Nature Communications - 14 March 2018

Advertisement Princeton University, Princeton Institute for the Science and Technology of Materials (PRISM), Nature Communications, Nature Materials, Nature Structural & Molecular Biology present: Princeton - Nature Conference: Frontiers in Electron Microscopy for the Physical and Life Sciences July 11-13, 2018, Princeton University, Princeton, NJ, USA Abstract submissions and registration is open. Register now to secure your place.        Weekly Content Alert Nature Communications is fully open access. Read more. 14 March 2018  Latest content: Articles Addendum Author Corrections Publisher Corrections Advertisement   Nature Outlook: Climate Change Discover how scientists that are tired of inaction on climate change are seeking technical and political solutions to a truly global problem.  Access the Outlook free online for six months  Journal homepage Recommend to library Web feed     Latest Review View all Articles         Nature Communications JOBS of the week Postdoctoral Fellow The Brigham and Women's Hospital Research Associate University of British Columbia (UBC) Postdoctoral position Universitätsspital Bern Research Fellow The University of Warwick Post-Doctoral Fellow University of Maryland Baltimore Assistant or Associate Professor Augusta University Postdoctoral Research Scientist The Earlham Institute Postdoctoral Fellows Ohio State University Biomedical Writer Phase V, ghg | greyhealth group Postdoctoral Fellow Cornell University More Science jobs from Nature Communications EVENT Health Leaders Research Congress 24.04.18 Berlin, Germany More science events from     Latest Articles View all Articles     Dark zone of the Greenland Ice Sheet controlled by distributed biologically-active impurities OPEN Jonathan C. Ryan, Alun Hubbard, Marek Stibal, Tristram D. Irvine-Fynn, Joseph Cook, Laurence C. Smith, Karen Cameron & Jason Box The surface types that comprise the dark zone of the Greenland Ice Sheet, an area of bare ice with low albedo, are unknown. Here, the authors use UAV imagery to show that, during the melt-season, biologically active surface impurities are responsible for spatial albedo patterns and the dark zone itself. 14 March 2018 | doi: 10.1038/s41467-018-03353-2 Cryospheric science  The preprophase band-associated kinesin-14 OsKCH2 is a processive minus-end-directed microtubule motor OPEN Kuo-Fu Tseng, Pan Wang, Yuh-Ru Julie Lee, Joel Bowen, Allison M. Gicking, Lijun Guo, Bo Liu & Weihong Qiu Land plants lack the cytoplasmic dynein motor in fungi and animals that shows processive minus-end-directed motility on microtubules. Here the authors demonstrate that land plants have evolved novel processive minus-end-directed kinesin-14 motors that likely compensate for the absence of dynein. 14 March 2018 | doi: 10.1038/s41467-018-03480-w Kinesin  Motor protein function  Plant cytoskeleton  Single-molecule biophysics  Magnon detection using a ferroic collinear multilayer spin valve OPEN Joel Cramer, Felix Fuhrmann, Ulrike Ritzmann, Vanessa Gall, Tomohiko Niizeki, Rafael Ramos, Zhiyong Qiu, Dazhi Hou, Takashi Kikkawa, Jairo Sinova, Ulrich Nowak, Eiji Saitoh & Mathias Kläui The Joule heating free magnon spintronics advances conventional electronics but demands more magnon-based logic operations. Here the authors achieved the magnon spin valve functionality in a YIG/CoO/Co structure where the amplitude of transmitted magnon from the YIG layer is dependent on the relative alignment of the YIG and Co magnetization. 14 March 2018 | doi: 10.1038/s41467-018-03485-5 Ferromagnetism  Spintronics  Predicting the spatiotemporal diversity of seizure propagation and termination in human focal epilepsy OPEN Timothée Proix, Viktor K. Jirsa, Fabrice Bartolomei, Maxime Guye & Wilson Truccolo A major goal of epilepsy research is understanding the spatiotemporal dynamics of seizure. Here, the authors extend the Epileptor neural mass model into a neural field model, in order to provide a unified and patient-specific model of seizure initiation, propagation, and termination. 14 March 2018 | doi: 10.1038/s41467-018-02973-y Dynamical systems  Epilepsy  Network models  Chemo-photothermal therapy combination elicits anti-tumor immunity against advanced metastatic cancer OPEN Jutaek Nam, Sejin Son, Lukasz J. Ochyl, Rui Kuai, Anna Schwendeman & James J. Moon Photothermal therapy (PTT) for cancer treatment is currently limited to local, accessible, tumors. Here the authors show that PTT combination with chemotherapy, by stimulating an immune response, is effective against distant tumors and establishes immune memory, thus providing a strategy to target metastatic disease. 14 March 2018 | doi: 10.1038/s41467-018-03473-9 Biomedical engineering  Cancer immunotherapy  Drug delivery  Micro-scale fusion in dense relativistic nanowire array plasmas OPEN Alden Curtis, Chase Calvi, James Tinsley, Reed Hollinger, Vural Kaymak, Alexander Pukhov, Shoujun Wang, Alex Rockwood, Yong Wang, Vyacheslav N. Shlyaptsev & Jorge J. Rocca Neutron beams are useful studying fundamental physics problems, fusion process and material properties. Here the authors use intense laser irradiation of deuterated nanowire array targets to create high energy density plasmas capable of efficient generation of ultrafast neutron pulses. 14 March 2018 | doi: 10.1038/s41467-018-03445-z Laser-produced plasmas  Nanowires  Plasma-based accelerators  Ultrafast lasers  Shallow very-low-frequency earthquakes accompany slow slip events in the Nankai subduction zone OPEN Masaru Nakano, Takane Hori, Eiichiro Araki, Shuichi Kodaira & Satoshi Ide Slow earthquakes are now increasingly recognised to occur at plate boundaries globally. Here, the authors examine seafloor observational data from the Nankai trough and find that very-low-frequency events and slow-slip events frequently occur together and share the same common source fault. 14 March 2018 | doi: 10.1038/s41467-018-03431-5 Geodynamics  Seismology  The choroid plexus is an important circadian clock component OPEN Jihwan Myung, Christoph Schmal, Sungho Hong, Yoshiaki Tsukizawa, Pia Rose, Yong Zhang, Michael J. Holtzman, Erik De Schutter, Hanspeter Herzel, Grigory Bordyugov & Toru Takumi The suprachiasmatic nucleus (SCN) has been thought of as the master circadian clock, but peripheral circadian clocks do exist. Here, the authors show that the choroid plexus displays oscillations more robust than the SCN and that can be described as a Poincaré oscillator with negative twist. 14 March 2018 | doi: 10.1038/s41467-018-03507-2 Circadian mechanisms  Oscillators  Improving atomic displacement and replacement calculations with physically realistic damage models OPEN Kai Nordlund, Steven J. Zinkle, Andrea E. Sand, Fredric Granberg, Robert S. Averback, Roger Stoller, Tomoaki Suzudo, Lorenzo Malerba, Florian Banhart, William J. Weber, Francois Willaime, Sergei L. Dudarev & David Simeone The Norgett−Robinson−Torrens displacements per atom model is the benchmark to assess radiation damage in metals but has well-known limitations. Here, the authors use molecular dynamics to introduce material-specific modifications to describe radiation damage more realistically. 14 March 2018 | doi: 10.1038/s41467-018-03415-5 Metals and alloys  Nuclear physics  Theory and computation  Intermembrane crosstalk drives inner-membrane protein organization in Escherichia coli OPEN Patrice Rassam, Kathleen R. Long, Renata Kaminska, David J. Williams, Grigorios Papadakos, Christoph G. Baumann & Colin Kleanthous Outer membrane proteins (OMPs) in Gram-negative bacteria have restricted lateral mobility. Here, Rassam et al. show that the bacteriocin ColE9, via its interactions with OMPs, imposes this restricted mobility on the inner membrane proteins of the Tol-Pal complex. 14 March 2018 | doi: 10.1038/s41467-018-03521-4 Biological fluorescence  Cellular microbiology  Membrane structure and assembly  Next generation histology methods for three-dimensional imaging of fresh and archival human brain tissues OPEN Hei Ming Lai, Alan King Lun Liu, Harry Ho Man Ng, Marc H. Goldfinger, Tsz Wing Chau, John DeFelice, Bension S. Tilley, Wai Man Wong, Wutian Wu & Steve M. Gentleman Current available tissue clearing techniques are mostly used for rodent tissues. Here, the authors develop OPTIClear solution for fresh and archival human brain tissue clearing and establish associated protocols for three-dimensional histological investigations. 