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Nature Communications - 01 March 2018

Nature Communications

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Springer Nature presents a custom webcast on: Sequencing Structural Variants for Disease Gene Discovery and Population Genetics

Date: Thursday, March 8, 2018 

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01 March 2018 
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Focal Point on Commercial Space Exploration in Japan 

Entering a new era of space development
Businesses are increasingly investing in space exploration and development 

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Nature Outline: Fatty liver disease

The worldwide rise in obesity and diabetes has led to a spike in the incidence of non-alcoholic fatty liver disease, which often progresses to the more severe non-alcoholic steatohepatitis. This Outline discusses diagnostic techniques and therapies.

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Springer Nature presents a custom webcast on: Precision over Bulk: Opportunities for Single-Cell DNA Analysis in Oncology

Date: Tuesday, March 13, 2018 

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Recent progress and perspectives of space electric propulsion systems based on smart nanomaterials OPEN
I. Levchenko, S. Xu, G. Teel, D. Mariotti, M. L. R. Walker & M. Keidar

Miniaturized spacecraft built from advanced nanomaterials are poised for unmanned space exploration. In this review, the authors examine the integration of nanotechnology in electric propulsion systems and propose the concept of self-healing and adaptive thrusters.

28 February 2018 | doi: 10.1038/s41467-017-02269-7
Aerospace engineering  Nanoscale materials 

Expanding frontiers in materials chemistry and physics with multiple anions OPEN
Hiroshi Kageyama, Katsuro Hayashi, Kazuhiko Maeda, J. Paul Attfield, Zenji Hiroi, James M. Rondinelli & Kenneth R. Poeppelmeier

Inorganic compounds with multiple anions have added a new dimension to the discovery of materials. Here the authors review the recent progress in the development of mixed-anion compounds, focusing on the roles of multiple anions in synthesis, characterization and properties.

22 February 2018 | doi: 10.1038/s41467-018-02838-4
Chemistry  Physics 
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A quantum light-emitting diode for the standard telecom window around 1,550 nm OPEN
T. Müller, J. Skiba-Szymanska, A. B. Krysa, J. Huwer, M. Felle, M. Anderson, R. M. Stevenson, J. Heffernan, D. A. Ritchie & A. J. Shields

Quantum light sources operating at telecom wavelength are a long-sought goal for quantum technologies. Here, the authors show electrically injected emission of single photons and entangled photon pairs from indium phosphide based quantum dots, operating up to a temperature of 93 K.

28 February 2018 | doi: 10.1038/s41467-018-03251-7
Optoelectronic devices and components  Quantum dots  Quantum information  Quantum optics 

Coupling between intra- and intermolecular motions in liquid water revealed by two-dimensional terahertz-infrared-visible spectroscopy OPEN
Maksim Grechko, Taisuke Hasegawa, Francesco D’Angelo, Hironobu Ito, Dmitry Turchinovich, Yuki Nagata & Mischa Bonn

Liquid water molecules are in constant vibrational motion, but probing how their local behaviour influences collective dynamics remains a challenge. Here, the authors present terahertz-infrared spectroscopy to elucidate coupling of the O-H stretch vibration to collective, delocalized intermolecular modes.

28 February 2018 | doi: 10.1038/s41467-018-03303-y
Chemical physics  Energy transfer  Infrared spectroscopy 

Two distinct domains contribute to the substrate acyl chain length selectivity of plant acyl-ACP thioesterase OPEN
Fuyuan Jing, Le Zhao, Marna D. Yandeau-Nelson & Basil J. Nikolau

The substrate specificity of acyl-ACP thioesterase (TE) plays a crucial role in determining the product profile of type II fatty acid synthase. Utilizing two FatB-type acyl-ACP TEs, the authors here define determinants of substrate specificity and create synthetic enzymes with distinct catalytic traits.

28 February 2018 | doi: 10.1038/s41467-018-03310-z
Biosynthesis  Enzyme mechanisms  Fatty acids  Protein design 

Uniform two-dimensional square assemblies from conjugated block copolymers driven by π–π interactions with controllable sizes OPEN
Liang Han, Meijing Wang, Xiangmeng Jia, Wei Chen, Hujun Qian & Feng He

Crystallization-driven processes play a vital role in preparing 2D nanostructures which makes structures with high symmetry hard to access. Here the authors present a non-crystallization approach which is based on π–π interactions of a copolymer for the fabrication of 2D symmetric structures with good dimensional control.

28 February 2018 | doi: 10.1038/s41467-018-03195-y
Conjugated polymers  Self-assembly  Supramolecular polymers 

Unattached kinetochores drive their own capturing by sequestering a CLASP OPEN
Caroline Kolenda, Jennifer Ortiz, Marina Pelzl, Sarina Norell, Verena Schmeiser & Johannes Lechner

Kinetochores (KT) that are not attached to microtubules prevent chromosome missegregation via the spindle assembly checkpoint. Here the authors show that Mps1 localizes Stu1 at unattached KTs together with Slk19, causing a reorganization of the nuclear MT network that favors the capturing of unattached KT.

28 February 2018 | doi: 10.1038/s41467-018-03108-z
Chromosome segregation  Kinetochores  Mitosis  Mitotic spindle 

Dual properties of a hydrogen oxidation Ni-catalyst entrapped within a polymer promote self-defense against oxygen OPEN
Alaa A. Oughli, Adrian Ruff, Nilusha Priyadarshani Boralugodage, Patricia Rodríguez-Maciá, Nicolas Plumeré, Wolfgang Lubitz, Wendy J. Shaw, Wolfgang Schuhmann & Olaf Rüdiger

Bio-inspired Ni-based molecular catalysts are efficient for H2 oxidation, but are suffering from the poor stability in the presence of O2. Here, the authors develop a strategy to boost greatly their stability by dispersing them in a hydrophobic and redox-silent polymer matrix.

28 February 2018 | doi: 10.1038/s41467-018-03011-7
Electrocatalysis  Energy  Fuel cells 

FcαRI co-stimulation converts human intestinal CD103+ dendritic cells into pro-inflammatory cells through glycolytic reprogramming OPEN
Ivo S. Hansen, Lisette Krabbendam, Jochem H. Bernink, Fabricio Loayza-Puch, Willianne Hoepel, Johan A. van Burgsteden, Elsa C. Kuijper, Christianne J. Buskens, Willem A. Bemelman, Sebastiaan A. J. Zaat, Reuven Agami, Gestur Vidarsson, Gijs R. van den Brink, Esther C. de Jong, Manon E. Wildenberg, Dominique L. P. Baeten, Bart Everts & Jeroen den Dunnen

Dendritic cells (DC) are important for maintaining immune homeostasis in the gut, but how they promote intestinal inflammation upon bacterial infection is still unclear. Here the authors show that IgA immune complexes induce proinflammatory cytokine production by metabolic reprogramming of otherwise tolerogenic human CD103+ DCs.

28 February 2018 | doi: 10.1038/s41467-018-03318-5
Antibodies  Dendritic cells  Mucosal immunology  Pattern recognition receptors 

Single cell polarity in liquid phase facilitates tumour metastasis OPEN
Anna Lorentzen , Paul F. Becker, Jan Kosla, Massimo Saini, Kathrin Weidele, Paolo Ronchi, Corinna Klein, Monika J. Wolf, Felix Geist, Bastian Seubert, Marc Ringelhan, Daniela Mihic-Probst, Knud Esser, Marko Roblek, Felix Kuehne, Gaia Bianco, Tracy O’Connor, Quentin Müller, Kathleen Schuck, Sebastian Lange et al.

Polarisation of metastasising cancer cells in circulation has not been investigated before. Here the authors identify single cell polarity as a distinct polarisation state of single cells in liquid phase, and show that perturbing single cell polarity affects attachment, adhesion, transmigration and metastasis in vitro and in vivo.

28 February 2018 | doi: 10.1038/s41467-018-03139-6
Actin  Cancer  Cell adhesion  Cell polarity 

Monovalent manganese based anodes and co-solvent electrolyte for stable low-cost high-rate sodium-ion batteries OPEN
Ali Firouzi, Ruimin Qiao, Shahrokh Motallebi, Christian W. Valencia, Hannah S. Israel, Mai Fujimoto, L. Andrew Wray, Yi-De Chuang, Wanli Yang & Colin D. Wessells

Sodium ion batteries offer more cost-effective storage than lithium and could be used for grid-scale energy storage. Here, the authors demonstrate a full cell based on a MnHCMn anode and an organic-aqueous cosolvent electrolyte. X-ray spectroscopy evidence further suggests the presence of Mn(I).

28 February 2018 | doi: 10.1038/s41467-018-03257-1
Batteries  Chemical physics  X-rays 

Cell-based glycan arrays for probing glycan–glycan binding protein interactions OPEN
Jennie Grace Briard, Hao Jiang, Kelley W. Moremen, Matthew Scott Macauley & Peng Wu

Glycans, interaction platforms protruding from the surface of cells, are hard to study due to their diverse architecture. Here, the authors present a method to obtain cells carrying defined glycans, which can then be used to find proteins specifically recognizing these tags.

28 February 2018 | doi: 10.1038/s41467-018-03245-5
Carbohydrates  Chemical biology  Chemical tools  Glycobiology  Screening 

All-optical control and super-resolution imaging of quantum emitters in layered materials OPEN
Mehran Kianinia, Carlo Bradac, Bernd Sontheimer, Fan Wang, Toan Trong Tran, Minh Nguyen, Sejeong Kim, Zai-Quan Xu, Dayong Jin, Andreas W. Schell, Charlene J. Lobo, Igor Aharonovich & Milos Toth

The photophysical properties of quantum emitters in layered van der Waals materials are receiving growing attention as they could be leveraged for nanophotonics applications. Here, the authors devise a two-laser super-resolution imaging setup capable of observing highly non-linear emission from hBN emitters.

28 February 2018 | doi: 10.1038/s41467-018-03290-0
Lasers, LEDs and light sources  Nanoscale materials  Optics and photonics 

Rational design of a trispecific antibody targeting the HIV-1 Env with elevated anti-viral activity OPEN
James J. Steinhardt, Javier Guenaga, Hannah L. Turner, Krisha McKee, Mark K. Louder, Sijy O’Dell, Chi-I Chiang, Lin Lei, Andrey Galkin, Alexander K. Andrianov, Nicole A. Doria-Rose, Robert T. Bailer, Andrew B. Ward, John R. Mascola & Yuxing Li

Broadly neutralizing antibodies targeting HIV Env could potentially be utilized as therapeutics. Here, Steinhardt et al. engineer a trispecific antibody with specificity for the receptor-binding site, a conserved Env glycan patch and the Env membrane proximal region with nearly pan-isolate neutralization breadth and high potency.

