomic layers in Fe3GeTe2 nanoflakes by varying the layer thickness.

19 April 2018 | doi: 10.1038/s41467-018-04018-w
Electronic and spintronic devices  Magnetic properties and materials  Two-dimensional materials 

Culturing of female bladder bacteria reveals an interconnected urogenital microbiota OPEN
Krystal Thomas-White, Samuel C. Forster, Nitin Kumar, Michelle Van Kuiken, Catherine Putonti, Mark D. Stares, Evann E. Hilt, Travis K. Price, Alan J. Wolfe & Trevor D. Lawley

The female bladder seems to harbor a poorly characterized indigenous microbiota. Here, the authors isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women, generating a culture collection representing two thirds of the bacterial diversity within the samples.

19 April 2018 | doi: 10.1038/s41467-018-03968-5
Bacterial genetics  Bladder  Metagenomics  Microbiome 

Aggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target OPEN
Olli Dufva , Matti Kankainen, Tiina Kelkka, Nodoka Sekiguchi, Shady Adnan Awad, Samuli Eldfors, Bhagwan Yadav, Heikki Kuusanmäki, Disha Malani, Emma I Andersson, Paavo Pietarinen, Leena Saikko, Panu E. Kovanen, Teija Ojala, Dean A. Lee, Thomas P. Loughran Jr., Hideyuki Nakazawa, Junji Suzumiya, Ritsuro Suzuki, Young Hyeh Ko et al.

Aggressive natural killer-cell leukemia (ANKL) has few targeted therapies. Here ANKL patients are reported to harbor STAT3, RAS-MAPK pathway, DDX3X and epigenetic modifier mutations; and drug sensitivity profiling uncovers the importance of the JAK-STAT pathway, revealing potential ANKL therapeutic targets.

19 April 2018 | doi: 10.1038/s41467-018-03987-2
Cancer genomics  High-throughput screening  Leukaemia 

Gene refashioning through innovative shifting of reading frames in mosses OPEN
Yanlong Guan, Li Liu, Qia Wang, Jinjie Zhao, Ping Li, Jinyong Hu, Zefeng Yang, Mark P. Running, Hang Sun & Jinling Huang

Extant representatives of the earliest land plant lineages adapt to various terrestrial habitats with structural and physiological innovations. Here the authors show a dual-coding gene in the moss Physcomitrella patens evolved from a hemerythrin gene, with effects on oil body biogenesis and dehydration resistance.

19 April 2018 | doi: 10.1038/s41467-018-04025-x
Evolutionary genetics  Plant evolution 

The E3 ubiquitin ligase Pellino2 mediates priming of the NLRP3 inflammasome OPEN
Fiachra Humphries, Ronan Bergin, Ruaidhri Jackson, Nezira Delagic, Bingwei Wang, Shuo Yang, Alice V. Dubois, Rebecca J. Ingram & Paul N. Moynagh

The NLRP3 inflammasome is important for inducing IL-1β and IL-18 inflammatory responses. Here the authors show, by generating and characterizing Peli2 deficient mice and immune cells, that an E3 ubiquitin ligase Pellino2 promotes inflammasome priming by inducing NLRP3 ubiquitination and by targeting IRAK1.

19 April 2018 | doi: 10.1038/s41467-018-03669-z
Immune cell death  Inflammasome  Monocytes and macrophages  Ubiquitylation 

Stereoselective photoredox ring-opening polymerization of O-carboxyanhydrides OPEN
Quanyou Feng, Lei Yang, Yongliang Zhong, Dong Guo, Guoliang Liu, Linghai Xie, Wei Huang & Rong Tong

The stereoselective synthesis of polyesters has been achieved via various methods; however, all routes show limited side-chain group functionality. Here the authors synthesize stereoblock polyesters by photoredox ring-opening polymerization of racemic O-carboxyanhydrides that have abundant side-chain functionality.