14 March 2018 | doi: 10.1038/s41467-018-03359-w Immunohistochemistry  Neurology  Neuroscience  Optical imaging  Structures of Teneurin adhesion receptors reveal an ancient fold for cell-cell interaction OPEN Verity A. Jackson, Dimphna H. Meijer, Maria Carrasquero, Laura S. van Bezouwen, Edward D. Lowe, Colin Kleanthous, Bert J. C. Janssen & Elena Seiradake Teneurins are cell-cell adhesion receptors that evolved through horizontal gene transfer in which a bacterial YD-repeat protein fused to a eukaryotic receptor. Here the authors present crystallographic and cryo-EM structures of two Teneurins, revealing an ancient YD-repeat protein super-fold. 14 March 2018 | doi: 10.1038/s41467-018-03460-0 Bacterial toxins  Development of the nervous system  Electron microscopy  X-ray crystallography  Internal climate variability and projected future regional steric and dynamic sea level rise OPEN Aixue Hu & Susan C. Bates As the global climate becomes warmer, the associated rising sea level could pose significant threats to island and coastal communities. Here the authors show that internal climate variability plays a key role in determining this sea level rise, especially in the next few decades. 14 March 2018 | doi: 10.1038/s41467-018-03474-8 Physical oceanography  Physics  The underappreciated potential of peatlands in global climate change mitigation strategies OPEN J. Leifeld & L. Menichetti Human activity, such as draining and mining of peatlands, is transforming these long-term carbon sinks into sources. Here, the authors assess current and future greenhouse gas (GHG) emissions from degrading peatlands and estimate the magnitude of potential GHG savings that could be achieved by restoring them. 14 March 2018 | doi: 10.1038/s41467-018-03406-6 Biogeochemistry  Carbon cycle  Clinically compliant spatial and temporal imaging of chimeric antigen receptor T-cells OPEN Nia Emami-Shahri, Julie Foster, Roxana Kashani, Patrycja Gazinska, Celia Cook, Jane Sosabowski, John Maher & Sophie Papa Adoptive transfer of chimeric antigen receptor (CAR) T cells has shown promising anticancer results in clinical trials. Here the authors use the human sodium iodide symporter (hNIS) as a reporter gene to image human CAR T cells in cancer-bearing mice using broadly available tracers and imaging platforms. 14 March 2018 | doi: 10.1038/s41467-018-03524-1 Cancer imaging  Cancer immunotherapy  Basal lamina remodeling at the skeletal muscle stem cell niche mediates stem cell self-renewal OPEN Shantisree Sandeepani Rayagiri, Daniele Ranaldi, Alexander Raven, Nur Izzah Farhana Mohamad Azhar, Olivier Lefebvre, Peter S Zammit & Anne-Gaëlle Borycki Extracellular matrix (ECM) remodelling is thought to have effects on muscle stem cells that support muscle homeostasis. Here the authors show ECM remodeling controls satellite cell self-renewal through deposition of laminin-α1 into the satellite cell niche. 14 March 2018 | doi: 10.1038/s41467-018-03425-3 Muscle stem cells  Self-renewal  Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis OPEN Meriem El Ghachi, Nicole Howe, Chia-Ying Huang, Vincent Olieric, Rangana Warshamanage, Thierry Touzé, Dietmar Weichert, Phillip J. Stansfeld, Meitian Wang, Fred Kerff & Martin Caffrey Bacterial cell wall components are assembled in a transmembrane cycle that involves the membrane integral pyrophosphorylase, BacA. Here the authors solve the crystal structure of BacA which shows an interdigitated inverted topology repeat that hints towards a flippase function for BacA. 14 March 2018 | doi: 10.1038/s41467-018-03477-5 Biochemistry  Structural biology  X-ray crystallography  Accumbens dopamine D2 receptors increase motivation by decreasing inhibitory transmission to the ventral pallidum OPEN Eduardo F. Gallo, Jozsef Meszaros, Jeremy D. Sherman, Muhammad O. Chohan, Eric Teboul, Claire S. Choi, Holly Moore, Jonathan A. Javitch & Christoph Kellendonk Dopamine D2 receptor activity in the nucleus accumbens is associated with regulation of motivated responding. Here the authors show that overexpression of D2 receptors specifically in ventral striatal projection neurons leads to an increase in the willingness to work by reducing inhibitory transmission to ventral pallidal neurons. 14 March 2018 | doi: 10.1038/s41467-018-03272-2 Cellular neuroscience  Motivation  Neural circuits  A non-conserved amino acid variant regulates differential signalling between human and mouse CD28 OPEN Nicla Porciello, Paola Grazioli, Antonio F. Campese, Martina Kunkl, Silvana Caristi, Marta Mastrogiovanni, Michela Muscolini, Francesca Spadaro, Cédric Favre, Jacques A. Nunès, Aldo Borroto, Balbino Alarcon, Isabella Screpanti & Loretta Tuosto CD28 transmits co-stimulatory signals for the activation of both mouse and human T cells, but in vivo hyperactivation of CD28 has opposite effects on system immunity. Here, the authors show that a single amino acid difference between mouse and human CD28 dictates this function distinction via differential recruitment of Nck. 14 March 2018 | doi: 10.1038/s41467-018-03385-8 Autoimmune diseases  CD4-positive T cells  NF-kappaB  Signal transduction  Cascading lake drainage on the Greenland Ice Sheet triggered by tensile shock and fracture OPEN Poul Christoffersen, Marion Bougamont, Alun Hubbard, Samuel H. Doyle, Shane Grigsby & Rickard Pettersson Lakes on the Greenland Ice Sheet transfer water to the bed when they drain, but the impact is unknown. Here, the authors use a 3D model to show that lakes drain when fractures form, causing a chain reaction in which cascading lake drainages extend inland and deliver water to previously isolated regions of the bed. 14 March 2018 | doi: 10.1038/s41467-018-03420-8 Cryospheric science  Environmental impact  Surface passivation engineering strategy to fully-inorganic cubic CsPbI3 perovskites for high-performance solar cells OPEN Bo Li, Yanan Zhang, Lin Fu, Tong Yu, Shujie Zhou, Luyuan Zhang & Longwei Yin Inorganic cesium lead iodide perovskite is inherently more stable than the hybrid perovskites but it undergoes phase transition that degrades the solar cell performance. Here Li et al. stabilize it with poly-vinylpyrrolidone and obtain high efficiency of 10.74% with excellent thermal and moisture stability. 14 March 2018 | doi: 10.1038/s41467-018-03169-0 Photovoltaics  Solar cells  Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways OPEN Atsumi Hirose, Takuya Kasai, Motohide Aoki, Tomonari Umemura, Kazuya Watanabe & Atsushi Kouzuma Whether electrochemically active bacteria (EAB) can gain energy according to electrode potentials is still unclear. Here, the authors show through transcriptome and deletion mutant analyses that EAB can sense electrode potentials by the Arc system and activate NADH-dependent catabolic pathway to generate ATP. 14 March 2018 | doi: 10.1038/s41467-018-03416-4 Applied microbiology  Bacterial physiology  Microarray analysis  Spin-liquid-like state in a spin-1/2 square-lattice antiferromagnet perovskite induced by d10–d0 cation mixing OPEN O. Mustonen, S. Vasala, E. Sadrollahi, K. P. Schmidt, C. Baines, H. C. Walker, I. Terasaki, F. J. Litterst, E. Baggio-Saitovitch & M. Karppinen Quantum spin liquids are predicted to form in frustrated square lattice magnets but this has been difficult to verify experimentally. Here the authors show that cation mixing in the square perovskite Sr2Cu(Te0.5W0.5)O6 can be used to tune it into the spin liquid regime. 14 March 2018 | doi: 10.1038/s41467-018-03435-1 Magnetic properties and materials  Materials chemistry  Hydrogen peroxide positively regulates brassinosteroid signaling through oxidation of the BRASSINAZOLE-RESISTANT1 transcription factor OPEN Yanchen Tian, Min Fan, Zhaoxia Qin, Hongjun Lv, Minmin Wang, Zhe Zhang, Wenying Zhou, Na Zhao, Xiaohui Li, Chao Han, Zhaojun Ding, Wenfei Wang, Zhi-Yong Wang & Ming-Yi Bai Hydrogen peroxide and brassinosteroids (BR) both regulate plant development and stress responses. Here Tian et al. show that hydrogen peroxide can trigger oxidation of the BR-responsive BZR1 transcription factor and promote its transcriptional activity, thereby linking BR and redox signaling. 