28 February 2018 | doi: 10.1038/s41467-018-03335-4
Antibodies  Antibody generation  Antibody therapy  HIV infections 

High capacity in G protein-coupled receptor signaling OPEN
Amiran Keshelava, Gonzalo P. Solis, Micha Hersch, Alexey Koval, Mikhail Kryuchkov, Sven Bergmann & Vladimir L. Katanaev

G protein-coupled receptors (GPCRs) activate intracellular signalling pathways upon extracellular stimulation. Here authors record single cell responses of GPCR signalling which allows the direct estimation of its channel capacity for each cell along with the reproducibility of its response.

28 February 2018 | doi: 10.1038/s41467-018-02868-y
Calcium signalling  Information theory 

Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds OPEN
Marina Naval-Sanchez , Quan Nguyen, Sean McWilliam, Laercio R. Porto-Neto, Ross Tellam, Tony Vuocolo, Antonio Reverter, Miguel Perez-Enciso, Rudiger Brauning, Shannon Clarke, Alan McCulloch, Wahid Zamani, Saeid Naderi, Hamid Reza Rezaei, Francois Pompanon, Pierre Taberlet, Kim C. Worley, Richard A. Gibbs, Donna M. Muzny, Shalini N. Jhangiani et al.

The domestication of plants and animals causes genomic changes underlying various morphologic, physiologic and behavioral changes. Here, Naval-Sanchez et al. provide a ChIP-Seq validated comparative functional annotation of the sheep genome, and show widespread evolution of proximal regulatory elements.

28 February 2018 | doi: 10.1038/s41467-017-02809-1
Computational biology and bioinformatics  Epigenomics  Molecular evolution  Systems biology 

Long-term optical brain imaging in live adult fruit flies OPEN
Cheng Huang, Jessica R. Maxey, Supriyo Sinha, Joan Savall, Yiyang Gong & Mark J. Schnitzer

Time-lapse imaging studies of more than a day in the fly brain have been infeasible until now. Here the authors present a laser microsurgery approach to create a permanent window in the fly cuticle to enable time-lapse imaging of neural architecture and dynamics for up to 10–50 days.

28 February 2018 | doi: 10.1038/s41467-018-02873-1
Olfactory system  Time-lapse imaging  Wide-field fluorescence microscopy 

PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers OPEN
Mohamad Moustafa Ali, Vijay Suresh Akhade, Subazini Thankaswamy Kosalai, Santhilal Subhash, Luisa Statello, Matthieu Meryet-Figuiere, Jonas Abrahamsson, Tanmoy Mondal & Chandrasekhar Kanduri

Although we know lncRNAs play a role in cancer, the identification of clinically relevant and functional lncRNAs is lacking. Here, the authors identify 633 prognostic markers, 570 S-phase cancer-associated lncRNAs, and show SCAT7 regulates FGF/FGFR and PI3K/AKT/MAPK pathways via interaction with hnRNPK/YBX1 complexes.

28 February 2018 | doi: 10.1038/s41467-018-03265-1
Cancer genomics  Oncogenes 

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen OPEN
Robert D. Stewart, Marc D. Auffret, Amanda Warr, Andrew H. Wiser, Maximilian O. Press, Kyle W. Langford, Ivan Liachko, Timothy J. Snelling, Richard J. Dewhurst, Alan W. Walker, Rainer Roehe & Mick Watson

Microbes in the cow rumen are crucial for the breakdown of plant material. Here, Stewart et al. assemble over 900 bacterial and archaeal genomes from the cow rumen microbiome, revealing new species and genes encoding enzymes with potential roles in carbohydrate metabolism.

28 February 2018 | doi: 10.1038/s41467-018-03317-6
Archaeal genomics  Bacterial genomics  Environmental microbiology  Metagenomics 

Spatial specificity of auxin responses coordinates wood formation OPEN
Klaus Brackmann, Jiyan Qi, Michael Gebert, Virginie Jouannet, Theresa Schlamp, Karin Grünwald, Eva-Sophie Wallner, Daria D. Novikova, Victor G. Levitsky, Javier Agustí, Pablo Sanchez, Jan U. Lohmann & Thomas Greb

Auxin activity controls plant stem cell function. Here the authors show that in the cambium, moderate auxin activity restricts cambial stem cell number via ARF5-dependent repression of the stem‐cell‐promoting factor WOX4, while ARF3 and ARF4 promote cambial activity outside of the WOX4‐expression domain.

28 February 2018 | doi: 10.1038/s41467-018-03256-2
Auxin  Plant stem cell 

Heritable DNA methylation marks associated with susceptibility to breast cancer OPEN
Jihoon E. Joo, James G. Dowty, Roger L. Milne, Ee Ming Wong, Pierre-Antoine Dugué, Dallas English, John L. Hopper, David E. Goldgar, Graham G. Giles & Melissa C. Southey

DNA methylation is associated with breast cancer risk. Here the authors measure DNA methylation in the blood of individuals from 25 Australian families with multiple cases of breast cancer but not known mutations associated with breast cancer risk to identify possible heritable methylation markers.

28 February 2018 | doi: 10.1038/s41467-018-03058-6
Breast cancer  Cancer genomics  DNA methylation  Genetics research 

Chloroquine modulates antitumor immune response by resetting tumor-associated macrophages toward M1 phenotype OPEN
Degao Chen, Jing Xie, Roland Fiskesund, Wenqian Dong, Xiaoyu Liang, Jiadi Lv, Xun Jin, Jinyan Liu, Siqi Mo, Tianzhen Zhang, Feiran Cheng, Yabo Zhou, Huafeng Zhang, Ke Tang, Jingwei Ma, Yuying Liu & Bo Huang

Tumour-associated macrophages (TAMs) display an M2 phenotype that promote tumour immune escape. Here the authors show that Chloroquine (CQ), a lysosome inhibitor used against malaria, inhibits tumour growth by switching TAMs into an M1 tumor-killing phenotype by repolarizing macrophages metabolism.

28 February 2018 | doi: 10.1038/s41467-018-03225-9
Cancer immunotherapy  Monocytes and macrophages  Tumour immunology 

Aggregating sequences that occur in many proteins constitute weak spots of bacterial proteostasis OPEN

Aggregation is sequence-specific and nucleated by short aggregating protein segments (APR). Here authors use a multidisciplinary approach to show that in E.coli some frequently occurring APRs lead to protein aggregation and ultimately bacterial cell death, which could serve as antibacterial strategy.

28 February 2018 | doi: 10.1038/s41467-018-03131-0
Bacterial infection  Chaperones  Molecular medicine  Protein aggregation 

3D printing of robotic soft actuators with programmable bioinspired architectures OPEN
Manuel Schaffner, Jakob A. Faber, Lucas Pianegonda, Patrick A. Rühs, Fergal Coulter & André R. Studart

3D-printed soft actuators have limited motion and are far from reaching the level of complexity found in biological systems. Here the authors present a multimaterial 3D printing platform for the fabrication of soft actuators displaying a wide range of motions that are programmable.

28 February 2018 | doi: 10.1038/s41467-018-03216-w
Actuators  Bioinspired materials  Mechanical engineering  Polymers 

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor OPEN
Megan Crow, Anirban Paul, Sara Ballouz, Z. Josh Huang & Jesse Gillis

Single cell RNA-sequencing analysis poses challenges in replication due to technical biases and analytic variability among bioinformatics pipelines. Here, Crow et al develop MetaNeighbor for measuring cell-type replication across datasets, and use it to identify marker genes for neuron subtypes with evidence of replication.

28 February 2018 | doi: 10.1038/s41467-018-03282-0
Data integration  Systems biology 

Genetic tagging of active neurons in auditory cortex reveals maternal plasticity of coding ultrasonic vocalizations OPEN
Gen-ichi Tasaka, Casey J. Guenthner, Amos Shalev, Omri Gilday, Liqun Luo & Adi Mizrahi

Fos-CreER knock-in mice enable tagging of neurons that are activated within a distinct time window. Here, the authors develop a Cre reporter mouse with low baseline activation and use it to reveal the specific coding properties of auditory cortex neurons that are activated by pup calls in both naive mice and mothers.

28 February 2018 | doi: 10.1038/s41467-018-03183-2
Auditory system  Neuroscience  Sensory processing 

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells OPEN
Ying Zhu, Paul D. Piehowski, Rui Zhao, Jing Chen, Yufeng Shen, Ronald J. Moore, Anil K. Shukla, Vladislav A. Petyuk, Martha Campbell-Thompson, Clayton E. Mathews, Richard D. Smith, Wei-Jun Qian & Ryan T. Kelly

There is a great need of developing highly sensitive mass spectrometry-based proteomics analysis for small cell populations. Here, the authors establish a robotically controlled chip-based nanodroplet processing platform and demonstrate its ability to profile the proteome from 10–100 mammalian cells.

28 February 2018 | doi: 10.1038/s41467-018-03367-w
Mass spectrometry  Proteomic analysis 

Highly stretchable carbon aerogels OPEN
Fan Guo, Yanqiu Jiang, Zhen Xu, Youhua Xiao, Bo Fang, Yingjun Liu, Weiwei Gao, Pei Zhao, Hongtao Wang & Chao Gao

Improved compressive elasticity was lately demonstrated for carbon aerogels but the problem of reversible stretchability remained a challenge. Here the authors use a hierarchical structure design and synergistic effects between carbon nanotubes and graphene to achieve high stretchability in carbon aerogels.

28 February 2018 | doi: 10.1038/s41467-018-03268-y
Mechanical and structural properties and devices  Structural properties 

Evidence that DNA polymerase δ contributes to initiating leading strand DNA replication in Saccharomyces cerevisiae OPEN
Marta A. Garbacz, Scott A. Lujan, Adam B. Burkholder, Phillip B. Cox, Qiuqin Wu, Zhi-Xiong Zhou, James E. Haber & Thomas A. Kunkel

DNA polymerases δ and ε (Pols δ and ε) are thought to be responsible for lagging and leading strand synthesis, respectively. Here the authors present evidence that Pol δ contributes to the initiation of leading strand replication in budding yeast by synthesizing DNA of both strands at replication origins.

