Wednesday, February 21, 2018

Nature Communications - 21 February 2018

Nature Communications

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Searching for an exotic spin-dependent interaction with a single electron-spin quantum sensor OPEN
Xing Rong, Mengqi Wang, Jianpei Geng, Xi Qin, Maosen Guo, Man Jiao, Yijin Xie, Pengfei Wang, Pu Huang, Fazhan Shi, Yi-Fu Cai, Chongwen Zou & Jiangfeng Du

Investigation of exotic electron–nucleon interactions with few-micrometers range requires micrometer-scale, highly-sensitive and well-isolated sensors. Here, the authors use an NV center to set limits on the monopole–dipole interaction between its electron spin and the nucleons of a half-ball lens.

21 February 2018 | doi: 10.1038/s41467-018-03152-9
Experimental particle physics  Quantum physics 

High-efficiency RNA-based reprogramming of human primary fibroblasts OPEN
Igor Kogut, Sandra M. McCarthy, Maryna Pavlova, David P. Astling, Xiaomi Chen, Ana Jakimenko, Kenneth L. Jones, Andrew Getahun, John C. Cambier, Anna M. G. Pasmooij, Marcel F. Jonkman, Dennis R. Roop & Ganna Bilousova

Induced pluripotent stem cells (iPSCs) have potential for regenerative medicine applications, but are generated with very low efficiency. Here, the authors show highly efficient reprogramming of human primary fibroblasts to iPSCs via the synergistic activity of synthetic modified mRNAs, mature miRNA mimics, and optimized culture methods.

21 February 2018 | doi: 10.1038/s41467-018-03190-3
Cell culture  Induced pluripotent stem cells  Reprogramming  Stem-cell biotechnology 

A neuronal mechanism underlying decision-making deficits during hyperdopaminergic states OPEN
Jeroen P. H. Verharen, Johannes W. de Jong, Theresia J. M. Roelofs, Christiaan F. M. Huffels, Ruud van Zessen, Mieneke C. M. Luijendijk, Ralph Hamelink, Ingo Willuhn, Hanneke E. M. den Ouden, Geoffrey van der Plasse, Roger A. H. Adan & Louk J. M. J. Vanderschuren

Aberrant increased dopaminergic function results in impaired value-based decision making. Here the authors report pathway-specific effects of VTA activation on distinct aspects of flexible value-based decisions in rats.

21 February 2018 | doi: 10.1038/s41467-018-03087-1
Cognitive neuroscience  Reward 

Chiral Ag23 nanocluster with open shell electronic structure and helical face-centered cubic framework OPEN
Chao Liu, Tao Li, Hadi Abroshan, Zhimin Li, Chen Zhang, Hyung J. Kim, Gao Li & Rongchao Jin

Chiral noble metal nanostructures are particularly interesting for optical materials and enantioselective catalysis. Here, the authors report the synthesis and crystal structure of a chiral Ag23 nanocluster, whose twisted fcc skeleton is responsible for its chiral nature–an unusual property for silver.

21 February 2018 | doi: 10.1038/s41467-018-03136-9
Inorganic chemistry  Nanoscience and technology 

A low cost and high performance polymer donor material for polymer solar cells OPEN
Chenkai Sun, Fei Pan, Haijun Bin, Jianqi Zhang, Lingwei Xue, Beibei Qiu, Zhixiang Wei, Zhi-Guo Zhang & Yongfang Li

A problem that hinders the commercialization of polymer solar cells is the complication in synthesis and thus the low yield and high cost of the polymers. Here, Sun et al. synthesize a new polymer via a two-step process with a yield close to 90% and show high photovoltaic performance with efficiency of 12%.

21 February 2018 | doi: 10.1038/s41467-018-03207-x
Conjugated polymers  Solar cells 

Microsecond dark-exciton valley polarization memory in two-dimensional heterostructures OPEN
Chongyun Jiang, Weigao Xu, Abdullah Rasmita, Zumeng Huang, Ke Li, Qihua Xiong & Wei-bo Gao

Owing to their valley degree of freedom, atomically thin transition metal dichalcogenides show promise for valleytronics. Here, the authors leverage the dark excitons of two-dimensional van der Waals heterostructures to demonstrate a microsecond valley polarization memory effect.