14 March 2018 | doi: 10.1038/s41467-018-03463-x Brassinosteroid  Plant signalling  Post-translational modifications  Circular DNA elements of chromosomal origin are common in healthy human somatic tissue OPEN Henrik Devitt Møller, Marghoob Mohiyuddin, Iñigo Prada-Luengo, M. Reza Sailani, Jens Frey Halling, Peter Plomgaard, Lasse Maretty, Anders Johannes Hansen, Michael P. Snyder, Henriette Pilegaard, Hugo Y. K. Lam & Birgitte Regenberg Somatic cells can accumulate structural variations such as deletions. Here, Møller et al. show that normal human cells generate large extrachromosomal circular DNAs (eccDNAs), most likely the products of excised DNA, that can be transcriptionally active and, thus, may have phenotypic consequences. 14 March 2018 | doi: 10.1038/s41467-018-03369-8 DNA damage and repair  Genomic instability  Structural variation  Compression force sensing regulates integrin αIIbβ3 adhesive function on diabetic platelets OPEN Lining Ju, James D. McFadyen, Saheb Al-Daher, Imala Alwis, Yunfeng Chen, Lotte L. Tønnesen, Sophie Maiocchi, Brianna Coulter, Anna C. Calkin, Eric I. Felner, Neale Cohen, Yuping Yuan, Simone M. Schoenwaelder, Mark E. Cooper, Cheng Zhu & Shaun P. Jackson Diabetes is associated with an increased thrombotic response, but the mechanism is unknown. Here the authors demonstrate that compressive force activates integrin αIIbβ3 on discoid diabetic platelets and that platelet aggregates can be eliminated by PI 3-kinase inhibition, but not by anti-thrombotics aspirin or clopidogrel. 14 March 2018 | doi: 10.1038/s41467-018-03430-6 Cardiovascular diseases  Integrins  Mechanisms of disease  Platelets  Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression OPEN Lingdi Zhang, Hengbo Zhou, Xueni Li, Rebecca L Vartuli, Michael Rowse, Yongna Xing, Pratyaydipta Rudra, Debashis Ghosh, Rui Zhao & Heide L Ford Eya proteins are characterised by phosphatase activity associated with both the evolutionary conserved region and the less conserved N-terminal domain (NTD). Here the authors show that NTD mediates the interaction with PP2A and regulates c-Myc phosphorylation and stability, potentially switching PP2A from a tumour suppressor to an oncogene. 13 March 2018 | doi: 10.1038/s41467-018-03327-4 Breast cancer  Functionally distinct and selectively phosphorylated GPCR subpopulations co-exist in a single cell OPEN Ao Shen, Madeline Nieves-Cintron, Yawen Deng, Qian Shi, Dhrubajyoti Chowdhury, Jinyi Qi, Johannes W. Hell, Manuel F. Navedo & Yang K. Xiang β2-adrenergic receptor (β2AR) can be phosphorylated by G protein receptor kinases and second messenger-dependent kinases. Here, the authors demonstrate that these phosphorylation events are specific to functionally distinct and spatially segregated subpopulations of β2AR that co-exist in a single cell. 13 March 2018 | doi: 10.1038/s41467-018-03459-7 Cellular neuroscience  G protein-coupled receptors  Phosphorylation  Single-molecule biophysics  GATA3 zinc finger 2 mutations reprogram the breast cancer transcriptional network OPEN Motoki Takaku, Sara A. Grimm, John D. Roberts, Kaliopi Chrysovergis, Brian D. Bennett, Page Myers, Lalith Perera, Charles J. Tucker, Charles M. Perou & Paul A. Wade In breast cancer GATA3 is known to be frequently mutated, but the function of these mutations is unclear. Here, the authors utilise CRISPR-Cas9 to model frame-shift mutations in zinc finger 2 of GATA3, highlighting that GATA3 mutation can have gain- or loss-of function effects in breast cancer. 13 March 2018 | doi: 10.1038/s41467-018-03478-4 Breast cancer  Cancer epigenetics  Transcriptional regulatory elements  Desmosomal cadherin association with Tctex-1 and cortactin-Arp2/3 drives perijunctional actin polymerization to promote keratinocyte delamination OPEN Oxana Nekrasova, Robert M. Harmon, Joshua A. Broussard, Jennifer L. Koetsier, Lisa M. Godsel, Gillian N. Fitz, Margaret L. Gardel & Kathleen J. Green The epidermis is a multi-layered epithelium formed by the differentiation of basal cells and movement into suprabasal layers. Here the authors define a role for the desmosomal cadherin desmoglein-1 in promoting the delamination of basal cells by remodeling the actin cytoskeleton through interactions with the dynein light chain Tctex-1 and cortactin. 13 March 2018 | doi: 10.1038/s41467-018-03414-6 Actin  Desmosomes  Dynein  A LATS biosensor screen identifies VEGFR as a regulator of the Hippo pathway in angiogenesis OPEN T. Azad, H. J. Janse van Rensburg, E. D. Lightbody, B. Neveu, A. Champagne, A. Ghaffari, V. R. Kay, Y. Hao, H. Shen, B. Yeung, B. A. Croy, K. L. Guan, F. Pouliot, J. Zhang, C. J. B. Nicol & X. Yang The Hippo pathway is a major orchestrator of organ development and homeostasis. Here Azad and colleagues develop a biosensor to monitor the activity of the Hippo pathway component LATS and identify VEGF signalling as an upstream regulator of LATS, supporting a role for Hippo signalling during angiogenesis. 13 March 2018 | doi: 10.1038/s41467-018-03278-w Angiogenesis  HIPPO signalling  Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors OPEN Julie George , Vonn Walter, Martin Peifer, Ludmil B. Alexandrov, Danila Seidel, Frauke Leenders, Lukas Maas, Christian Müller, Ilona Dahmen, Tiffany M. Delhomme, Maude Ardin, Noemie Leblay, Graham Byrnes, Ruping Sun, Aurélien De Reynies, Anne McLeer-Florin, Graziella Bosco, Florian Malchers, Roopika Menon, Janine Altmüller et al. The molecular nature of large-cell neuroendocrine lung carcinomas (LCNEC) has remained unclear. Here, the authors show LCNECs represent a distinct transcriptional subgroup among lung cancers and comprise two molecular subgroups, type I (TP53 and STK11/KEAP1 alterations) and type II (TP53 and RB1 inactivation). 13 March 2018 | doi: 10.1038/s41467-018-03099-x Cancer genomics  Small-cell lung cancer  Structure-based design of chimeric antigens for multivalent protein vaccines OPEN S. Hollingshead, I. Jongerius, R. M. Exley, S. Johnson, S. M. Lea & C. M. Tang Factor H binding protein (fHbp) and PorA are components of experimental serogroup B N. meningitidis vaccines. Here the authors graft the VR2 loop of PorA onto an fHBp-based scaffold to demonstrate proof-of-principle of a chimeric antigen strategy and vaccination against meningococcal disease. 13 March 2018 | doi: 10.1038/s41467-018-03146-7 Meningitis  Protein vaccines  Atrx inactivation drives disease-defining phenotypes in glioma cells of origin through global epigenomic remodeling OPEN Carla Danussi, Promita Bose, Prasanna T. Parthasarathy, Pedro C. Silberman, John S. Van Arnam, Mark Vitucci, Oliver Y. Tang, Adriana Heguy, Yuxiang Wang, Timothy A. Chan, Gregory J. Riggins, Erik P. Sulman, Frederick Lang, Chad J. Creighton, Benjamin Deneen, C. Ryan Miller, David J. Picketts, Kasthuri Kannan & Jason T. Huse ATRX inactivation frequently occurs in glioma. Here, the authors explore the role of ATRX inactivation in oncogenesis, highlighting ATRX deficiency driven epigenomic changes that influence the expression of genes crucial to the oncogenic phenotype. 13 March 2018 | doi: 10.1038/s41467-018-03476-6 Cancer genomics  CNS cancer  Differentiation  Epigenomics  RHO signalling  Uniaxial strain control of spin-polarization in multicomponent nematic order of BaFe2As2 OPEN T. Kissikov, R. Sarkar, M. Lawson, B. T. Bush, E. I. Timmons, M. A. Tanatar, R. Prozorov, S. L. Bud’ko, P. C. Canfield, R. M. Fernandes & N. J. Curro A fundamental understanding of nematic order is one of the most important issues to explore in the high temperature superconductors. Here, the authors unveil an internal spin structure of the nematic order in BaFe2As2 by using nuclear magnetic resonance under precisely controlled tunable strain. 