27 February 2018 | doi: 10.1038/s41467-018-03270-4
DNA synthesis  Replisome 

Multi-indicator sustainability assessment of global food systems OPEN
Abhishek Chaudhary, David Gustafson & Alexander Mathys

The development of sustainable food systems requires an understanding of potential trade-off between various objectives. Here, Chaudhary et al. examine how different nations score on food system performance across several domains, including environment, nutrition, and sociocultural wellbeing.

27 February 2018 | doi: 10.1038/s41467-018-03308-7
Climate-change policy  Environmental impact  Socioeconomic scenarios  Sustainability 

Attosecond recorder of the polarization state of light OPEN
Álvaro Jiménez-Galán, Gopal Dixit, Serguei Patchkovskii, Olga Smirnova, Felipe Morales & Misha Ivanov

Attosecond pulses are useful in exploring processes involving ultrafast electron motion in atomic and molecular systems. Here the authors discuss a method to characterize the complex time-varying polarization state of broadband attosecond pulses by using asymmetry in photoelectron spectra.

27 February 2018 | doi: 10.1038/s41467-018-03167-2
Attosecond science  Optical physics  Ultrafast lasers 

Chiral DOTA chelators as an improved platform for biomedical imaging and therapy applications OPEN
Lixiong Dai, Chloe M. Jones, Wesley Ting Kwok Chan, Tiffany A. Pham, Xiaoxi Ling, Eric M. Gale, Nicholas J. Rotile, William Chi-Shing Tai, Carolyn J. Anderson, Peter Caravan & Ga-Lai Law

MRI contrast agents containing the rare earth metal gadolinium are very effective, yet unstable and thus potentially hazardous. Here, the authors developed complexes between gadolinium and the scaffolding compound DOTA with increased stability, which also lend themselves to radiometal labelling.

27 February 2018 | doi: 10.1038/s41467-018-03315-8
Ligands  Magnetic resonance imaging  Molecular imaging 

Frequency multiplexing for quasi-deterministic heralded single-photon sources OPEN
Chaitali Joshi, Alessandro Farsi, Stéphane Clemmen, Sven Ramelow & Alexander L. Gaeta

The aim of multiplexing is to boost capabilities of probabilistic single photon sources, but is vexed by rapidly increasing switching losses. Here, the authors propose and implement an in-fiber frequency-multiplexing scheme where total losses are independent of the number of multiplexed modes.

27 February 2018 | doi: 10.1038/s41467-018-03254-4
Nonlinear optics  Quantum optics  Single photons and quantum effects 

A G-protein pathway determines grain size in rice OPEN
Shengyuan Sun, Lei Wang, Hailiang Mao, Lin Shao, Xianghua Li, Jinghua Xiao, Yidan Ouyang & Qifa Zhang

Grain size is a major determinant of cereal yield. Here the authors characterize five subunits of the rice heterotrimeric G proteins and find that manipulating the three Gγ proteins can achieve designed grain size, which provides a predictable approach to improving grain yield and quality.

27 February 2018 | doi: 10.1038/s41467-018-03141-y
Agricultural genetics  Natural variation in plants  Plant breeding 

G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice OPEN
Qian Liu, Ruixi Han, Kun Wu, Jianqing Zhang, Yafeng Ye, Shuansuo Wang, Jianfeng Chen, Yajun Pan, Qi Li, Xiaopeng Xu, Jiawu Zhou, Dayun Tao, Yuejin Wu & Xiangdong Fu

Cereal crops' grain yield and quality are traits that are usually considered to be negatively correlated. Here, the authors show that interaction of G-protein βγ subunits with an alternatively spliced MADS1lgy3 protein can increase rice grain yield and quality simultaneously in field conditions.

27 February 2018 | doi: 10.1038/s41467-018-03047-9
Agricultural genetics  Natural variation in plants  Plant breeding 

Bonding dissimilar polymer networks in various manufacturing processes OPEN
Qihan Liu, Guodong Nian, Canhui Yang, Shaoxing Qu & Zhigang Suo

Hydrogels and hydrophobic elastomers of various shapes are difficult to bond in arbitrary sequences. Here the authors mix silane coupling agents into a precursor to form hydrogel resins with robust properties that can be spun, coated and printed in air.

27 February 2018 | doi: 10.1038/s41467-018-03269-x
Mechanical engineering  Soft materials 

Solid-phase synthesis of protein-polymers on reversible immobilization supports OPEN
Hironobu Murata, Sheiliza Carmali, Stefanie L. Baker, Krzysztof Matyjaszewski & Alan J. Russell

Synthesis of protein-polymer conjugates typically relies on multi-step processes in solution and on challenging purification strategies. Here the authors show a robust synthesis approach which eliminates purification processes by immobilizing proteins reversibly on modified agarose beads before grafting from polymers via ATRP.

27 February 2018 | doi: 10.1038/s41467-018-03153-8
Biomaterials  Enzymes 

Opponent control of behavioral reinforcement by inhibitory and excitatory projections from the ventral pallidum OPEN
Lauren Faget, Vivien Zell, Elizabeth Souter, Adam McPherson, Reed Ressler, Navarre Gutierrez-Reed, Ji Hoon Yoo, Davide Dulcis & Thomas S. Hnasko

The ventral palladium (VP) is involved in reward and contains mostly GABAergic neurons, but also glutamatergic neurons. Here, the authors characterize glutamatergic VP neurons and show that glutamatergic versus GABAergic projections play roles in avoidance and reinforcement, respectively.

27 February 2018 | doi: 10.1038/s41467-018-03125-y
Neural circuits  Reward 

Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere OPEN
Jônatas Abrahão, Lorena Silva, Ludmila Santos Silva, Jacques Yaacoub Bou Khalil, Rodrigo Rodrigues, Thalita Arantes, Felipe Assis, Paulo Boratto, Miguel Andrade, Erna Geessien Kroon, Bergmann Ribeiro, Ivan Bergier, Herve Seligmann, Eric Ghigo, Philippe Colson, Anthony Levasseur, Guido Kroemer, Didier Raoult & Bernard La Scola

Giant viruses are the largest viruses of the known virosphere and their genetic analysis can provide insights into virus evolution. Here, the authors discover Tupanvirus, a unique giant virus that has an unusually long tail and contains the largest translational apparatus of the known virosphere.

27 February 2018 | doi: 10.1038/s41467-018-03168-1
Evolution  Microbial genetics  Virology 

NAD+ analog reveals PARP-1 substrate-blocking mechanism and allosteric communication from catalytic center to DNA-binding domains OPEN
Marie-France Langelier, Levani Zandarashvili, Pedro M. Aguiar, Ben E. Black & John M. Pascal

Poly(ADP-ribose) polymerases (PARPs) catalyse ADP-ribose posttranslational modifications using NAD+ as a substrate. Here, the authors present the crystal structure of PARP-1 bound to the non-hydrolyzable NAD+ analog BAD and provide insights into the mechanism of PARP-1 allosteric regulation.

27 February 2018 | doi: 10.1038/s41467-018-03234-8
Enzyme mechanisms  X-ray crystallography 

On the relative motions of long-lived Pacific mantle plumes OPEN
Kevin Konrad, Anthony A. P. Koppers, Bernhard Steinberger, Valerie A. Finlayson, Jasper G. Konter & Matthew G. Jackson

Using mantle plumes to reconstruct past plate motion is complicated, because plumes may not be fixed. Here, the authors demonstrate using 40Ar/39Ar ages that the Rurutu plume is relatively stable compared to the rapidly moving Hawaiian plume, yet it has a similar deep mantle origin.

27 February 2018 | doi: 10.1038/s41467-018-03277-x
Geodynamics  Tectonics 

Biological methane production under putative Enceladus-like conditions OPEN
Ruth-Sophie Taubner, Patricia Pappenreiter, Jennifer Zwicker, Daniel Smrzka, Christian Pruckner, Philipp Kolar, Sébastien Bernacchi, Arne H. Seifert, Alexander Krajete, Wolfgang Bach, Jörn Peckmann, Christian Paulik, Maria G. Firneis, Christa Schleper & Simon K.-M. R. Rittmann

Many methanogenic archaea use H2 and CO2 to produce methane. Here, Taubner et al. show that Methanothermococcus okinawensis produces methane under conditions extrapolated for Saturn’s icy moon, Enceladus, and estimate that serpentinization may produce sufficient H2 for biological methane production.

27 February 2018 | doi: 10.1038/s41467-018-02876-y
Archaeal physiology  Astrobiology  Rings and moons 

The interdependence of excitation and inhibition for the control of dynamic breathing rhythms OPEN
Nathan Andrew Baertsch, Hans Christopher Baertsch & Jan Marino Ramirez

Excitatory neurons in the preBötzinger Complex generate bursting activity responsible for breathing, but these alone cannot generate physiological breathing frequencies. Here the authors show how inhibition regulates refractory properties of excitatory neurons to allow dynamic breathing rhythms.

26 February 2018 | doi: 10.1038/s41467-018-03223-x
Cellular neuroscience  Central pattern generators  Inhibition–excitation balance  Intrinsic excitability  Respiration 

Sodium enhances indium-gallium interdiffusion in copper indium gallium diselenide photovoltaic absorbers OPEN
Diego Colombara, Florian Werner, Torsten Schwarz, Ingrid Cañero Infante, Yves Fleming, Nathalie Valle, Conrad Spindler, Erica Vacchieri, Germain Rey, Mael Guennou, Muriel Bouttemy, Alba Garzón Manjón, Inmaculada Peral Alonso, Michele Melchiorre, Brahime El Adib, Baptiste Gault, Dierk Raabe, Phillip J. Dale & Susanne Siebentritt

Sodium doping is necessary to achieve high performance in polycrystalline chalcopyrite solar cells, but retards gallium interdiffusion, and thus efficiency optimisation. Here, Colombara et al. show that in contrast to the polycrystalline case, sodium accelerates atomic interdiffusion in monocrystalline samples.

26 February 2018 | doi: 10.1038/s41467-018-03115-0
Solar cells  Surfaces, interfaces and thin films 

Comprehensive integrative analyses identify GLT8D1 and CSNK2B as schizophrenia risk genes OPEN
Cui-Ping Yang, Xiaoyan Li, Yong Wu, Qiushuo Shen, Yong Zeng, Qiuxia Xiong, Mengping Wei, Chunhui Chen, Jiewei Liu, Yongxia Huo, Kaiqin Li, Gui Xue, Yong-Gang Yao, Chen Zhang, Ming Li, Yongbin Chen & Xiong-Jian Luo

More than 100 risk loci for schizophrenia have been identified by genome-wide association studies. Here, the authors apply an integrative genomic approach to prioritize risk genes and validate GLT8D1 and CSNK2B as candidate causal genes by in vitro studies in neural stem cells.