21 February 2018 | doi: 10.1038/s41467-018-03174-3
Electronic properties and materials  Optical physics  Two-dimensional materials 

Nanoscale kinetic segregation of TCR and CD45 in engaged microvilli facilitates early T cell activation OPEN
Yair Razvag, Yair Neve-Oz, Julia Sajman, Meital Reches & Eilon Sherman

T cell activation is critically controlled by T cell receptor (TCR) signalling. Here the authors show, using live cell imaging, atomic force microscopy and modelling simulation, a prompt separation of TCR and CD45 that negatively correlates with TCR activation, supporting a refined kinetic segregation model of TCR signalling.

21 February 2018 | doi: 10.1038/s41467-018-03127-w
Imaging the immune system  Lymphocyte activation  Membrane structure and assembly  Signal transduction 

Effector CD4+ T cells recognize intravascular antigen presented by patrolling monocytes OPEN
Clare L. V. Westhorpe, M. Ursula Norman, Pam Hall, Sarah L. Snelgrove, Michaela Finsterbusch, Anqi Li, Camden Lo, Zhe Hao Tan, Songhui Li, Susan K. Nilsson, A. Richard Kitching & Michael J. Hickey

Monocytes constitutively adhere and crawl along the glomerular endothelium and are thought to contribute to glomerulonephritis. Here the authors use multiphoton microscopy to show local antigen presentation by MHCII+ monocytes to T cells in glomerular capillaries of mice.

21 February 2018 | doi: 10.1038/s41467-018-03181-4
Antigen processing and presentation  Imaging the immune system 

Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus OPEN
Yan Zhang, Lin An, Jie Xu, Bo Zhang, W. Jim Zheng, Ming Hu, Jijun Tang & Feng Yue

Despite its popularity for measuring the spatial organization of mammalian genomes, the resolution of most Hi-C datasets is coarse due to sequencing cost. Here, Zhang et al. develop HiCPlus, a computational approach based on deep convolutional neural network, to infer high-resolution Hi-C interaction matrices from low-resolution Hi-C data.

21 February 2018 | doi: 10.1038/s41467-018-03113-2
Computational biology and bioinformatics  Computational models 

Identification of the fungal ligand triggering cytotoxic PRR-mediated NK cell killing of Cryptococcus and Candida OPEN
Shu Shun Li, Henry Ogbomo, Michael K. Mansour, Richard F. Xiang, Lian Szabo, Fay Munro, Priyanka Mukherjee, Roy A. Mariuzza, Matthias Amrein, Jatin M. Vyas, Stephen M. Robbins & Christopher H. Mody

Natural killer (NK) cells has been show to mediate fungi killing via the activating receptor NKp30, but the fungal target for NKp30 is still unclear. Here the authors show, using atomic force microscopy and live cell imaging, that β-1,3-glucan is expressed by Cryptococcus neoformans and Candida albicans and responsible for NKp30-mediated NK killing.

21 February 2018 | doi: 10.1038/s41467-018-03014-4
Antimicrobial responses  Fungal infection  Innate immunity  NK cells 

Analysis of cardiomyocyte clonal expansion during mouse heart development and injury OPEN
Konstantina-Ioanna Sereti, Ngoc B. Nguyen, Paniz Kamran, Peng Zhao, Sara Ranjbarvaziri, Shuin Park, Shan Sabri, James L. Engel, Kevin Sung, Rajan P. Kulkarni, Yichen Ding, Tzung K. Hsiai, Kathrin Plath, Jason Ernst, Debashis Sahoo, Hanna K.A. Mikkola, M. Luisa Iruela-Arispe & Reza Ardehali

During cardiac tissue formation it is unclear whether newly generated myocytes originate from cardiac progenitor cells or from pre-existing cardiomyocytes. Here, the authors use a stochastic four-colour reporter system (Rainbow) to identify the source of new cardiomyocytes during mouse development.