13 March 2018 | doi: 10.1038/s41467-018-03377-8 Magnetic properties and materials  Phase transitions and critical phenomena  Warm Arctic episodes linked with increased frequency of extreme winter weather in the United States OPEN Judah Cohen, Karl Pfeiffer & Jennifer A. Francis Whether accelerated Arctic warming is favorable for more frequent severe winter weather remains controversial. Here the authors present an observational analysis that links Arctic warming to severe winter weather, showing that extreme weather is 2–4 times more likely in the eastern US when the Arctic is warm. 13 March 2018 | doi: 10.1038/s41467-018-02992-9 Atmospheric dynamics  Climate and Earth system modelling  Role of monkeys in the sylvatic cycle of chikungunya virus in Senegal OPEN Benjamin M. Althouse, Mathilde Guerbois, Derek A. T. Cummings, Ousmane M. Diop, Ousmane Faye, Abdourahmane Faye, Diawo Diallo, Bakary Djilocalisse Sadio, Abdourahmane Sow, Oumar Faye, Amadou A. Sall, Mawlouth Diallo, Brenda Benefit, Evan Simons, Douglas M. Watts, Scott C. Weaver & Kathryn A. Hanley The authors examine the role of monkey populations in the sylvatic cycle of chikungunya virus in the Kédougou region, Senegal. The authors show that monkeys are amplification hosts, as opposed to reservoir hosts for infection. These findings expand our knowledge of the transmission dynamics of chikungunya virus in this region of Senegal. 13 March 2018 | doi: 10.1038/s41467-018-03332-7 Ecological epidemiology  Epidemiology  Viral infection  Virology  Benchmarking common quantification strategies for large-scale phosphoproteomics OPEN Alexander Hogrebe, Louise von Stechow, Dorte B. Bekker-Jensen, Brian T. Weinert, Christian D. Kelstrup & Jesper V. Olsen Quantitative phosphoproteomics has become a standard method in molecular and cell biology. Here, the authors compare performance and parameters of phosphoproteome quantification by LFQ, SILAC, and MS2-/MS3-based TMT and introduce a TMT-adapted algorithm for calculating phosphorylation site stoichiometry. 13 March 2018 | doi: 10.1038/s41467-018-03309-6 DNA damage response  Mass spectrometry  Phosphorylation  Proteomics  Integrated genomics and functional validation identifies malignant cell specific dependencies in triple negative breast cancer OPEN Nirmesh Patel , Daniel Weekes, Konstantinos Drosopoulos, Patrycja Gazinska, Elodie Noel, Mamun Rashid, Hasan Mirza, Jelmar Quist, Fara Brasó-Maristany, Sumi Mathew, Riccardo Ferro, Ana Mendes Pereira, Cynthia Prince, Farzana Noor, Erika Francesch-Domenech, Rebecca Marlow, Emanuele de Rinaldis, Anita Grigoriadis, Spiros Linardopoulos, Pierfrancesco Marra et al. Triple negative breast cancers harbor multiple copy number aberrations driving gene expression changes thought to underpin their malignant phenotypes. Here the authors integrate these features, finding and functionally validating 37 gene addictions among which they identify the mechanism of addiction to KIFC1, a potential selective drug target. 13 March 2018 | doi: 10.1038/s41467-018-03283-z Breast cancer  Cancer genomics  Target identification  Target validation  Targeted therapies  Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont OPEN Benjamin Pluvinage, Julie M. Grondin, Carolyn Amundsen, Leeann Klassen, Paul E. Moote, Yao Xiao, Dallas Thomas, Nicholas A. Pudlo, Anuoluwapo Anele, Eric C. Martens, G. Douglas Inglis, Richard E. R. Uwiera, Alisdair B. Boraston & D. Wade Abbott Polysaccharides are the primary structural cell wall and energy storage molecules of seaweed. Here, the authors show how the geographically restricted dietary polysaccharide agarose is selectively utilized by the human intestinal bacterium Bacteroides uniformis, providing insight into how carbohydrate metabolism evolves within the human microbiome. 13 March 2018 | doi: 10.1038/s41467-018-03366-x Bacteria  Hydrolases  Microbial ecology  Polysaccharides  Structural change as a key component for agricultural non-CO2 mitigation efforts OPEN Stefan Frank, Robert Beach, Petr Havlík, Hugo Valin, Mario Herrero, Aline Mosnier, Tomoko Hasegawa, Jared Creason, Shaun Ragnauth & Michael Obersteiner To achieve the climate target of the Paris Agreement substantial emission reductions will be required across economic sectors. Here the authors show that agriculture can make a significant contribution to non-CO2 mitigation efforts through structural change in the livestock sector and the deployment of technical options. 13 March 2018 | doi: 10.1038/s41467-018-03489-1 Agriculture  Carbon cycle  Climate-change mitigation  Scalable WDM phase regeneration in a single phase-sensitive amplifier through optical time lenses OPEN Pengyu Guan, Francesco Da Ros, Mads Lillieholm, Niels-Kristian Kjøller, Hao Hu, Kasper Meldgaard Røge, Michael Galili, Toshio Morioka & Leif Katsuo Oxenløwe Scalable solutions for data regeneration of multiple parallel channels are elusive. Here the authors report a scalable wavelength-division multiplexing technique for phase regeneration and demonstrate the highest reported number of regenerated wavelength-division multiplexed channels in a single phase regenerator. 13 March 2018 | doi: 10.1038/s41467-018-03458-8 Fibre optics and optical communications  Nonlinear optics  A meta-analysis of birth-origin effects on reproduction in diverse captive environments OPEN Katherine A. Farquharson, Carolyn J. Hogg & Catherine E. Grueber Aquaculture, conservation, and biological research are reliant on the successful breeding of animals in captivity. Here, Farquharson et al. report that, in captivity, captive-born animals have decreased reproductive success compared to wild-born individuals, across diverse species and contexts. 13 March 2018 | doi: 10.1038/s41467-018-03500-9 Evolution  Zoology  Wing bone geometry reveals active flight in Archaeopteryx OPEN Dennis F. A. E. Voeten, Jorge Cubo, Emmanuel de Margerie, Martin Röper, Vincent Beyrand, Stanislav Bureš, Paul Tafforeau & Sophie Sanchez Archaeopteryx had a mix of traits seen in non-flying dinosaurs and flying birds, leading to debate on whether it had powered flight. Here, Voeten et al. compare wing bone architecture from Archaeopteryx and both flying and non-flying archosaurs, supporting that Archaeopteryx had powered flight but with a different stroke than that of modern birds. 13 March 2018 | doi: 10.1038/s41467-018-03296-8 Biomechanics  Palaeontology  miR200-regulated CXCL12β promotes fibroblast heterogeneity and immunosuppression in ovarian cancers OPEN Anne-Marie Givel, Yann Kieffer, Alix Scholer-Dahirel, Philemon Sirven, Melissa Cardon, Floriane Pelon, Ilaria Magagna, Géraldine Gentric, Ana Costa, Claire Bonneau, Virginie Mieulet, Anne Vincent-Salomon & Fatima Mechta-Grigoriou Cancer-associated fibroblasts (CAFs) are an important part of the tumor microenvironment. Here the authors characterize four subsets of CAFs across human samples of ovarian cancer subtypes and show in the mesenchymal subtype a specific CAF-S1 population that attracts immunosuppressive Tregs via CXCL12β. 13 March 2018 | doi: 10.1038/s41467-018-03348-z Cancer microenvironment  Ovarian cancer  Tumour heterogeneity  Efficient molecular evolution to generate enantioselective enzymes using a dual-channel microfluidic droplet screening platform OPEN Fuqiang Ma, Meng Ting Chung, Yuan Yao, Robert Nidetz, Lap Man Lee, Allen P. Liu, Yan Feng, Katsuo Kurabayashi & Guang-Yu Yang Optimizing an enzyme usually requires testing thousands of variants, thus consuming large amounts of material and time. Here, the authors present a method that allows for measuring two different activities of the same enzyme simultaneously instead of doing two consecutive rounds of screening. 12 March 2018 | doi: 10.1038/s41467-018-03492-6 High-throughput screening  Hydrolases  Protein design  A systematic approach to the development of a safe live attenuated Zika vaccine OPEN Swee Sen Kwek, Satoru Watanabe, Kuan Rong Chan, Eugenia Z. Ong, Hwee Cheng Tan, Wy Ching Ng, Mien T. X. Nguyen, Esther S. Gan, Summer L. Zhang, Kitti W. K. Chan, Jun Hao Tan, October M. Sessions, Menchie Manuel, Julien Pompon, Camillus Chua, Sharifah Hazirah, Karl Tryggvason, Subhash G. Vasudevan & Eng Eong Ooi A Zika virus (ZIKV) vaccine should provide long-lasting immunity, which may be achieved with a live-attenuated vaccine. Here, Kwek et al. select an interferon-restricted, attenuated ZIKV variant and evaluate replication and immunogenicity in mouse and mosquito models. 12 March 2018 | doi: 10.1038/s41467-018-03337-2 Live attenuated vaccines  Viral host response  Viral infection  Disentangling the role of floral sensory stimuli in pollination networks OPEN Aphrodite Kantsa, Robert A. Raguso, Adrian G. Dyer, Jens M. Olesen, Thomas Tscheulin & Theodora Petanidou Can floral phenotype predict the most influential species for maintaining plant–pollinator communities? Here, Kantsa et al. develop a methodology for trait-based analysis, revealing the critical role of floral scent, and floral colour as perceived by insects, in shaping visitation networks. 