26 February 2018 | doi: 10.1038/s41467-018-03247-3
Genetics of the nervous system  Genetics research  Genome-wide association studies  Schizophrenia 

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes OPEN
Ibrahim Numanagić, Salem Malikić, Michael Ford, Xiang Qin, Lorraine Toji, Milan Radovich, Todd C. Skaar, Victoria M. Pratt, Bonnie Berger, Steve Scherer & S. Cenk Sahinalp

Many genes of functional and clinical significance are highly polymorphic and experience structural alterations. Here, Numanagić et al. develop Aldy, a computational tool for resolving the copy number and the sequence content of each copy of a gene by analyzing whole or targeted genome sequencing data.

26 February 2018 | doi: 10.1038/s41467-018-03273-1
Computational models  Software 

Fatty Acid Synthase induced S6Kinase facilitates USP11-eIF4B complex formation for sustained oncogenic translation in DLBCL OPEN
Bandish Kapadia, Nahid M. Nanaji, Kavita Bhalla, Binny Bhandary, Rena Lapidus, Afshin Beheshti, Andrew M. Evens & Ronald B. Gartenhaus

Aberrant protein translation and uncontrolled lipid metabolism are hallmarks of cancer growth. Here, in diffuse large B-cell lymphoma, the authors show that fatty acid synthase increases USP11 interaction with and stability of eIF4B via PI3K-S6Kinase signaling, promoting oncogenic protein translation.

26 February 2018 | doi: 10.1038/s41467-018-03028-y
Cancer  Lymphoma 

Widespread erosion on high plateaus during recent glaciations in Scandinavia OPEN
Jane L. Andersen, David L. Egholm, Mads F. Knudsen, Henriette Linge, John D. Jansen, Vivi K. Pedersen, Søren B. Nielsen, Dmitry Tikhomirov, Jesper Olsen, Derek Fabel & Sheng Xu

The contribution of surface processes to the long-term evolution of plateau surfaces on high-latitude passive margins is poorly understood. Here, the authors show that recent glacial erosion on plateaus in western Scandinavia was widespread and may have contributed substantially to the sediment flux to the oceans.

26 February 2018 | doi: 10.1038/s41467-018-03280-2
Geochemistry  Geomorphology 

How ligand binds to the type 1 insulin-like growth factor receptor OPEN
Yibin Xu, Geoffrey K.-W. Kong, John G. Menting, Mai B. Margetts, Carlie A. Delaine, Lauren M. Jenkin, Vladislav V. Kiselyov, Pierre De Meyts, Briony E. Forbes & Michael C. Lawrence

The human type 1 insulin-like growth factor receptor (IGF-1R) is important for normal human growth and development. Here, the authors present the crystal structures of the IGF-1R ectodomain both in its apo form and in complex with its ligand insulin-like growth factor I and discuss the receptor activation mechanism.

26 February 2018 | doi: 10.1038/s41467-018-03219-7
Kinases  X-ray crystallography 

MSD1 regulates pedicellate spikelet fertility in sorghum through the jasmonic acid pathway OPEN
Yinping Jiao, Young Koung Lee, Nicholas Gladman, Ratan Chopra, Shawn A. Christensen, Michael Regulski, Gloria Burow, Chad Hayes, John Burke, Doreen Ware & Zhanguo Xin

Inflorescence architecture affects crop grain yield. Here, the authors deploy whole-genome sequencing-based bulk segregant analysis to identify the causal gene of a sorghum multi-seeded (msd) mutant and suggest MSD1 regulating the fertility of the pedicellate spikelets through jasmonic acid pathway.

26 February 2018 | doi: 10.1038/s41467-018-03238-4
Agricultural genetics  Jasmonic acid 

EGFL7 reduces CNS inflammation in mouse OPEN
Catherine Larochelle, Timo Uphaus, Bieke Broux, Elizabeth Gowing, Magdalena Paterka, Laure Michel, Nevenka Dudvarski Stankovic, Frank Bicker, Florent Lemaître, Alexandre Prat, Mirko H. H. Schmidt & Frauke Zipp

Endothelial cells release extracellular matrix components that regulate inflammation. Here the authors demonstrate that the extracellular matrix component epidermal growth factor-like protein 7 regulates inflammation in experimental autoimmune encephalomyelitis in the mouse.

26 February 2018 | doi: 10.1038/s41467-018-03186-z
Blood–brain barrier  Extracellular matrix  Multiple sclerosis  Neuroimmunology 

Non-catalytic hydrogenation of VO2 in acid solution OPEN
Yuliang Chen, Zhaowu Wang, Shi Chen, Hui Ren, Liangxin Wang, Guobin Zhang, Yalin Lu, Jun Jiang, Chongwen Zou & Yi Luo

Hydrogenation is an effective way to tune the property of metal oxides. Here, the authors report a simple approach to hydrogenate VO2 in acid solution under ambient conditions by placing a small piece of low workfunction metal on VO2 surface.

26 February 2018 | doi: 10.1038/s41467-018-03292-y
Chemical physics  Electronic properties and materials  Phase transitions and critical phenomena 

Agrochemicals increase risk of human schistosomiasis by supporting higher densities of intermediate hosts OPEN
Neal T. Halstead, Christopher M. Hoover, Arathi Arakala, David J. Civitello, Giulio A. De Leo, Manoj Gambhir, Steve A. Johnson, Nicolas Jouanard, Kristin A. Loerns, Taegan A. McMahon, Raphael A. Ndione, Karena Nguyen, Thomas R. Raffel, Justin V. Remais, Gilles Riveau, Susanne H. Sokolow & Jason R. Rohr

Agrochemicals can affect the life cycle of human parasites in unexpected ways. Here, Halstead et al. show in mesocosm experiments that agrochemicals increase the density of snails hosting schistosome parasites, and modeling analysis suggests this could lead to increased risk of human schistosomiasis.

26 February 2018 | doi: 10.1038/s41467-018-03189-w
Agroecology  Community ecology  Ecological epidemiology 

Spatiotemporal regulation of Aurora B recruitment ensures release of cohesion during C. elegans oocyte meiosis OPEN
Nuria Ferrandiz, Consuelo Barroso, Oana Telecan, Nan Shao, Hyun-Min Kim, Sarah Testori, Peter Faull, Pedro Cutillas, Ambrosious P. Snijders, Monica P. Colaiácovo & Enrique Martinez-Perez

During meiosis, step-wise release of sister chromatid cohesion mediated by REC-8 cohesin is required for the formation of haploid gametes. Here, the authors show that in C. elegans oocytes, regulated recruitment of Aurora B kinase ensures the correct distribution of REC-8 phosphorylation, which promotes cohesion release.

26 February 2018 | doi: 10.1038/s41467-018-03229-5
Caenorhabditis elegans  Chromosome segregation  Meiosis  Oogenesis 

Superplastic nanoscale pore shaping by ion irradiation OPEN
Morteza Aramesh, Yashar Mayamei, Annalena Wolff & Kostya (Ken) Ostrikov

When nanomaterials are exposed to ionizing radiation, they often sustain mesoscopic changes not seen in their bulk form. Here, the authors use a helium ion microscope to induce and examine transformations in nanoporous alumina, drawing connections between atomic structure and nano- and microscale behavior in materials under irradiation.

26 February 2018 | doi: 10.1038/s41467-018-03316-7
Nanoscale materials  Structural properties  Surfaces, interfaces and thin films 

The influence of the molecular packing on the room temperature phosphorescence of purely organic luminogens OPEN
Jie Yang, Xu Zhen, Bin Wang, Xuming Gao, Zichun Ren, Jiaqiang Wang, Yujun Xie, Jianrong Li, Qian Peng, Kanyi Pu & Zhen Li

Organic luminogens with persistent room temperature phosphorescence will find wide applications in optoelectronic devices and bioimaging, but they are still scarce. Here, the authors synthesize seven organic luminogens and investigate their different properties and potential imaging applications.

26 February 2018 | doi: 10.1038/s41467-018-03236-6
Bioanalytical chemistry  Fluorescent labelling  Imaging studies 

Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation OPEN
Diana M. Mitrea, Jaclyn A. Cika, Christopher B. Stanley, Amanda Nourse, Paulo L. Onuchic, Priya R. Banerjee, Aaron H. Phillips, Cheon-Gil Park, Ashok A. Deniz & Richard W. Kriwacki

The nucleolus is a membrane-less organelle formed through liquid–liquid phase separation (LLPS). Here the authors use biophysical methods and show that the nucleolar protein nucleophosmin (NPM1) also undergoes LLPS through homotypic, inter-NPM1 interactions and discuss implications for the ribosome biogenesis process.

26 February 2018 | doi: 10.1038/s41467-018-03255-3
Intrinsically disordered proteins  Molecular conformation  SAXS  Single-molecule biophysics  Supramolecular assembly 

Sculpting nanoparticle dynamics for single-bacteria-level screening and direct binding-efficiency measurement OPEN
Y. Z. Shi, S. Xiong, Y. Zhang, L. K. Chin, Y. –Y. Chen, J. B. Zhang, T. H. Zhang, W. Ser, A. Larson, L. S. Hoi, J. H. Wu, T. N. Chen, Z. C. Yang, Y. L. Hao, B. Liedberg, P. H. Yap, D. P. Tsai, C.-W. Qiu & A. Q. Liu

Optical trapping is a versatile tool for biomedical applications. Here, the authors use an optofluidic lattice to achieve controllable multi-particle hopping and demonstrate single-bacteria-level screening and measurement of binding efficiency of biological binding agents through particle-enabled bacteria hopping.

26 February 2018 | doi: 10.1038/s41467-018-03156-5
Biological techniques  Optical manipulation and tweezers  Optofluidics 

A randomized and open-label phase II trial reports the efficacy of neoadjuvant lobaplatin in breast cancer OPEN
Xiujuan Wu, Peng Tang, Shifei Li, Shushu Wang, Yueyang Liang, Ling Zhong, Lin Ren, Ting Zhang & Yi Zhang

Triple-negative breast cancer (TNBC) is one of the most aggressive and difficult to treat types of breast cancer. Here, a phase 2 clinical trial in TNBC patients reveals that the addition of lobaplatin to docetaxel and epirubicin regime improves pCR and ORR rates with tolerable side-effects.