19 April 2018 | doi: 10.1038/s41467-018-03879-5
Photocatalysis  Polymer synthesis  Polymerization mechanisms 

A proteomics landscape of circadian clock in mouse liver OPEN
Yunzhi Wang, Lei Song, Mingwei Liu, Rui Ge, Quan Zhou, Wanlin Liu, Ruiyang Li, Jingbo Qie, Bei Zhen, Yi Wang, Fuchu He, Jun Qin & Chen Ding

As a circadian organ, liver functions are regulated by circadian clock. Here, the authors present a comprehensive proteomics landscape of the mouse liver, including transcription factor binding profiles, phosphorylation and ubiquitylation patterns, nuclear and whole proteome, and the transcriptome.

19 April 2018 | doi: 10.1038/s41467-018-03898-2
Physiology  Post-translational modifications  Proteomics  Transcriptomics 

Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote OPEN
Yueyong Xin, Yang Shi, Tongxin Niu, Qingqiang Wang, Wanqiang Niu, Xiaojun Huang, Wei Ding, Lei Yang, Robert E. Blankenship, Xiaoling Xu & Fei Sun

Filamentous anoxygenic phototrophs (FAPs) are phylogenetically distant from other anoxygenic photosynthetic bacteria. Here the authors present the 4.1 Å cryo-EM structure of the photosynthetic core complex from the FAP Roseiflexus castenholzii and propose a model for energy and electron transfer.

19 April 2018 | doi: 10.1038/s41467-018-03881-x
Cryoelectron microscopy  Membrane biophysics 

Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions OPEN
Dongjie Zhu, Xiangxi Wang, Qianglin Fang, James L Van Etten, Michael G Rossmann, Zihe Rao & Xinzheng Zhang

Conventional reconstruction methods used in cryo-EM single particle analysis do not take the depth of field effect into account. Here the authors present a block-based reconstruction method to deal with the depth of field effect and show that this approach can improve the resolution of cryo-EM virus structures.

19 April 2018 | doi: 10.1038/s41467-018-04051-9
Cryoelectron microscopy 

Spontaneous formation of gold nanostructures in aqueous microdroplets OPEN
Jae Kyoo Lee, Devleena Samanta, Hong Gil Nam & Richard N. Zare

Reactions in aqueous microdroplets can significantly differ from those in bulk. Here, the authors report microdroplets that not only accelerate gold nanoparticle formation by several orders of magnitude but also promote spontaneous nanostructure formation with no reducing agents or template.

19 April 2018 | doi: 10.1038/s41467-018-04023-z
Materials chemistry  Nanoparticle synthesis  Nanoscale materials 

Nanoscale zero-field electron spin resonance spectroscopy OPEN
Fei Kong, Pengju Zhao, Xiangyu Ye, Zhecheng Wang, Zhuoyang Qin, Pei Yu, Jihu Su, Fazhan Shi & Jiangfeng Du

Demonstrations of sensing devices using nitrogen vacancy centres have shown significantly improved sensitivity compared to traditional methods. Here the authors demonstrate an approach for performing nanoscale electron spin resonance without magnetic fields in order to achieve better spectral resolution.

19 April 2018 | doi: 10.1038/s41467-018-03969-4
Applied physics  Optical properties of diamond  Techniques and instrumentation 

Gold-nanofève surface-enhanced Raman spectroscopy visualizes hypotaurine as a robust anti-oxidant consumed in cancer survival OPEN
Megumi Shiota , Masayuki Naya, Takehiro Yamamoto, Takako Hishiki, Takeharu Tani, Hiroyuki Takahashi, Akiko Kubo, Daisuke Koike, Mai Itoh, Mitsuyo Ohmura, Yasuaki Kabe, Yuki Sugiura, Nobuyoshi Hiraoka, Takayuki Morikawa, Keiyo Takubo, Kentaro Suina, Hideaki Nagashima, Oltea Sampetrean, Osamu Nagano, Hideyuki Saya et al.

Surface-enhanced Raman spectroscopy (SERS) visualizes fingerprints of intermolecular vibrations of many metabolites. Here the authors report a SERS imaging technique that enables the visualization of metabolites distribution and automated extraction of tumour boundaries in frozen tissues.