12 March 2018 | doi: 10.1038/s41467-018-03448-w Community ecology  Ecological networks  Plant ecology  Vesicular glutamate release from central axons contributes to myelin damage OPEN Sean Doyle, Daniel Bloch Hansen, Jasmine Vella, Peter Bond, Glenn Harper, Christian Zammit, Mario Valentino & Robert Fern Neuronal activity can lead to vesicular release of glutamate. Here the authors demonstrate that vesicular release of glutamate occurs in axons during ischemic conditions, and that an allosteric modulator of GluN2C/D is protective in models of ischemic injury. 12 March 2018 | doi: 10.1038/s41467-018-03427-1 Myelin biology and repair  Stroke  Development of the social brain from age three to twelve years OPEN Hilary Richardson, Grace Lisandrelli, Alexa Riobueno-Naylor & Rebecca Saxe Though adults’ brains process the internal states of others’ bodies versus others’ minds in distinct brain regions, it is not clear when this functional dissociation emerges. Here, authors study 3–12 year olds and show that these networks are distinct by age 3 and become even more distinct with age. 12 March 2018 | doi: 10.1038/s41467-018-03399-2 Agency  Cognitive neuroscience  Empathy  Psychology  Label-free analysis of physiological hyaluronan size distribution with a solid-state nanopore sensor OPEN Felipe Rivas, Osama K. Zahid, Heidi L. Reesink, Bridgette T. Peal, Alan J. Nixon, Paul L. DeAngelis, Aleksander Skardal, Elaheh Rahbar & Adam R. Hall Involved in various diseases, hyaluronic acid is an important indicator of pathophysiology. Here, the authors report on a solid-state nanopore for the detection of the molecular weight and abundance of hyaluronic acid and demonstrate the system by studying an equine model of osteoarthritis 12 March 2018 | doi: 10.1038/s41467-018-03439-x Biosensors  Nanopores  Proteomics  CoA synthase regulates mitotic fidelity via CBP-mediated acetylation OPEN Chao-Chieh Lin, Mayumi Kitagawa, Xiaohu Tang, Ming-Hsin Hou, Jianli Wu, Dan Chen Qu, Vinayaka Srinivas, Xiaojing Liu, J. Will Thompson, Bernard Mathey-Prevot, Tso-Pang Yao, Sang Hyun Lee & Jen-Tsan Chi The temporal activation of kinases and timely ubiquitin-mediated degradation is central to faithful mitosis. Here the authors show that acetylation controlled by Coenzyme A synthase (COASY) and acetyltransferase CBP constitutes a mechanism that ensures faithful mitosis. 12 March 2018 | doi: 10.1038/s41467-018-03422-6 Acetylation  Mitosis  Divergent T-cell receptor recognition modes of a HLA-I restricted extended tumour-associated peptide OPEN Kok Fei Chan, Benjamin S. Gully, Stephanie Gras, Dennis X. Beringer, Lars Kjer-Nielsen, Jonathan Cebon, James McCluskey, Weisan Chen & Jamie Rossjohn Human leukocyte antigen (HLA) presents peptides to activate T cells, but many aspects in the T cell receptor (TCR)/HLA interaction remain unclear. Here the authors show, via structural data, that two TCRs differentially recognize the same tumour peptide/HLA complex and induce contrasting conformation changes of the peptide. 12 March 2018 | doi: 10.1038/s41467-018-03321-w Adaptive immunity  Antigen processing and presentation  Tumour immunology  X-ray crystallography  Inhibition of neuronal FLT3 receptor tyrosine kinase alleviates peripheral neuropathic pain in mice OPEN Cyril Rivat , Chamroeun Sar, Ilana Mechaly, Jean-Philippe Leyris, Lucie Diouloufet, Corinne Sonrier, Yann Philipson, Olivier Lucas, Sylvie Mallié, Antoine Jouvenel, Adrien Tassou, Henri Haton, Stéphanie Venteo, Jean-Philippe Pin, Eric Trinquet, Fabienne Charrier-Savournin, Alexandre Mezghrani, Willy Joly, Julie Mion, Martine Schmitt et al. Sensitisation of dorsal root ganglia neurons contributes to neuropathic pain. Here the authors demonstrate the cytokine FL contributes to sensitisation of DRGs via its receptor FLT3 expressed on neurons, and identify a novel FLT3 inhibitor that attenuates neuropathic pain in mice. 12 March 2018 | doi: 10.1038/s41467-018-03496-2 Chronic pain  Neuroimmunology  Structural basis for the recognition of LDL-receptor family members by VSV glycoprotein OPEN Jovan Nikolic, Laura Belot, Hélène Raux, Pierre Legrand, Yves Gaudin & Aurélie A. Albertini Glycoprotein G of vesicular stomatitis virus (VSV) enables viral entry by binding to the major VSV receptor LDL-R. Here the authors present crystal structures of G in complex with two distinct CR domains of LDL-R, identifying structural determinants for VSV infectivity in mammalian and insect cells. 12 March 2018 | doi: 10.1038/s41467-018-03432-4 Viral proteins  Virus–host interactions  X-ray crystallography  TRiC controls transcription resumption after UV damage by regulating Cockayne syndrome protein A OPEN Alex Pines, Madelon Dijk, Matthew Makowski, Elisabeth M. Meulenbroek, Mischa G. Vrouwe, Yana van der Weegen, Marijke Baltissen, Pim J. French, Martin E. van Royen, Martijn S. Luijsterburg, Leon H. Mullenders, Michiel Vermeulen, Wim Vermeulen, Navraj S. Pannu & Haico van Attikum An integrated network of chaperones and protein degradation machineries called the proteostasis network (PN) is required to maintain protein homeostasis. Here the authors show that one of the components of the PN, the chaperonin TRiC, interacts with the core transcription-coupled nucleotide excision repair protein CSA to ensure its assembly into the CRLCSA complex. 12 March 2018 | doi: 10.1038/s41467-018-03484-6 Chaperones  Nucleotide excision repair  Evidence for ephemeral middle Eocene to early Oligocene Greenland glacial ice and pan-Arctic sea ice OPEN Aradhna Tripati & Dennis Darby With rapidly disappearing ice, understanding the past behavior of the cryosphere is critical. Here, the authors indicate the initiation and disappearance of glaciation on Greenland and Arctic sea ice coincided in the past, synchronous with Antarctic ice and global ice volume, and a CO2 threshold of ~500 p.p.m.v. 12 March 2018 | doi: 10.1038/s41467-018-03180-5 Cryospheric science  Palaeoceanography  Palaeoclimate  Capture Hi-C identifies putative target genes at 33 breast cancer risk loci OPEN Joseph S. Baxter, Olivia C. Leavy, Nicola H. Dryden, Sarah Maguire, Nichola Johnson, Vita Fedele, Nikiana Simigdala, Lesley-Ann Martin, Simon Andrews, Steven W. Wingett, Ioannis Assiotis, Kerry Fenwick, Ritika Chauhan, Alistair G. Rust, Nick Orr, Frank Dudbridge, Syed Haider & Olivia Fletcher Risk loci for breast cancer have been identified by genome-wide association studies. Here, the authors use Capture Hi-C to identify 110 putative target genes at 33 loci and assessed associations of gene expression, SNP genotype, and survival, providing evidence of mechanisms that may influence the prognosis and risk of breast cancer. 12 March 2018 | doi: 10.1038/s41467-018-03411-9 Breast cancer  Cancer genetics  Large enhancement of response times of a protein conformational switch by computational design OPEN Alex J. DeGrave, Jeung-Hoi Ha, Stewart N. Loh & Lillian T. Chong The rational optimization of response times of protein conformational switches is a major challenge for biomolecular switch design. Here the authors present a generally applicable computational design strategy that in combination with biophysical experiments can improve response times using a Ca2+-sensor as an example. 09 March 2018 | doi: 10.1038/s41467-018-03228-6 Computational biophysics  Molecular biophysics  Paracrine cellular senescence exacerbates biliary injury and impairs regeneration OPEN Sofia Ferreira-Gonzalez, Wei-Yu Lu, Alexander Raven, Benjamin Dwyer, Tak Yung Man, Eoghan O’Duibhir, Philip J. Starkey Lewis, Lara Campana, Tim J. Kendall, Thomas G. Bird, Nuria Tarrats, Juan-Carlos Acosta, Luke Boulter & Stuart J. Forbes Senescence has been suggested as causing biliary cholangiopathies but how this is regulated is unclear. Here, the authors generate a mouse model of biliary senescence by deleting Mdm2 in bile ducts and show that inhibiting TGFβ limits senescence-dependent aggravation of cholangiopathies. 09 March 2018 | doi: 10.1038/s41467-018-03299-5 Bile ducts  Liver fibrosis  Mechanisms of disease  Senescence  Statistical ensembles without typicality OPEN Paul Boes, Henrik Wilming, Jens Eisert & Rodrigo Gallego The minimal amount of assumptions to justify the use of maximum-entropy ensembles is still debated. Here, the authors show that the transitions that a partially known system environment can undergo are the same allowed for the maximum entropy state which is compatible with the known information. 