26 February 2018 | doi: 10.1038/s41467-018-03210-2
Breast cancer  Randomized controlled trials 

Clonally diverse CD38+HLA-DR+CD8+ T cells persist during fatal H7N9 disease OPEN
Zhongfang Wang , Lingyan Zhu, Thi H. O. Nguyen, Yanmin Wan, Sneha Sant, Sergio M. Quiñones-Parra, Jeremy Chase Crawford, Auda A. Eltahla, Simone Rizzetto, Rowena A. Bull, Chenli Qiu, Marios Koutsakos, E. Bridie Clemens, Liyen Loh, Tianyue Chen, Lu Liu, Pengxing Cao, Yanqin Ren, Lukasz Kedzierski, Tom Kotsimbos et al.

Virus-specific CD8+ T cells are crucial during H7N9 influenza infection, but CD8+ T cell dysfunction is associated with poor prognosis. Here, the authors use molecular and phenotypic analysis to establish persistence of clonally diverse CD8+ T cell populations during fatal infection.

26 February 2018 | doi: 10.1038/s41467-018-03243-7
CD8-positive T cells  Influenza virus  T-cell receptor  Viral infection 

An olfactory virtual reality system for mice OPEN
Brad A. Radvansky & Daniel A. Dombeck

Odor-guided spatial behaviours are difficult to study due to the challenge of controlling chemical concentrations in space and time. Here the authors present a precise odor delivery system to generate a olfactory virtual landscape that engages hippocampal place cells in mice.

26 February 2018 | doi: 10.1038/s41467-018-03262-4
Behavioural methods  Hippocampus  Olfactory system 

A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets OPEN
Fruzsina Hobor, Andre Dallmann, Neil J. Ball, Carla Cicchini, Cecilia Battistelli, Roksana W. Ogrodowicz, Evangelos Christodoulou, Stephen R. Martin, Alfredo Castello, Marco Tripodi, Ian A. Taylor & Andres Ramos

Syncrip is a conserved RNA-binding protein that mediates selective miRNA loading into cell-secreted exosomes, which is important for cell–cell communication. Here the authors provide mechanistic insights into how Syncrip recognises its target miRNAs by combining NMR and crystallography.

26 February 2018 | doi: 10.1038/s41467-018-03182-3
Extracellular signalling molecules  miRNAs  Solution-state NMR  X-ray crystallography 

Lkb1 deficiency confers glutamine dependency in polycystic kidney disease OPEN
Ebony M. Flowers, Jessica Sudderth, Lauren Zacharias, Glenda Mernaugh, Roy Zent, Ralph J. DeBerardinis & Thomas J. Carroll

Polycystic kidney disease (PKD) is characterized by the formation of large fluid-filled cysts. Here Flowers and colleagues show that loss of Lkb1, downregulated in PKD, renders kidney cells dependent on glutamine for growth, and suggest that inhibition of glutamine metabolism may prevent cyst development in PKD.

26 February 2018 | doi: 10.1038/s41467-018-03036-y
Metabolomics  Polycystic kidney disease 

A dual mechanism promotes switching of the Stormorken STIM1 R304W mutant into the activated state OPEN
Marc Fahrner, Michael Stadlbauer, Martin Muik, Petr Rathner, Peter Stathopulos, Mitsu Ikura, Norbert Müller & Christoph Romanin

Stormorken syndrome is associated with the R304W mutation in STIM1, which is a Calcium sensor in the endoplasmic reticulum. Here authors use FRET and electrophysiology to show that R304W induces STIM1 conformational extension by a dual mechanism resulting in constitutive activation of Ca2+ channels.

26 February 2018 | doi: 10.1038/s41467-018-03062-w
Calcium signalling  Diseases 

Marangoni-driven flower-like patterning of an evaporating drop spreading on a liquid substrate OPEN
F. Wodlei, J. Sebilleau, J. Magnaudet & V. Pimienta

In liquid–liquid systems, Marangoni effects induced by surface tension gradients may result in the formation of peculiar self-assembled patterns. Wodlei et al. utilize this effect to draw a ‘flower’ by letting an oil droplet evaporate on an aqueous substrate in the presence of a cationic surfactant.

26 February 2018 | doi: 10.1038/s41467-018-03201-3
Chemical physics  Fluid dynamics 

Control over multiple molecular states with directional changes driven by molecular recognition OPEN
Takehiro Hirao, Dong Sub Kim, Xiaodong Chi, Vincent M. Lynch, Kazuaki Ohara, Jung Su Park, Kentaro Yamaguchi & Jonathan L. Sessler

Multistate molecular systems usually rely on external energy inputs to switch between states. Here, the authors show that a bispyridyl calixpyrrole system directed by only weak noncovalent interactions and metal coordination can access six discrete structural states, with directional and sequential control.

26 February 2018 | doi: 10.1038/s41467-018-03220-0
Molecular capsules  Self-assembly 

Encapsulation of catalyst in block copolymer micelles for the polymerization of ethylene in aqueous medium OPEN
Camille Boucher-Jacobs, Muhammad Rabnawaz, Joshua S. Katz, Ralph Even & Damien Guironnet

Olefin and emulsion polymerizations are incompatible due to the water sensitivity of olefin polymerization catalysts and thus direct synthesis of semi-crystalline polyolefin latexes is difficult. Here, the authors encapsulate a catalyst precursor in micelles which act as nanoreactors for ethylene polymerization in water.

26 February 2018 | doi: 10.1038/s41467-018-03253-5
Polymer synthesis  Polymerization mechanisms 

Cardiolipin exposure on the outer mitochondrial membrane modulates α-synuclein OPEN
Tammy Ryan, Vladimir V. Bamm, Morgan G. Stykel, Carla L. Coackley, Kayla M. Humphries, Rhiannon Jamieson-Williams, Rajesh Ambasudhan, Dick D. Mosser, Stuart A. Lipton, George Harauz & Scott D. Ryan

Cardiolipin is a phospholipid component of the inner mitochondrial membrane. Here the authors demonstrate that cardiolipin interacts with mutant α-synuclein, and that impaired cardiolipin function can lead to spread of α-synuclein between neurons.

26 February 2018 | doi: 10.1038/s41467-018-03241-9
Mitochondria  Parkinson's disease 

Hypoxia-inducible factor 2-alpha-dependent induction of amphiregulin dampens myocardial ischemia-reperfusion injury OPEN
Michael Koeppen, Jae W. Lee, Seong-Wook Seo, Kelley S. Brodsky, Simone Kreth, Ivana V. Yang, Peter M. Buttrick, Tobias Eckle & Holger K. Eltzschig

Myocardial ischemia–reperfusion injury stabilizes the hypoxia-inducible factor HIF2-alpha. Here, the authors show that HIF2-alpha protects the heart from injury via induction of the epidermal growth factor amphiregulin, and that amphiregulin administration is cardioprotective in mice.

26 February 2018 | doi: 10.1038/s41467-018-03105-2
Myocardial infarction  Stress signalling 

Effect of friction on oxidative graphite intercalation and high-quality graphene formation OPEN
Steffen Seiler, Christian E. Halbig, Fabian Grote, Philipp Rietsch, Felix Börrnert, Ute Kaiser, Bernd Meyer & Siegfried Eigler

Scalable graphene production from graphite via an intercalation-oxidation-reduction process is still hampered by low reproducibility and many lattice defects. Here, the authors show that reducing molecular friction by using highly crystalline graphite and mild oxidizing conditions is the key to high quality graphene.

26 February 2018 | doi: 10.1038/s41467-018-03211-1
Molecular dynamics  Synthesis of graphene  Two-dimensional materials 

Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms OPEN
Brandon L. Pierce, Lin Tong, Maria Argos, Kathryn Demanelis, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwar, Md. Tariqul Islam, Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, Md. Yunus, Muhammad G. Kibriya, Lin S. Chen & Habibul Ahsan

Most expression QTLs (eQTLs) co-occur with a DNA methylation QTL (meQTL), suggesting a common causal variant. Here the authors analyse DNA and RNA from blood and identify eQTL-meQTL pairs likely to share a causal variant, finding that expression and methylation are often genetically co-regulated.

23 February 2018 | doi: 10.1038/s41467-018-03209-9
DNA methylation  Epigenomics  Gene regulation  Quantitative trait 

A family of unconventional deubiquitinases with modular chain specificity determinants OPEN
Thomas Hermanns, Christian Pichlo, Ilka Woiwode, Karsten Klopffleisch, Katharina F. Witting, Huib Ovaa, Ulrich Baumann & Kay Hofmann

Deubiquitinating enzymes (DUBs) are essential to modulate ubiquitin signaling. While known DUBs can be grouped into six families, the authors here present biochemical and structural evidence for a seventh DUB family, defining determinants of substrate specificity for two representative enzymes.

23 February 2018 | doi: 10.1038/s41467-018-03148-5
Deubiquitylating enzymes  Enzyme mechanisms  Ubiquitylation  X-ray crystallography 

Evolution of Barrett’s esophagus through space and time at single-crypt and whole-biopsy levels OPEN
Pierre Martinez, Diego Mallo, Thomas G. Paulson, Xiaohong Li, Carissa A. Sanchez, Brian J. Reid, Trevor A. Graham, Mary K. Kuhner & Carlo C. Maley

Clonal dynamics of Barrett’s esophagus (BE) leading to cancer are poorly understood. Here, they report BE segments are clonal, have frequent mutations at the gastro-esophageal junction, genomic instability precedes genome doubling/clonal expansion, and a correlation between inter- and intra-biopsy genetic diversity.

23 February 2018 | doi: 10.1038/s41467-017-02621-x
Cancer genomics  Oesophageal cancer  Phylogenetics  Tumour heterogeneity 

MEMS-tunable dielectric metasurface lens OPEN
Ehsan Arbabi, Amir Arbabi, Seyedeh Mahsa Kamali, Yu Horie, MohammadSadegh Faraji-Dana & Andrei Faraon

Conventional refractive elements are bulky, thick and offer limited active tunability. Here, the authors demonstrate MEMS-based tunable metasurface doublets with more than 60 diopters change in the optical power upon a 1-micron movement of a membrane with one of the metasurface elements.

23 February 2018 | doi: 10.1038/s41467-018-03155-6
Engineering  Integrated optics  Metamaterials  Sub-wavelength optics 

Molecular demultiplexer as a terminator automaton OPEN
Ilke S. Turan, Gurcan Gunaydin, Seylan Ayan & Engin U. Akkaya

Nanorobots will likely play a major role in future therapeutic approaches. Here, the authors develop a molecular automaton based on Zinc-BODIPY complexes that can autonomously switch between singlet oxygen generation and fluorescence emission, i.e., therapeutic and diagnostic modes.