21 February 2018 | doi: 10.1038/s41467-018-02891-z
Cardiac regeneration  Gene ontology  Heart development 

Bio-inspired counter-current multiplier for enrichment of solutes OPEN
Kyle Brubaker, Armand Garewal, Rachel C. Steinhardt & Aaron P. Esser-Kahn

Improving the efficiency of gas separation technology is needed, since existing methods represent a significant portion of the world’s energy consumption. Here, the authors report an enhancement in the release rate of carbon dioxide and oxygen using a counter-current amplification method inspired by fish.

21 February 2018 | doi: 10.1038/s41467-018-03052-y
Chemical engineering  Process chemistry 

High-performance graphdiyne-based electrochemical actuators OPEN
Chao Lu, Ying Yang, Jian Wang, Ruoping Fu, Xinxin Zhao, Lei Zhao, Yue Ming, Ying Hu, Hongzhen Lin, Xiaoming Tao, Yuliang Li & Wei Chen

Transduction efficiency in electrochemical actuators hardly exceeds 1% because the current electrode materials do not allow to efficiently exploit microstructural changes to achieve large actuation effects. Here the authors demonstrate transduction efficiencies up to 6% in actuators by using graphdiyne as electrode material.

21 February 2018 | doi: 10.1038/s41467-018-03095-1
Actuators  Electronic properties and materials  Two-dimensional materials 

Induction of long-lived room temperature phosphorescence of carbon dots by water in hydrogen-bonded matrices OPEN
Qijun Li, Ming Zhou, Mingyang Yang, Qingfeng Yang, Zhixun Zhang & Jing Shi

A long phosphorescence lifetime is desirable for imaging and detection, however, phosphorescence is often quenched in aqueous environments limiting applications. Here, Li et al. present a strategy for the long-lived phosphorescence of carbon dots in water due to multiple hydrogen-bonding interactions

21 February 2018 | doi: 10.1038/s41467-018-03144-9
Nanoparticles  Photochemistry  Supramolecular assembly 

PARP1 and PARP2 stabilise replication forks at base excision repair intermediates through Fbh1-dependent Rad51 regulation OPEN
George E. Ronson, Ann Liza Piberger, Martin R. Higgs, Anna L. Olsen, Grant S. Stewart, Peter J. McHugh, Eva Petermann & Nicholas D. Lakin

PARP1 has a well characterised role in DNA break repair and base excision repair, whereas the role of PARP2 is less well understood. Here, the authors show a requirement for PARP2 in stabilising replication forks that encounter base excision repair intermediates.

21 February 2018 | doi: 10.1038/s41467-018-03159-2
Base excision repair  DNA damage response 

Human Semaphorin-4A drives Th2 responses by binding to receptor ILT-4 OPEN
Ning Lu, Ying Li, Zhiqiang Zhang, Junji Xing, Ying Sun, Sheng Yao & Lieping Chen

Semaphorin-4A is a cell surface protein with known functions in neural development and immune regulation, but the mechanism for immune modulation is unclear. Here the authors show that ILT-4, previously found on myeloid cells, is the receptor of Semaphorin-4A on activate human CD4 T cells for mediating T cell co-stimulation.

21 February 2018 | doi: 10.1038/s41467-018-03128-9
Chronic inflammation  Interleukins  Signal transduction  T-helper 2 cells 

Dynamic air/liquid pockets for guiding microscale flow OPEN
Xu Hou, Jianyu Li, Alexander B. Tesler, Yuxing Yao, Miao Wang, Lingli Min, Zhizhi Sheng & Joanna Aizenberg

Fouling of solid surfaces is a problem when designing microchannel systems for applications such as bioassays and drug delivery. Here Hou et al. propose a way to overcome this issue by controlling fluid flow by means of an immiscible functional liquid partly infiltrated in a porous solid matrix.

21 February 2018 | doi: 10.1038/s41467-018-03194-z
Bioinspired materials  Fluid dynamics 

Long-distance propagation of short-wavelength spin waves OPEN

Short-wavelength spin waves with high group velocity are one of the key ingredients for the spin-wave based memory-logics. Here the authors demonstrate the propagation of spin waves with wavelength down to 50 nm and group velocity up to 2600 m s−1 using ferromagnetic nanowires grown on a thin Y3Fe5O12 film strip structure.