09 March 2018 | doi: 10.1038/s41467-018-03230-y Information theory and computation  Quantum mechanics  Statistical physics, thermodynamics and nonlinear dynamics  MRN complex-dependent recruitment of ubiquitylated BLM helicase to DSBs negatively regulates DNA repair pathways OPEN Vivek Tripathi, Himanshi Agarwal, Swati Priya, Harish Batra, Priyanka Modi, Monica Pandey, Dhurjhoti Saha, Sathees C. Raghavan & Sagar Sengupta Bloom helicase is recruited to double strand breaks in an ATM dependent manner. Here the authors show that Bloom helicase is recruited to double strand breaks in an ATM and MRN dependent manner with HR and NHEJ regulated by the helicase depending on the phase of the cell cycle. 09 March 2018 | doi: 10.1038/s41467-018-03393-8 DNA recombination  Double-strand DNA breaks  Homologous recombination  Non-homologous-end joining  p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage OPEN Marina E. Borisova, Andrea Voigt, Maxim A. X. Tollenaere, Sanjeeb Kumar Sahu, Thomas Juretschke, Nastasja Kreim, Niels Mailand, Chunaram Choudhary, Simon Bekker-Jensen, Masato Akutsu, Sebastian A. Wagner & Petra Beli UV-light-induced DNA damage affects RNA metabolism but the underlying signalling pathways are largely unexplored. Here, the authors show that UV light triggers p38-MK2-mediated phosphorylation of the NELF complex, promoting its release from chromatin and concurrent transcriptional elongation. 09 March 2018 | doi: 10.1038/s41467-018-03417-3 DNA damage response  Phosphorylation  Proteomics  RNA metabolism  Brain and eyes of Kerygmachela reveal protocerebral ancestry of the panarthropod head OPEN Tae-Yoon S. Park, Ji-Hoon Kihm, Jusun Woo, Changkun Park, Won Young Lee, M. Paul Smith, David A. T. Harper, Fletcher Young, Arne T. Nielsen & Jakob Vinther The arthropod head is complex and its evolution has been difficult to reconstruct. Here, Park et al. describe new specimens of the Cambrian stem-group euarthropod Kerygmachela that preserve evidence of primitive compound eyes and a unipartite brain, providing insight into the structure of the early arthropod head. 09 March 2018 | doi: 10.1038/s41467-018-03464-w Evolutionary developmental biology  Palaeontology  Risk of nontyphoidal Salmonella bacteraemia in African children is modified by STAT4 OPEN James J. Gilchrist , Anna Rautanen, Benjamin P. Fairfax, Tara C. Mills, Vivek Naranbhai, Holly Trochet, Matti Pirinen, Esther Muthumbi, Salim Mwarumba, Patricia Njuguna, Neema Mturi, Chisomo L. Msefula, Esther N. Gondwe, Jenny M. MacLennan, Stephen J. Chapman, Malcolm E. Molyneux, Julian C. Knight, Chris C. A. Spencer, Thomas N. Williams, Calman A. MacLennan et al. Nontyphoidal Salmonella (NTS) is a major cause of bacteraemia in children and HIV-infected adults in Africa. Here, Gilchrist et al. conduct a genome-wide association study and show that genetic variation in STAT4 is a determinant of NTS in Kenyan and Malawian children. 09 March 2018 | doi: 10.1038/s41467-017-02398-z Bacterial infection  Genome-wide association studies  Stabilizing spin spirals and isolated skyrmions at low magnetic field exploiting vanishing magnetic anisotropy OPEN Marie Hervé, Bertrand Dupé, Rafael Lopes, Marie Böttcher, Maximiliano D. Martins, Timofey Balashov, Lukas Gerhard, Jairo Sinova & Wulf Wulfhekel Skyrmions are promising for spintronics but usually require large spin-orbit coupling of 5d-metals and external magnetic field. Here the authors realize stabilization of isolated skyrmions at a 4d-metal interface of weak chiral interaction and magnetic anisotropy down to vanishing field. 09 March 2018 | doi: 10.1038/s41467-018-03240-w Ferromagnetism  Spintronics  Surfaces, interfaces and thin films  MYC-driven epigenetic reprogramming favors the onset of tumorigenesis by inducing a stem cell-like state OPEN Vittoria Poli, Luca Fagnocchi, Alessandra Fasciani, Alessandro Cherubini, Stefania Mazzoleni, Sara Ferrillo, Annarita Miluzio, Gabriella Gaudioso, Valentina Vaira, Alice Turdo, Miriam Giaggianesi, Aurora Chinnici, Elisa Lipari, Silvio Bicciato, Silvano Bosari, Matilde Todaro & Alessio Zippo Breast cancer tumors originating from mammary luminal epithelial cells are highly heterogeneous. Here, the authors show MYC-driven tumor initiation is reliant on cell reprogramming via an epigenetic program which leads to mammary luminal epithelial cells acquiring basal/stem cell-like properties. 09 March 2018 | doi: 10.1038/s41467-018-03264-2 Breast cancer  Histone post-translational modifications  Reprogramming  Transcriptional regulatory elements  Ultrafast nonlinear optical response of Dirac fermions in graphene OPEN Matthias Baudisch, Andrea Marini, Joel D. Cox, Tony Zhu, Francisco Silva, Stephan Teichmann, Mathieu Massicotte, Frank Koppens, Leonid S. Levitov, F. Javier García de Abajo & Jens Biegert Graphene possesses a nonlinear optical response arising from its electronic dispersion. Here, the authors measure the response of graphene to an ultrafast optical field and provide an explanation of the quantum dynamics of Dirac carriers mediating the material’s nonlinear response. 09 March 2018 | doi: 10.1038/s41467-018-03413-7 Nonlinear optics  Optical properties and devices  CDK6 inhibits white to beige fat transition by suppressing RUNX1 OPEN Xiaoli Hou, Yongzhao Zhang, Wei Li, Alexander J. Hu, Chi Luo, Wenhui Zhou, Jamie K. Hu, Stefano G. Daniele, Jinfeng Wang, Jinghao Sheng, Yongsheng Fan, Andrew S. Greenberg, Stephen R. Farmer & Miaofen G. Hu Beige adipocytes can arise from transdifferentiation of mature white adipocytes. Here the authors identify CDK6 as a key molecule involved in the white-to-beige adipocyte transdifferentiation and, therefore, as a regulator of organismal energy homeostasis in mice. 09 March 2018 | doi: 10.1038/s41467-018-03451-1 Mechanisms of disease  Metabolic disorders  Obesity  Insc:LGN tetramers promote asymmetric divisions of mammary stem cells OPEN Simone Culurgioni, Sara Mari, Paola Bonetti, Sara Gallini, Greta Bonetto, Martha Brennich, Adam Round, Francesco Nicassio & Marina Mapelli During asymmetric divisions fate determinants and niche contacts segregate unequally between daughter cells, but the mechanism is unclear. Here the authors show that Insc:LGN tetramers promote assembly of Par3-Insc-LGN-GαiGDP complexes and asymmetric fate specification independently of microtubule motors. 09 March 2018 | doi: 10.1038/s41467-018-03343-4 Cell division  Structural biology  p63 is a key regulator of iRHOM2 signalling in the keratinocyte stress response OPEN Paola Arcidiacono, Catherine M. Webb, Matthew A. Brooke, Huiqing Zhou, Paul J. Delaney, Keat-Eng Ng, Diana C. Blaydon, Andrew Tinker, David P. Kelsell & Anissa Chikh Mutations in the gene encoding iRHOM2 are associated with hyperproliferative epidermal disorders. Here, the authors show that iRHOM2 is a target gene of p63, that together they regulate inflammation, cell survival and response to oxidative stress, and inhibition of p63-iRHOM2 signalling with an antioxidant reduces epidermal inflammation. 09 March 2018 | doi: 10.1038/s41467-018-03470-y Cell proliferation  Intermediate filaments  Skin diseases  Sedimentary noise and sea levels linked to land–ocean water exchange and obliquity forcing OPEN Mingsong Li, Linda A. Hinnov, Chunju Huang & James G. Ogg The origin of large, long-term sea-level oscillations during non-glacial times remains uncertain. Here, the authors develop geological evidence that reveals astronomically forced land–ocean water exchange as a potential missing link for reconciling geological records and models of sea-level change. 08 March 2018 | doi: 10.1038/s41467-018-03454-y Palaeoceanography  Palaeoclimate  HCN2 Rescues brain defects by enforcing endogenous voltage pre-patterns OPEN Vaibhav P. Pai, Alexis Pietak, Valerie Willocq, Bin Ye, Nian-Qing Shi & Michael Levin The authors have previously shown that membrane voltage can influence embryonic patterning during development. Here, the authors computationally model how nicotine disrupts Xenopus embryogenesis by perturbing voltage gradients, and rescue nicotine-inducted defects with HCN2 channel expression. 