19 April 2018 | doi: 10.1038/s41467-018-03899-1
Cancer metabolism  Molecular medicine 

Histone demethylase JMJD1A coordinates acute and chronic adaptation to cold stress via thermogenic phospho-switch OPEN
Yohei Abe, Yosuke Fujiwara, Hiroki Takahashi, Yoshihiro Matsumura, Tomonobu Sawada, Shuying Jiang, Ryo Nakaki, Aoi Uchida, Noriko Nagao, Makoto Naito, Shingo Kajimura, Hiroshi Kimura, Timothy F. Osborne, Hiroyuki Aburatani, Tatsuhiko Kodama, Takeshi Inagaki & Juro Sakai

JMJD1A is essential for thermogenic gene induction in brown adipose tissue. Here the authors show that white adipose tissue beige-ing requires both β-adrenergic-dependent phosphorylation of S265 and demethylation activity of JMJD1A while brown adipose tissue-driven thermogenesis requires β-adrenergic dependent phosphorylation of S265 but is independent of H3K9me2 demethylation.

19 April 2018 | doi: 10.1038/s41467-018-03868-8
Fat metabolism  Phosphorylation 

Interplay of orbital effects and nanoscale strain in topological crystalline insulators OPEN
Daniel Walkup, Badih A. Assaf, Kane L. Scipioni, R. Sankar, Fangcheng Chou, Guoqing Chang, Hsin Lin, Ilija Zeljkovic & Vidya Madhavan

The role of orbital degrees of freedom in determining the electronic structure remains obscured. Here, Walkup et al. report strain-induced band structure changes in a topological crystalline insulator SnTe, whose surprising behavior reflects the  orbital nature of bands.

19 April 2018 | doi: 10.1038/s41467-018-03887-5
Electronic properties and materials  Topological matter 

Reduced oxidative capacity in macrophages results in systemic insulin resistance OPEN
Saet-Byel Jung, Min Jeong Choi, Dongryeol Ryu, Hyon-Seung Yi, Seong Eun Lee, Joon Young Chang, Hyo Kyun Chung, Yong Kyung Kim, Seul Gi Kang, Ju Hee Lee, Koon Soon Kim, Hyun Jin Kim, Cuk-Seong Kim, Chul-Ho Lee, Robert W. Williams, Hail Kim, Heung Kyu Lee, Johan Auwerx & Minho Shong

M1-like polarization of macrophages is thought to control adipose inflammation and associated insulin resistance and metabolic syndrome. Here the authors show that macrophage-specific deletion of the OxPhos-related gene Crif1 results in an M1-like phenotype in mice, and that the effects can be reversed by recombinant GDF15.

19 April 2018 | doi: 10.1038/s41467-018-03998-z
Chronic inflammation  Metabolic syndrome  Obesity  Type 2 diabetes 

How high energy fluxes may affect Rayleigh–Taylor instability growth in young supernova remnants OPEN
C. C. Kuranz , H.-S. Park, C. M. Huntington, A. R. Miles, B. A. Remington, T. Plewa, M. R. Trantham, H. F. Robey, D. Shvarts, A. Shimony, K. Raman, S. MacLaren, W. C. Wan, F. W. Doss, J. Kline, K. A. Flippo, G. Malamud, T. A. Handy, S. Prisbrey, C. M. Krauland et al.

Radiation and conduction are generally considered as the main energy transport mechanisms for the evolution of early supernova remnants. Here the authors experimentally show the role of electron heat transfer on the growth of Rayleigh–Taylor instability in young supernova remnants.

19 April 2018 | doi: 10.1038/s41467-018-03548-7
Astronomy and planetary science  Laser-produced plasmas 

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition OPEN
Pooja Kumari, Florian Aeschimann, Dimos Gaidatzis, Jeremy J. Keusch, Pritha Ghosh, Anca Neagu, Katarzyna Pachulska-Wieczorek, Janusz M. Bujnicki, Heinz Gut, Helge Großhans & Rafal Ciosk

The C. elegans LIN-41 and its homologs, including human TRIM71/LIN41, contain the RNA binding NHL domain. Here the authors combine computational analysis, structural biology and in vivo studies, to explain how these proteins bind RNA and how rapid evolution of NHL domains resulted in different solutions to RNA recognition.