23 February 2018 | doi: 10.1038/s41467-018-03259-z
Excited states  Nanoscale devices  Single-molecule fluorescence 

Quantum and electrochemical interplays in hydrogenated graphene OPEN
Lin Jiang, Wangyang Fu, Yuvraj Y. Birdja, Marc T. M. Koper & Grégory F. Schneider

Electrochemically-gated graphene field-effect transistors show promise for sensing of charged species in real time. Here, the authors leverage the interplay between electrical in-plane transport and electrochemical activity to explore the sensing performance of hydrogenated graphene.

23 February 2018 | doi: 10.1038/s41467-018-03026-0
Electrochemistry  Graphene 

Vps3 and Vps8 control integrin trafficking from early to recycling endosomes and regulate integrin-dependent functions OPEN
C. T. H. Jonker, R. Galmes, T. Veenendaal, C. ten Brink, R. E. N. van der Welle, N. Liv, J. de Rooij, A. A. Peden, P. van der Sluijs, C. Margadant & J. Klumperman

The CORVET complex is a multi-subunit complex that regulates fusion between early endosomes. Here the authors show that the CORVET subunits Vps3 and Vps8 also regulate vesicular transport from early to recycling endosomes and are required for recycling integrins to the plasma membrane.

23 February 2018 | doi: 10.1038/s41467-018-03226-8
Endosomes  Integrins  Transport carrier 

Experimental evidence of quantum radiation reaction in aligned crystals OPEN
Tobias N. Wistisen, Antonino Di Piazza, Helge V. Knudsen & Ulrik I. Uggerhøj

The experimental evidence of radiation reaction has so far been elusive. Here the authors provide the signature of radiation reaction in quantum electrodynamics by observing the radiation reaction effects when high-energy positrons emit radiation while propagating through a  silicon crystal.

23 February 2018 | doi: 10.1038/s41467-018-03165-4
Matter waves and particle beams  Single photons and quantum effects 

Increasing temperature of cooling granular gases OPEN
Nikolai V. Brilliantov, Arno Formella & Thorsten Pöschel

Granular gases—dilute systems composed of dissipatively colliding particles—exhibit anomalous dynamics and numerous surprising phenomena. Here, Brilliantov et al. show that the aggregation mechanism can induce increase of the gas temperature despite the fact that the total kinetic energy decreases.

23 February 2018 | doi: 10.1038/s41467-017-02803-7
Statistical physics  Thermodynamics 

Correlating chemical diversity with taxonomic distance for discovery of natural products in myxobacteria OPEN
Thomas Hoffmann, Daniel Krug, Nisa Bozkurt, Srikanth Duddela, Rolf Jansen, Ronald Garcia, Klaus Gerth, Heinrich Steinmetz & Rolf Müller

It is thought that the chances for discovery of novel natural products increase by screening rare organisms. Here the authors analyse metabolites produced by over 2300 myxobacterial strains and, indeed, find a correlation between taxonomic distance and production of distinct secondary metabolite families.

23 February 2018 | doi: 10.1038/s41467-018-03184-1
Bacteria  Drug discovery  Metabolomics  Natural products 

Membrane sculpting by curved DNA origami scaffolds OPEN
Henri G. Franquelim, Alena Khmelinskaia, Jean-Philippe Sobczak, Hendrik Dietz & Petra Schwille

BAR domain proteins feature a “banana-like” shape which is thought to aid membrane scaffolding and membrane tubulation. Here authors use DNA origami mimicking BAR domains, giant unilamellar vesicles and fluorescence imaging to study how different BAR domain shapes bind and deform membranes.

23 February 2018 | doi: 10.1038/s41467-018-03198-9
DNA nanostructures  Nanoscale biophysics 

Direct observation of single-molecule hydrogen-bond dynamics with single-bond resolution OPEN
Ce Zhou, Xingxing Li, Zhongliang Gong, Chuancheng Jia, Yuanwei Lin, Chunhui Gu, Gen He, Yuwu Zhong, Jinlong Yang & Xuefeng Guo

Hydrogen-bonds are widely found in many systems, such as DNAs and supramolecular assemblies, but it remains challenging to detect their dynamics at a molecular level. Here, Zhou et al. study the stochastic arrangement of hydrogen bonds using single-molecule junctions connected to graphene electrodes.

23 February 2018 | doi: 10.1038/s41467-018-03203-1
Reaction kinetics and dynamics  Self-assembly 

Precipitation of binary quasicrystals along dislocations OPEN
Zhiqing Yang, Lifeng Zhang, Matthew F. Chisholm, Xinzhe Zhou, Hengqiang Ye & Stephen J. Pennycook

Quasicrystal precipitation in alloys should be favored at dislocations, which break crystal symmetry, but almost all precipitates at dislocations are periodic. Here, the authors show rare quasicrystal formation along dislocations in a magnesium zinc alloy with atomic resolution.

23 February 2018 | doi: 10.1038/s41467-018-03250-8
Metals and alloys  Structure of solids and liquids 

Zebrafish and medaka offer insights into the neurobehavioral correlates of vertebrate magnetoreception OPEN
Ahne Myklatun, Antonella Lauri, Stephan H. K. Eder, Michele Cappetta, Denis Shcherbakov, Wolfgang Wurst, Michael Winklhofer & Gil G. Westmeyer

Advances in animal magnetoreception have been limited by a lack of tractable vertebrate laboratory models. Here, the authors demonstrate light-independent magnetoreception in mature zebrafish and medaka, as well as magnetosensitive locomotion in juvenile medaka associated with neuronal activation in the lateral hindbrain.

23 February 2018 | doi: 10.1038/s41467-018-03090-6
Animal behaviour  Model vertebrates  Navigation  Sensory processing 

Probing of sub-picometer vertical differential resolutions using cavity plasmons OPEN
Wen Chen, Shunping Zhang, Qian Deng & Hongxing Xu

Plasmon rulers can be used for resolving ultrasmall material changes. Here, the authors show how cavity plasmons in a metal nanowire-on-mirror setup can be used to probe vertical dimensional changes with sub-picometer differential resolution using two carefully chosen material systems.

23 February 2018 | doi: 10.1038/s41467-018-03227-7
Nanophotonics and plasmonics  Nanosensors  Optical sensors 

Cobalt-catalyzed electrooxidative C-H/N-H [4+2] annulation with ethylene or ethyne OPEN
Shan Tang, Dan Wang, Yichang Liu, Li Zeng & Aiwen Lei

Catalytic methodologies that incorporate commodity chemicals ethylene and ethyne into fine chemicals are quite limited. Here, the authors show a cobalt-catalyzed electrochemical C-H/N–H [4+2] annulation of aryl/vinyl amides with ethylene or ethyne to produce N-heterocycles in absence of oxidants.

23 February 2018 | doi: 10.1038/s41467-018-03246-4
Electrocatalysis  Synthetic chemistry methodology  Reaction mechanisms 

Development differentially sculpts receptive fields across early and high-level human visual cortex OPEN
Jesse Gomez, Vaidehi Natu, Brianna Jeska, Michael Barnett & Kalanit Grill-Spector

Population receptive fields (pRFs) in the visual system are key information-processors, but how they develop is unknown. Here, authors use fMRI and pRF modeling in children and adults to show that in the ventral stream only pRFs in face- and word-selective regions continue to develop, mirroring changes in viewing behavior.

23 February 2018 | doi: 10.1038/s41467-018-03166-3
Extrastriate cortex  Striate cortex 

Membrane cholesterol mediates the cellular effects of monolayer graphene substrates OPEN
Kristina E. Kitko, Tu Hong, Roman M. Lazarenko, Da Ying, Ya-Qiong Xu & Qi Zhang

Understanding the biological role of graphene in eukaryotic cells is essential for future biomedicine applications. Here, the authors investigate the interaction of neurons and fibroblasts with graphene substrates, which increase cell membrane cholesterol and potentiate neurotransmitter release and receptor signaling.

23 February 2018 | doi: 10.1038/s41467-018-03185-0
Calcium signalling  Nanostructures  Synaptic vesicle exocytosis 

Retrosynthesis of multi-component metal−organic frameworks OPEN
Shuai Yuan, Jun-Sheng Qin, Jialuo Li, Lan Huang, Liang Feng, Yu Fang, Christina Lollar, Jiandong Pang, Liangliang Zhang, Di Sun, Ali Alsalme, Tahir Cagin & Hong-Cai Zhou

The crystal engineering of metal–organic frameworks has led to the construction of complex structures, but has yet to reach the same level of sophistication as organic synthesis. Here, Zhou and colleagues use retrosynthetic chemistry to design and produce complex multi-component frameworks.

23 February 2018 | doi: 10.1038/s41467-018-03102-5
Coordination chemistry  Crystal engineering  Metal–organic frameworks  Solid-state chemistry 

Bounding cross-shelf transport time and degradation in Siberian-Arctic land-ocean carbon transfer OPEN
Lisa Bröder, Tommaso Tesi, August Andersson, Igor Semiletov & Örjan Gustafsson

The fate of terrestrial organic carbon in marine sediments is debated due to large uncertainties in its degradation during transport. Here, using compound-specific radiocarbon dating of terrestrial biomarkers, the authors show that transport across the East Siberian Arctic shelf takes 3600 ± 300 years.

23 February 2018 | doi: 10.1038/s41467-018-03192-1
Carbon cycle 

A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle OPEN
Benjamin Goode , Gourish Mondal, Michael Hyun, Diego Garrido Ruiz, Yu-Hsiu Lin, Jessica Van Ziffle, Nancy M. Joseph, Courtney Onodera, Eric Talevich, James P. Grenert, Iman H. Hewedi, Matija Snuderl, Daniel J. Brat, Bette K. Kleinschmidt-DeMasters, Fausto J. Rodriguez, David N. Louis, William H. Yong, M. Beatriz Lopes, Marc K. Rosenblum, Nicholas Butowski et al.

Chordoid glioma is a rare low-grade brain tumor that originates from the anterior wall of the third ventricle where surgical resection is challenging; the clinical outcome of patients after subtotal resection or disease recurrence is poor. Here the authors identify a recurrent missense mutation in PRKCA that may serve as a potential therapeutic target in this uncommon brain cancer.

23 February 2018 | doi: 10.1038/s41467-018-02826-8
Cancer genetics  CNS cancer  Oncogenes  Targeted therapies 

Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis OPEN
Fumitaka Mizoguchi , Kamil Slowikowski, Kevin Wei, Jennifer L. Marshall, Deepak A. Rao, Sook Kyung Chang, Hung N. Nguyen, Erika H. Noss, Jason D. Turner, Brandon E. Earp, Philip E. Blazar, John Wright, Barry P. Simmons, Laura T. Donlin, George D. Kalliolias, Susan M. Goodman, Vivian P. Bykerk, Lionel B. Ivashkiv, James A. Lederer, Nir Hacohen et al.