08 March 2018 | doi: 10.1038/s41467-018-03334-5 Brain  Ion channels  Regeneration  Regeneration and repair in the nervous system  Aberrant GlyRS-HDAC6 interaction linked to axonal transport deficits in Charcot-Marie-Tooth neuropathy OPEN Zhongying Mo, Xiaobei Zhao, Huaqing Liu, Qinghua Hu, Xu-Qiao Chen, Jessica Pham, Na Wei, Ze Liu, Jiadong Zhou, Robert W. Burgess, Samuel L. Pfaff, C. Thomas Caskey, Chengbiao Wu, Ge Bai & Xiang-Lei Yang Mutations in glycyl-tRNA synthetase (GlyRS) cause Charcot-Marie-Tooth disease, a neuromuscular disorder characterized by axonal degeneration. Here the authors show that mutant GlyRS interacts with histone deacetylase 6, resulting in increased deacetylation of α-tubulin and axonal transport deficits. 08 March 2018 | doi: 10.1038/s41467-018-03461-z Acetylation  Molecular neuroscience  Neurodegeneration  Design and validation of a foldable and photovoltaic wide-field epiretinal prosthesis OPEN Laura Ferlauto, Marta Jole Ildelfonsa Airaghi Leccardi, Naïg Aurelia Ludmilla Chenais, Samuel Charles Antoine Gilliéron, Paola Vagni, Michele Bevilacqua, Thomas J. Wolfensberger, Kevin Sivula & Diego Ghezzi Retinal prostheses are being developed to fight severe retinal diseases where wider visual field and higher visual acuity are desired. Here Ferlauto et al. design a foldable and wide-field epiretinal prosthesis that can meet the performance and safety requirements and show a long lifetime of 2 years. 08 March 2018 | doi: 10.1038/s41467-018-03386-7 Biomedical engineering  Polymers  Retina  Activation of serotonin neurons promotes active persistence in a probabilistic foraging task OPEN Eran Lottem, Dhruba Banerjee, Pietro Vertechi, Dario Sarra, Matthijs oude Lohuis & Zachary F. Mainen Serotonin (5-HT) has been suggested to promote waiting through behavioral inhibition. Here, the authors use an active foraging task and optogenetic activation of 5-HT neurons to show that rather than passivity, these neurons enhance persistence in the face of delay. 08 March 2018 | doi: 10.1038/s41467-018-03438-y Motivation  Reward  An accurate and robust imputation method scImpute for single-cell RNA-seq data OPEN Wei Vivian Li & Jingyi Jessica Li Despite being widely performed in exploring cell heterogeneity and gene expression stochasticity, single cell RNA-seq analysis is complicated by excess zero counts (dropouts). Here, Li and Li develop scImpute for statistical imputation of dropouts in scRNA-seq data. 08 March 2018 | doi: 10.1038/s41467-018-03405-7 Statistical methods  Nanoscale kinetics of asymmetrical corrosion in core-shell nanoparticles OPEN Hao Shan, Wenpei Gao, Yalin Xiong, Fenglei Shi, Yucong Yan, Yanling Ma, Wen Shang, Peng Tao, Chengyi Song, Tao Deng, Hui Zhang, Deren Yang, Xiaoqing Pan & Jianbo Wu Understanding how catalysts corrode during use is crucial in developing new, durable devices. Here, the authors studied the real-time corrosion of core-shell palladium-platinum nanocubes by electron microscopy and found two competitive etching mechanisms to dominate catalyst degradation behavior. 08 March 2018 | doi: 10.1038/s41467-018-03372-z Corrosion  Electrocatalysis  Fuel cells  Nanoparticles  Phosphorylation of conserved phosphoinositide binding pocket regulates sorting nexin membrane targeting OPEN Marc Lenoir, Cansel Ustunel, Sandya Rajesh, Jaswant Kaur, Dimitri Moreau, Jean Gruenberg & Michael Overduin Sorting nexin 3 (SNX3) is a phosphatidylinositol 3-phosphate binding protein that localizes to early endosomes. Here the authors use NMR to resolve SNX3′s membrane interactions, revealing that membrane binding is regulated through phosphorylation of a conserved serine by its lipid recognition site. 08 March 2018 | doi: 10.1038/s41467-018-03370-1 Endosomes  Solution-state NMR  Strong phenotypic plasticity limits potential for evolutionary responses to climate change OPEN Vicencio Oostra, Marjo Saastamoinen, Bas J. Zwaan & Christopher W. Wheat Phenotypic plasticity—the ability to express multiple phenotypes from the same genome—is a widespread adaptation to environmental variability. Here, Oostra et al analyze transcriptomes of an African butterfly with distinct seasonal phenotypes, and observe lack of variation for plasticity, limiting potential for evolutionary responses to climate change. 08 March 2018 | doi: 10.1038/s41467-018-03384-9 Environmental health  Evolutionary ecology  Evolutionary genetics  Phenology  Transcriptomics  Expansion of functional personalized cells with specific transgene combinations OPEN Christoph Lipps , Franziska Klein, Tom Wahlicht, Virginia Seiffert, Milada Butueva, Jeannette Zauers, Theresa Truschel, Martin Luckner, Mario Köster, Roderick MacLeod, Jörn Pezoldt, Jochen Hühn, Qinggong Yuan, Peter Paul Müller, Henning Kempf, Robert Zweigerdt, Oliver Dittrich-Breiholz, Thomas Pufe, Rainer Beckmann, Wolf Drescher et al. Personalised medicine requires cell cultures from defined genetic backgrounds, but providing sufficient numbers of cells is a challenge. Here the authors develop gene cocktails to expand primary cells from a variety of different tissues and species, and show that expanded endothelial and hepatic cells retain properties of the differentiated phenotype. 08 March 2018 | doi: 10.1038/s41467-018-03408-4 Cell culture  Cell therapies  Regenerative medicine  The H2B deubiquitinase Usp22 promotes antibody class switch recombination by facilitating non-homologous end joining OPEN Conglei Li, Thergiory Irrazabal, Clare C. So, Maribel Berru, Likun Du, Evelyn Lam, Alexanda K. Ling, Jennifer L. Gommerman, Qiang Pan-Hammarström & Alberto Martin Class switch recombination (CSR) requires break and repair of immunoglobulin DNA. Here the authors show that the histone deubiquitinase Usp22 is involved in V(D)J recombination and CSR of IgG and IgE, but not IgA, and that IgG CSR is dependent on the canonical c-NHEJ pathway, whereas IgA CSR is more dependent on the alternative A-EJ pathway. 08 March 2018 | doi: 10.1038/s41467-018-03455-x B-cell receptor  Class switch recombination  An HDAC9-MALAT1-BRG1 complex mediates smooth muscle dysfunction in thoracic aortic aneurysm OPEN Christian L. Lino Cardenas, Chase W. Kessinger, Yisha Cheng, Carolyn MacDonald, Thomas MacGillivray, Brian Ghoshhajra, Luai Huleihel, Saifar Nuri, Ashish S. Yeri, Farouc A. Jaffer, Naftali Kaminski, Patrick Ellinor, Neal L. Weintraub, Rajeev Malhotra, Eric M. Isselbacher & Mark E. Lindsay Vascular smooth muscle cell (VSMC) dysfunction is a common feature of thoracic aortic aneurysms (TAAs). Here, Lino Cardenas and colleagues show that the formation of a HDAC9-MALAT1-BRG1 complex promotes VSMC dysfunction in TAA by epigenetically altering the expression of key components of the cytoskeleton in VSMCs. 08 March 2018 | doi: 10.1038/s41467-018-03394-7 Actin  Aneurysm  Long non-coding RNAs  Surface plasmon resonance extension through two-block metal-conducting polymer nanorods OPEN Insub Jung, Minkyung Kim, Min Kwak, Geonwoo Kim, Minsun Jang, Sang Min Kim, Doo Jae Park & Sungho Park Localized surface plasmon resonance can be exploited for a range of applications, but remains difficult to tailor in metal-organic nanostructures. Here the authors synthesize gold-polypyrrole nanorods and observe a unique extended surface plasmon resonance, which they find to be tunable through doping. 08 March 2018 | doi: 10.1038/s41467-018-03453-z Materials chemistry  Nanophotonics and plasmonics  Nanoscale materials  Oscillating modes of driven colloids in overdamped systems OPEN Johannes Berner, Boris Müller, Juan Ruben Gomez-Solano, Matthias Krüger & Clemens Bechinger The motion of microparticles suspended in liquids is assumed to be dominated by viscous forces. Here, Berner et al. challenge this consensus by observing underdamped particle oscillations in a viscoelastic fluid and attributing it to the non-equilibrium fluctuations of liquid excited by particles. 08 March 2018 | doi: 10.1038/s41467-018-03345-2 Fluid dynamics  Thermodynamics  Transient rheology of the Sumatran mantle wedge revealed by a decade of great earthquakes OPEN Qiang Qiu, James D. P. Moore, Sylvain Barbot, Lujia Feng & Emma M. Hill The rheology of the upper mantle is key to understanding how plate tectonics may evolve. Here, using GPS and tide-gauge measurements along the Sumatran subduction zone, the authors’ show that a bi-viscous rheology model is needed to explain the stress and strain evolution of the upper mantle following earthquakes. 