19 April 2018 | doi: 10.1038/s41467-018-03920-7
Computational biology and bioinformatics  RNA  X-ray crystallography 

The molecular basis of JAK/STAT inhibition by SOCS1 OPEN
Nicholas P. D. Liau, Artem Laktyushin, Isabelle S. Lucet, James M. Murphy, Shenggen Yao, Eden Whitlock, Kimberley Callaghan, Nicos A. Nicola, Nadia J. Kershaw & Jeffrey J. Babon

Cytokines are key molecules in controlling haematopoiesis that signal via the JAK/STAT pathway. Here the authors present the structures of SOCS1 bound to its JAK1 target as well as in complex with elonginB and elonginC, providing a molecular explanation for the potent JAK- inhibitory activity of SOCS1.

19 April 2018 | doi: 10.1038/s41467-018-04013-1
Biochemistry  Structural biology  X-ray crystallography 
  Latest Correspondence    
Reply to ‘Pitfalls in the quantitative imaging of glutathione in living cells’ OPEN
Xiqian Jiang, Jianwei Chen & Jin Wang
23 April 2018 | doi: 10.1038/s41467-018-04037-7
Biosensors  Chemical tools  Fluorescent dyes 

Pitfalls in the quantitative imaging of glutathione in living cells OPEN
Cristina Cossetti, Gianna Di Giovamberardino, Rossella Rota & Anna Pastore
23 April 2018 | doi: 10.1038/s41467-018-04035-9
Biosensors  Chemical tools  Fluorescent dyes 

Reply to ‘Anisotropy governs strain stiffening in nanotwinned-materials’ OPEN
Bing Li, Hong Sun & Changfeng Chen
23 April 2018 | doi: 10.1038/s41467-018-03967-6
Nanoscale materials  Theory and computation 

Anisotropy governs strain stiffening in nanotwinned-materials OPEN
Seyedeh Mohadeseh Taheri Mousavi, Guijin Zou, Haofei Zhou & Huajian Gao
23 April 2018 | doi: 10.1038/s41467-018-03972-9
Nanoscale materials  Theory and computation 
  Latest Author Correction    
Author Correction: Cardioprotection induced in a mouse model of neuropathic pain via anterior nucleus of paraventricular thalamus OPEN
Yi-Fen Cheng, Ya-Ting Chang, Wei-Hsin Chen, Hsi-Chien Shih, Yen-Hui Chen, Bai-Chuang Shyu & Chien-Chang Chen
23 April 2018 | doi: 10.1038/s41467-018-04160-5
Chronic pain  Myocardial infarction 
  Latest Publisher Corrections    
Publisher Correction: Nfat/calcineurin signaling promotes oligodendrocyte differentiation and myelination by transcription factor network tuning OPEN
Matthias Weider , Laura Julia Starost, Katharina Groll, Melanie Küspert, Elisabeth Sock, Miriam Wedel, Franziska Fröb, Christian Schmitt, Tina Baroti, Anna C. Hartwig, Simone Hillgärtner, Sandra Piefke, Tanja Fadler, Marc Ehrlich, Corinna Ehlert, Martin Stehling, Stefanie Albrecht, Ammar Jabali, Hans R. Schöler, Jürgen Winkler et al.
23 April 2018 | doi: 10.1038/s41467-018-03871-z
Differentiation  Oligodendrocyte 

Publisher Correction: Spin-controlled atom–ion chemistry OPEN
Tomas Sikorsky, Ziv Meir, Ruti Ben-shlomi, Nitzan Akerman & Roee Ozeri
23 April 2018 | doi: 10.1038/s41467-018-04165-0
Atomic and molecular collision processes  Reaction kinetics and dynamics  Physics  Ultracold gases 

Publisher Correction: JMJD5 is a human arginyl C-3 hydroxylase OPEN
Sarah E. Wilkins, Md. Saiful Islam, Joan M. Gannon, Suzana Markolovic, Richard J. Hopkinson, Wei Ge, Christopher J. Schofield & Rasheduzzaman Chowdhury
23 April 2018 | doi: 10.1038/s41467-018-04196-7
Enzyme mechanisms  High-throughput screening  Nanocrystallography  Post-translational modifications  Proteomics 

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