Synovial fibroblasts are thought to be central mediators of joint destruction in rheumatoid arthritis (RA). Here the authors use single-cell transcriptomics and flow cytometry to identify synovial fibroblast subsets that are expanded and display distinct tissue distribution and function in patients with RA.

23 February 2018 | doi: 10.1038/s41467-018-02892-y
Functional clustering  Rheumatoid arthritis 

Bioinspired leaves-on-branchlet hybrid carbon nanostructure for supercapacitors OPEN
Guoping Xiong, Pingge He, Zhipeng Lyu, Tengfei Chen, Boyun Huang, Lei Chen & Timothy S. Fisher

One way to improve the performance of supercapacitors is to use hybrid carbon nanomaterials. Here the authors show a bioinspired electrode design with graphene petals and carbon nanotube arrays serving as leaves and branchlets, respectively. The structure affords excellent electrochemical characteristics.

23 February 2018 | doi: 10.1038/s41467-018-03112-3
Power distribution  Supercapacitors 

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging OPEN
Irene Franco, Anna Johansson, Karl Olsson, Peter Vrtačnik, Pär Lundin, Hafdis T. Helgadottir, Malin Larsson, Gwladys Revêchon, Carla Bosia, Andrea Pagnani, Paolo Provero, Thomas Gustafsson, Helene Fischer & Maria Eriksson

Aging skeletal muscle shows declining numbers and activity of satellite cells. Here, Franco et al. show that in satellite cells of the human leg muscle vastus lateralis, somatic mutations accumulate with age and that these mutations become enriched in exons and promoters of genes involved in muscle function.

23 February 2018 | doi: 10.1038/s41467-018-03244-6
Ageing  Genetics research  Muscle stem cells  Next-generation sequencing 

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation OPEN
William Stephenson, Laura T. Donlin, Andrew Butler, Cristina Rozo, Bernadette Bracken, Ali Rashidfarrokhi, Susan M. Goodman, Lionel B. Ivashkiv, Vivian P. Bykerk, Dana E. Orange, Robert B. Darnell, Harold P. Swerdlow & Rahul Satija

Droplet-based single-cell RNA-seq is a powerful tool for cellular heterogeneity profiling in disease but is limited by instrumentation required. Here the authors develop a 3D printed microfluidic platform for massive parallel sequencing of rheumatoid arthritis tissues.

23 February 2018 | doi: 10.1038/s41467-017-02659-x
Autoimmunity  Gene expression profiling  Microfluidics 

Landscape topography structures the soil microbiome in arctic polygonal tundra OPEN
Neslihan Taş, Emmanuel Prestat, Shi Wang, Yuxin Wu, Craig Ulrich, Timothy Kneafsey, Susannah G. Tringe, Margaret S. Torn, Susan S. Hubbard & Janet K. Jansson

The role of ecosystem structure in microbial activity related to greenhouse gas production is poorly understood. Here, Taş and colleagues show that microbial communities and ecosystem function vary across fine-scale topography in a polygonal tundra.

22 February 2018 | doi: 10.1038/s41467-018-03089-z
Biogeochemistry  Boreal ecology  Metagenomics  Microbial ecology 

Timescales of water accumulation in magmas and implications for short warning times of explosive eruptions OPEN
M. Petrelli, K. El Omari, L. Spina, Y. Le Guer, G. La Spina & D. Perugini

Volatiles such as water play a key role in magma ascent and ultimately triggering explosive eruptions. Here, the authors show that water-rich melts with water concentrations of 6–9 wt.% can ascend rapidly to the surface over the timescales of hours to days with very short warning times.

22 February 2018 | doi: 10.1038/s41467-018-02987-6
Natural hazards  Petrology  Volcanology 

Periosteum contains skeletal stem cells with high bone regenerative potential controlled by Periostin OPEN
Oriane Duchamp de Lageneste, Anaïs Julien, Rana Abou-Khalil, Giulia Frangi, Caroline Carvalho, Nicolas Cagnard, Corinne Cordier, Simon J. Conway & Céline Colnot

The periosteum, a tissue lining the bone surface, and the bone marrow are known to contain bone-forming cells. Here the authors show that skeletal stem cells reside in the mouse periosteum, and that periosteal cells have common embryonic origins with bone marrow stromal/stem cells (BMSCs), but are better at bone repair and long-term integration than BMSCs.

22 February 2018 | doi: 10.1038/s41467-018-03124-z
Bone  Mesenchymal stem cells  Regeneration 

The assassin bug Pristhesancus plagipennis produces two distinct venoms in separate gland lumens OPEN
Andrew A. Walker, Mark L. Mayhew, Jiayi Jin, Volker Herzig, Eivind A. B. Undheim, Andy Sombke, Bryan G. Fry, David J. Meritt & Glenn F. King

Venom can be used both offensively for prey capture and defensively to deter predators. Here, Walker and colleagues demonstrate that the assassin bug Pristhesancus plagipennis has two distinct venom glands that produce venoms with distinct compositions that can be elicited by different stimuli.

22 February 2018 | doi: 10.1038/s41467-018-03091-5
Animal behaviour  Chemical ecology  Entomology  Evolutionary ecology 

Quantum phase transitions in highly crystalline two-dimensional superconductors OPEN
Yu Saito, Tsutomu Nojima & Yoshihiro Iwasa

Superconductor-insulator transitions predominantly occur in highly disordered thin films. Here, Saito et al. report that a quantum metallic state transforms via the quantum Griffiths state to a weakly localized metal at high magnetic fields in a crystalline two-dimensional superconductor.

22 February 2018 | doi: 10.1038/s41467-018-03275-z
Phase transitions and critical phenomena  Superconducting properties and materials  Two-dimensional materials 

The structure of iPLA2β reveals dimeric active sites and suggests mechanisms of regulation and localization OPEN
Konstantin R. Malley, Olga Koroleva, Ian Miller, Ruslan Sanishvili, Christopher M. Jenkins, Richard W. Gross & Sergey Korolev

Calcium-independent phospholipase A2β (iPLA2β) is involved in many physiological and pathological processes but the underlying mechanisms are largely unknown. Here, the authors present the structure of dimeric iPLA2β, providing insights into the regulation of its activity and cellular localization.

22 February 2018 | doi: 10.1038/s41467-018-03193-0
Calcium signalling  Enzyme mechanisms  Lipid signalling  X-ray crystallography 

Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility OPEN
Vivek Behera, Perry Evans, Carolyne J. Face, Nicole Hamagami, Laavanya Sankaranarayanan, Cheryl A. Keller, Belinda Giardine, Kai Tan, Ross C. Hardison, Junwei Shi & Gerd A. Blobel

Single nucleotide variants (SNVs) can affect chromatin occupancy by transcription factors (TF). Here the authors mine naturally occurring SNVs to probe cis elements and define contextual sequences that govern in vivo transcription factor chromatin occupancy and chromatin accessibility.

22 February 2018 | doi: 10.1038/s41467-018-03082-6
Data mining  Epigenetics  Epigenomics  Gene regulation 

Thermal influences on spontaneous rock dome exfoliation OPEN
Brian D. Collins, Greg M. Stock, Martha-Cary Eppes, Scott W. Lewis, Skye C. Corbett & Joel B. Smith

Thermal triggering of rock exfoliation has long been discounted as relevant to the evolution of rock domes. Here, the authors documented and measured recent fracturing events in California, USA to show that hot summer periods can lead to thermal stresses and cause seemingly spontaneous rock exfoliation.

22 February 2018 | doi: 10.1038/s41467-017-02728-1
Geomorphology  Natural hazards 

Input–output maps are strongly biased towards simple outputs OPEN
Kamaludin Dingle, Chico Q. Camargo & Ard A. Louis

Algorithmic information theory measures the complexity of strings. Here the authors provide a practical bound on the probability that a randomly generated computer program produces a given output of a given complexity and apply this upper bound to RNA folding and financial trading algorithms.

22 February 2018 | doi: 10.1038/s41467-018-03101-6
Applied mathematics  Computer science  Information theory and computation 

Reshaping the phonon energy landscape of nanocrystals inside a terahertz plasmonic nanocavity OPEN
Xin Jin, Andrea Cerea, Gabriele C. Messina, Andrea Rovere, Riccardo Piccoli, Francesco De Donato, Francisco Palazon, Andrea Perucchi, Paola Di Pietro, Roberto Morandotti, Stefano Lupi, Francesco De Angelis, Mirko Prato, Andrea Toma & Luca Razzari

Here the authors show that the dipole-active phonon resonance of semiconducting nanocrystals can be hybridized by a strongly concentrated terahertz vacuum field of a plasmonic nanocavity, thus achieving strong plasmon–phonon coupling even in the absence of direct terahertz illumination.

22 February 2018 | doi: 10.1038/s41467-018-03120-3
Nanocavities  Nanophotonics and plasmonics  Sub-wavelength optics 

Ocean submesoscales as a key component of the global heat budget OPEN
Zhan Su, Jinbo Wang, Patrice Klein, Andrew F. Thompson & Dimitris Menemenlis

Oceanic motions associated with horizontal scales smaller than 50 km remain unresolved in climate models. Here the authors show that motions in this scale range are critical to the global transport of heat between the ocean interior and the atmosphere, and are thus a key component of the Earth’s climate.

22 February 2018 | doi: 10.1038/s41467-018-02983-w
Climate and Earth system modelling  Fluid dynamics  Physical oceanography 

Directed gas phase formation of silicon dioxide and implications for the formation of interstellar silicates OPEN
Tao Yang, Aaron M. Thomas, Beni B. Dangi, Ralf I. Kaiser, Alexander M. Mebel & Tom J. Millar

Interstellar silicates play a key role in star formation, however their synthetic routes are not fully understood. Here, the authors provide evidence for the formation of SiO2 along with SiO via low-temperature gas phase chemistry.

22 February 2018 | doi: 10.1038/s41467-018-03172-5
Interstellar medium  Reaction kinetics and dynamics  Reaction mechanisms 

Mutant p53 cancers reprogram macrophages to tumor supporting macrophages via exosomal miR-1246 OPEN
Tomer Cooks, Ioannis S. Pateras, Lisa M. Jenkins, Keval M. Patel, Ana I. Robles, James Morris, Tim Forshew, Ettore Appella, Vassilis G. Gorgoulis & Curtis C. Harris

p53 gain of function mutants (mutp53) are involved in the pathogenesis of most human cancers. Here, the authors show that mutp53 regulates the tumor microenvironment by inducing the release of specific exosomes containing miR-1246 that once received by macrophages turns them into tumor supportive macrophages.