08 March 2018 | doi: 10.1038/s41467-018-03298-6 Geophysics  Tectonics  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. Diffuse-type gastric cancer (DGC) accounts for 30% of gastric cancers and has few treatment options. Here the authors present a mutation and proteome dataset for 84 patients, identifying three major classes of DGC and indicating potential targets for therapy. 08 March 2018 | doi: 10.1038/s41467-018-03121-2 Gastric cancer  Proteomics  Turning microplastics into nanoplastics through digestive fragmentation by Antarctic krill OPEN Amanda L. Dawson, So Kawaguchi, Catherine K. King, Kathy A. Townsend, Robert King, Wilhelmina M. Huston & Susan M. Bengtson Nash Microplastics are emerging ocean contaminants, but their fates in the ocean environment are poorly understood. Here the authors show that Antarctic krill digest micro plastics into nano plastics, thereby generating particles of a size that can cross biological and physical barriers. 08 March 2018 | doi: 10.1038/s41467-018-03465-9 Ecology  Environmental impact  Marine biology  Cation vacancy stabilization of single-atomic-site Pt1/Ni(OH)x catalyst for diboration of alkynes and alkenes OPEN Jian Zhang, Xi Wu, Weng-Chon Cheong, Wenxing Chen, Rui Lin, Jia Li, Lirong Zheng, Wensheng Yan, Lin Gu, Chen Chen, Qing Peng, Dingsheng Wang & Yadong Li Development of single-atomic-site catalysts with high metal loading remains a challenge. Here, the authors report a nickel hydroxide nanoboard with abundant Ni2+ vacancy defects serving as the support to achieve high platinum loading by simple wet impregnation. 08 March 2018 | doi: 10.1038/s41467-018-03380-z Heterogeneous catalysis  Materials chemistry  Materials for energy and catalysis  The oxidized phospholipid oxPAPC protects from septic shock by targeting the non-canonical inflammasome in macrophages OPEN Lan H. Chu, Mohanalaxmi Indramohan, Rojo A. Ratsimandresy, Anu Gangopadhyay, Emily P. Morris, Denise M. Monack, Andrea Dorfleutner & Christian Stehlik Non-canonical inflammasome activation is mediated by caspase-11 in mice and caspase-4 in humans. Here the authors show that oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine (oxPAPC) competes with LPS for binding to these caspases and in so doing is a negative regulator of non-canonical inflammasome activation in macrophages, but not in dendritic cells. 08 March 2018 | doi: 10.1038/s41467-018-03409-3 Inflammasome  Pattern recognition receptors  Mutual potentiation drives synergy between trimethoprim and sulfamethoxazole OPEN Yusuke Minato, Surendra Dawadi, Shannon L. Kordus, Abiram Sivanandam, Courtney C. Aldrich & Anthony D. Baughn The antibiotics trimethoprim (TMP) and sulfamethoxazole (SMX) synergistically inhibit bacterial tetrahydrofolate biosynthesis, apparently because SMX potentiates TMP activity. Here, Minato et al. identify a metabolic feedback loop in this pathway, revealing that TMP also potentiates SMX activity. 08 March 2018 | doi: 10.1038/s41467-018-03447-x Antibiotics  Bacteria  Bacteriology  Metabolic pathways      Latest Addendum       Addendum: Application of bio-orthogonal proteome labeling to cell transplantation and heterochronic parabiosis OPEN Yan Liu, Michael J. Conboy, Melod Mehdipour, Yutong Liu, Thanhtra P. Tran, Aaron Blotnick, Prasanna Rajan, Thalie Cavalcante Santos & Irina M. Conboy 13 March 2018 | doi: 10.1038/s41467-017-02779-4 Ageing  Proteome  Transgenic organisms      Latest Author Corrections       Author Correction: Liquid crystal elastomer coatings with programmed response of surface profile OPEN Greta Babakhanova, Taras Turiv, Yubing Guo, Matthew Hendrikx, Qi-Huo Wei, Albert P. H. J. Schenning, Dirk J. Broer & Oleg D. Lavrentovich 14 March 2018 | doi: 10.1038/s41467-018-03634-w Liquid crystals  Polymers  Author Correction: Super-achromatic monolithic microprobe for ultrahigh-resolution endoscopic optical coherence tomography at 800 nm OPEN Wu Yuan, Robert Brown, Wayne Mitzner, Lonny Yarmus & Xingde Li 14 March 2018 | doi: 10.1038/s41467-018-03637-7 Biomedical engineering  Biophotonics  Endoscopy  Author Correction: Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology OPEN Jeong-Ki Kim, Arghavan Louhghalam, Geonhui Lee, Benjamin W. Schafer, Denis Wirtz & Dong-Hwee Kim 13 March 2018 | doi: 10.1038/s41467-018-03450-2 Nuclear envelope  Nucleoskeleton  Stress fibres  Author Correction: Restoration of patterned vision with an engineered photoactivatable G protein-coupled receptor OPEN Michael H. Berry, Amy Holt, Joshua Levitz, Johannes Broichhagen, Benjamin M. Gaub, Meike Visel, Cherise Stanley, Krishan Aghi, Yang Joon Kim, Kevin Cao, Richard H Kramer, Dirk Trauner, John Flannery & Ehud Y. Isacoff 13 March 2018 | doi: 10.1038/s41467-018-03585-2 Molecular neuroscience  Protein design  Retina  Author Correction: Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations OPEN Fabian Paul, Christoph Wehmeyer, Esam T. Abualrous, Hao Wu, Michael D. Crabtree, Johannes Schöneberg, Jane Clarke, Christian Freund, Thomas R. Weikl & Frank Noé 09 March 2018 | doi: 10.1038/s41467-018-03452-0 Biological physics  Chemical physics  Computational biophysics  Reaction kinetics and dynamics  Author Correction: Energy use and life cycle greenhouse gas emissions of drones for commercial package delivery OPEN Joshuah K. Stolaroff, Constantine Samaras, Emma R. O’Neill, Alia Lubers, Alexandra S. Mitchell & Daniel Ceperley 08 March 2018 | doi: 10.1038/s41467-018-03457-9 Climate-change mitigation  Energy efficiency  Energy science and technology      Latest Publisher Corrections       Publisher Correction: Discordant congenital Zika syndrome twins show differential in vitro viral susceptibility of neural progenitor cells OPEN Luiz Carlos Caires-Júnior , Ernesto Goulart, Uirá Souto Melo, Bruno Henrique Silva Araujo, Lucas Alvizi, Alessandra Soares-Schanoski, Danyllo Felipe de Oliveira, Gerson Shigeru Kobayashi, Karina Griesi-Oliveira, Camila Manso Musso, Murilo Sena Amaral, Lucas Ferreira daSilva, Renato Mancini Astray, Sandra Fernanda Suárez-Patiño, Daniella Cristina Ventini, Sérgio Gomes da Silva, Guilherme Lopes Yamamoto, Suzana Ezquina, Michel Satya Naslavsky, Kayque Alves Telles-Silva et al. 13 March 2018 | doi: 10.1038/s41467-018-03497-1 Neural stem cells  Viral host response  Publisher Correction: Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid OPEN Youngzee Song, Huihao Zhou, My-Nuong Vo, Yi Shi, Mir Hussain Nawaz, Oscar Vargas-Rodriguez, Jolene K. Diedrich, John R. Yates III, Shuji Kishi, Karin Musier-Forsyth & Paul Schimmel 13 March 2018 | doi: 10.1038/s41467-018-03594-1 Enzyme mechanisms  Proteins  tRNAs  X-ray crystallography  Publisher Correction: Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes OPEN Hua Li & Sharon Aviran 13 March 2018 | doi: 10.1038/s41467-018-03519-y Computational science  Statistical methods  Publisher Correction: Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets OPEN Zachary R. Crook, Gregory P. Sevilla, Della Friend, Mi-Youn Brusniak, Ashok D. Bandaranayake, Midori Clarke, Mesfin Gewe, Andrew J. Mhyre, David Baker, Roland K. Strong, Philip Bradley & James M. Olson 09 March 2018 | doi: 10.1038/s41467-018-03350-5 Drug development  High-throughput screening  Protein design  Recombinant peptide therapy  Publisher Correction: Identification of a peptide recognizing cerebrovascular changes in mouse models of Alzheimer’s disease OPEN Aman P. Mann, Pablo Scodeller, Sazid Hussain, Gary B. Braun, Tarmo Mölder, Kadri Toome, Rajesh Ambasudhan, Tambet Teesalu, Stuart A. Lipton & Erkki Ruoslahti 09 March 2018 | doi: 10.1038/s41467-018-03517-0 Alzheimer's disease  Neuro–vascular interactions      Advertisement nature.com webcasts Nature Research Custom presents a webcast on: Precision Health: Using Blood Biomarkers to Detect and Prevent Disease Date: Thursday, March 29, 2018  Register for FREE Sponsored by: Quanterix    Advertisement Nature Machine Intelligence launching Launching in January 2019, Nature Machine Intelligence will publish research from a wide range of topics underpinning machine learning, robotics and AI. 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