22 February 2018 | doi: 10.1038/s41467-018-03224-w
Colon cancer  Tumour immunology 

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells OPEN
Stephen J. Clark, Ricard Argelaguet, Chantriolnt-Andreas Kapourani, Thomas M. Stubbs, Heather J. Lee, Celia Alda-Catalinas, Felix Krueger, Guido Sanguinetti, Gavin Kelsey, John C. Marioni, Oliver Stegle & Wolf Reik

Relationships between DNA methylation and transcription, and methylation and DNA accessibility can be probed but interrogating all three in the same single cells has not been possible. Here, the authors report the first single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling.

22 February 2018 | doi: 10.1038/s41467-018-03149-4
Chromatin analysis  DNA methylation  Methylation analysis  Nucleosomes 

Programmed hierarchical patterning of bacterial populations OPEN
Christian R. Boehm, Paul K. Grant & Jim Haseloff

Biological self-organization uses hierarchical induction of gene expression but this has not been exploited by synthetic biology. Here the authors use an AND gate based on a split T7 RNA polymerase to organize programmed hierarchical patterning of gene expression across a bacterial population.

22 February 2018 | doi: 10.1038/s41467-018-03069-3
Pattern formation  Synthetic biology 

Single-molecule theory of enzymatic inhibition OPEN
Tal Robin, Shlomi Reuveni & Michael Urbakh

Single molecule approaches demonstrated that enzymatic catalysis is stochastic which could lead to deviations from classical predictions. Here authors rebuild the theory of enzymatic inhibition to show that stochastic fluctuations on the single enzyme level could make inhibitors act as activators.

22 February 2018 | doi: 10.1038/s41467-018-02995-6
Biological physics  Statistical physics 

Wetter summers can intensify departures from natural variability in a warming climate OPEN
Colin R. Mahony & Alex J. Cannon

Climate change can drive local climates outside the range of their historical variability, straining the adaptive capacity of ecological communities. Here the authors show dependencies between climate variables can produce larger and earlier departures from natural variability than is detectable in individual variables.

22 February 2018 | doi: 10.1038/s41467-018-03132-z
Climate-change impacts  Hydrology  Projection and prediction 

A non-invasive method to directly quantify surface heterogeneity of porous materials OPEN
Wei-Shan Chiang, Daniel Georgi, Taner Yildirim, Jin-Hong Chen & Yun Liu

Surface heterogeneity significantly influences the properties of porous materials, but remains extremely difficult to characterize. Here, the authors extend Porod’s scattering law from homogeneous to heterogeneous porous materials, allowing for surface variation to be non-invasively probed.

22 February 2018 | doi: 10.1038/s41467-018-03151-w
Characterization and analytical techniques  Porous materials 

Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks OPEN
Benedict Borer, Robin Tecon & Dani Or

Spatial organisation of bacteria could contribute to the persistence of anoxic hotspots in soils, however such processes are difficult to observe directly. Here, the authors develop an experimental platform mimicking resource gradients postulated in soil aggregates to assess bacterial spatial organisation.

22 February 2018 | doi: 10.1038/s41467-018-03187-y
Carbon cycle  Element cycles  Microbial ecology  Soil microbiology 

Sumoylation regulates FMRP-mediated dendritic spine elimination and maturation OPEN

Fragile X syndrome patients display intellectual disability and autism, caused by mutations in the RNA-binding protein fragile X mental retardation protein (FMRP). Here, the authors show that FMRP sumoylation is required for regulating spine density and maturation.

22 February 2018 | doi: 10.1038/s41467-018-03222-y
Cellular neuroscience  Sumoylation 

An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion OPEN

LPMOs catalyze the oxidative breakdown of polysaccharides, thereby facilitating biomass degradation. By analyzing the digestive proteome of firebrats, the authors here identify a yet uncharacterized LPMO family and provide phylogenetic, structural and biochemical insights into its origin and functions.

22 February 2018 | doi: 10.1038/s41467-018-03142-x
Enzymes  Phylogeny  Polysaccharides  Proteomics 

Polyrotaxane-based supramolecular theranostics OPEN
Guocan Yu, Zhen Yang, Xiao Fu, Bryant C. Yung, Jie Yang, Zhengwei Mao, Li Shao, Bin Hua, Yijing Liu, Fuwu Zhang, Quli Fan, Sheng Wang, Orit Jacobson, Albert Jin, Changyou Gao, Xiaoying Tang, Feihe Huang & Xiaoyuan Chen

Multifunctional nanomedicine platforms are highly promising for anticancer therapy. Here, the authors design polyrotaxane-based theranostic nanoparticles that combine targeted drug delivery with photothermal behaviour to exhibit potent anti-tumour effects in vivo.

22 February 2018 | doi: 10.1038/s41467-018-03119-w
Drug delivery  Nanotechnology in cancer  Supramolecular chemistry 

Active colloids as mobile microelectrodes for unified label-free selective cargo transport OPEN
Alicia M. Boymelgreen, Tov Balli, Touvia Miloh & Gilad Yossifon

Janus particles have a surface with two distinct physical or chemical properties; when one side is conducting and the other dielectric, the particles can be guided by an electric field. Here the authors polarize the metallic hemisphere of the particle which enables selective pickup and release of cargo.

22 February 2018 | doi: 10.1038/s41467-018-03086-2
Colloids  Fluidics  Self-assembly 

Painting with light-powered bacteria OPEN
Jochen Arlt, Vincent A. Martinez, Angela Dawson, Teuta Pilizota & Wilson C. K. Poon

The ability to generate microscale patterns and control microswimmers may be useful for engineering smart materials. Here Arlt et al. use genetically modified bacteria with fast response to changes in light intensity to produce light-induced patterns.

22 February 2018 | doi: 10.1038/s41467-018-03161-8
Self-assembly  Statistical physics 

A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast OPEN
Fabien Moretto, N. Ezgi Wood, Gavin Kelly, Andreas Doncic & Folkert J. van Werven

Transcription of lncRNAs is known to regulate local gene expression. Here the authors describe how orchestrated transcription of two contiguous lncRNAs facilitates a regulatory circuit by which the master regulator for entry into meiosis, IME1, directs the decision to enter meiosis in yeast.

22 February 2018 | doi: 10.1038/s41467-018-03213-z
Differentiation  Gene regulation  Long non-coding RNAs  Transcriptional regulatory elements 

Kinetics of lithium peroxide oxidation by redox mediators and consequences for the lithium–oxygen cell OPEN
Yuhui Chen, Xiangwen Gao, Lee R. Johnson & Peter G. Bruce

The kinetics of Li2O2 oxidation is of high importance to the operation of Li–O2 batteries. Here the authors work on different types of mediators revealing the dependence of the kinetics on the nature of the redox active site and its steric hindrance.

22 February 2018 | doi: 10.1038/s41467-018-03204-0
Batteries  Energy 

HDAC1 and HDAC2 integrate checkpoint kinase phosphorylation and cell fate through the phosphatase-2A subunit PR130 OPEN
Anja Göder, Claudia Emmerich, Teodora Nikolova, Nicole Kiweler, Maria Schreiber, Toni Kühl, Diana Imhof, Markus Christmann, Thorsten Heinzel, Günter Schneider & Oliver H. Krämer

Checkpoint kinases control cell cycle progression via the regulation of many key regulators. Here the authors demonstrate how HDAC1 and HDAC2 modulate checkpoint kinase signalling via the suppression of PR130, a regulatory subunit of the trimeric serine/threonine phosphatase 2.

22 February 2018 | doi: 10.1038/s41467-018-03096-0
Checkpoint signalling  Colon cancer 

EGF receptor kinase suppresses ciliogenesis through activation of USP8 deubiquitinase OPEN
Kousuke Kasahara, Hiromasa Aoki, Tohru Kiyono, Shujie Wang, Harumi Kagiwada, Mizuki Yuge, Toshio Tanaka, Yuhei Nishimura, Akira Mizoguchi, Naoki Goshima & Masaki Inagaki

The trichoplein-Aurora A pathway inhibits ciliogenesis in proliferating cells. Here the authors EGFR-mediated phosphorylation of the deubiquitinating enzyme USP8 leads to its activation, and this suppresses trichoplein degradation, allowing inhibition of ciliogenesis.

22 February 2018 | doi: 10.1038/s41467-018-03117-y
Cilia  Phosphorylation 
  Latest Author Corrections    
Author Correction: Low frequency transcranial electrical stimulation does not entrain sleep rhythms measured by human intracranial recordings OPEN
Belen Lafon, Simon Henin, Yu Huang, Daniel Friedman, Lucia Melloni, Thomas Thesen, Werner Doyle, György Buzsáki, Orrin Devinsky, Lucas C. Parra & Anli Liu
28 February 2018 | doi: 10.1038/s41467-018-03392-9
Consolidation  Electroencephalography – EEG  Epilepsy  Non-REM sleep 

Author Correction: Tropical explosive volcanic eruptions can trigger El Niño by cooling tropical Africa OPEN
Myriam Khodri, Takeshi Izumo, Jérôme Vialard, Serge Janicot, Christophe Cassou, Matthieu Lengaigne, Juliette Mignot, Guillaume Gastineau, Eric Guilyardi, Nicolas Lebas, Alan Robock & Michael J. McPhaden
22 February 2018 | doi: 10.1038/s41467-018-03365-y
Atmospheric dynamics  Natural hazards 

Author Correction: Muscle pathology from stochastic low level DUX4 expression in an FSHD mouse model OPEN
Darko Bosnakovski, Sunny S. K. Chan, Olivia O. Recht, Lynn M. Hartweck, Collin J. Gustafson, Laura L. Athman, Dawn A. Lowe & Michael Kyba
22 February 2018 | doi: 10.1038/s41467-018-03449-9
Disease model  Neuromuscular disease  Skeletal muscle 
  Latest Publisher Correction    
Publisher Correction: Direct quantum process tomography via measuring sequential weak values of incompatible observables OPEN
Yosep Kim, Yong-Su Kim, Sang-Yun Lee, Sang-Wook Han, Sung Moon, Yoon-Ho Kim & Young-Wook Cho
22 February 2018 | doi: 10.1038/s41467-018-03305-w
Quantum information  Quantum optics  Single photons and quantum effects 

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