21 February 2018 | doi: 10.1038/s41467-018-03199-8
Magnetic devices  Magnetic properties and materials  Spintronics 

Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy OPEN
Rajani Ravi, Kimberly A. Noonan, Vui Pham, Rishi Bedi, Alex Zhavoronkov, Ivan V. Ozerov, Eugene Makarev, Artem V. Artemov, Piotr T. Wysocki, Ranee Mehra, Sridhar Nimmagadda, Luigi Marchionni, David Sidransky, Ivan M. Borrello, Evgeny Izumchenko & Atul Bedi

Antitumor T cells can be inhibited by a TGFβ rich tumor microenvironment. The authors develop bifunctional proteins comprising CTLA-4 or PD-L1 immune checkpoint-targeted antibodies fused to a “TGFβ trap” and show that they counteract tumor immune tolerance and enhance the efficacy of these antibodies.

21 February 2018 | doi: 10.1038/s41467-017-02696-6
Cancer immunotherapy  Tumour immunology 

Basal condensation of Numb and Pon complex via phase transition during Drosophila neuroblast asymmetric division OPEN
Zelin Shan, Yuting Tu, Ying Yang, Ziheng Liu, Menglong Zeng, Huisha Xu, Jiafu Long, Mingjie Zhang, Yu Cai & Wenyu Wen

Polarized localization of Numb and Pon in Drosophila neuroblasts (NBs) enables their unequal segregation during asymmetric cell divisions. Here, the authors demonstrate liquid-liquid phase separation of Pon and Numb in NBs mediated by multivalent intermolecular interactions is required for their basal condensation.

21 February 2018 | doi: 10.1038/s41467-018-03077-3
Apicobasal polarity  Biophysical chemistry  Mitosis  Neural stem cells  X-ray crystallography 

Genetic variations in ARE1 mediate grain yield by modulating nitrogen utilization in rice OPEN
Qing Wang, Jinqiang Nian, Xianzhi Xie, Hong Yu, Jian Zhang, Jiaoteng Bai, Guojun Dong, Jiang Hu, Bo Bai, Lichao Chen, Qingjun Xie, Jian Feng, Xiaolu Yang, Juli Peng, Fan Chen, Qian Qian, Jiayang Li & Jianru Zuo

Understanding the regulatory mechanisms of nitrogen assimilation is crucial for developing crop cultivars with improved nitrogen utilization efficiency (NUE). Here the authors identify a new negative regulator of NUE and mutation of this gene increases 10–20% rice grain yield under nitrogen-limiting field conditions.

21 February 2018 | doi: 10.1038/s41467-017-02781-w
Agricultural genetics  Field trials  Natural variation in plants 

Prostaglandin D2 amplifies lupus disease through basophil accumulation in lymphoid organs OPEN
Christophe Pellefigues, Barbara Dema, Yasmine Lamri, Fanny Saidoune, Nathalie Chavarot, Charlotte Lohéac, Emeline Pacreau, Michael Dussiot, Caroline Bidault, Florian Marquet, Mathieu Jablonski, Jonathan M. Chemouny, Fanny Jouan, Antoine Dossier, Marie-Paule Chauveheid, Delphine Gobert, Thomas Papo, Hajime Karasuyama, Karim Sacré, Eric Daugas et al.

In a lupus environment, basophils accumulate in secondary lymphoid organs where they affect pathogenesis by stimulating autoantibody production. Here the authors show this accumulation is driven by PGD2-induced CXCR4 surface expression and trafficking of basophils.

20 February 2018 | doi: 10.1038/s41467-018-03129-8
Innate immune cells  Lupus nephritis  Translational immunology 

Near-100 MeV protons via a laser-driven transparency-enhanced hybrid acceleration scheme OPEN

It is a challenge to scale up laser-ion acceleration to higher ion energies. Here the authors demonstrate a hybrid acceleration scheme based on the relativistic induced transparency mechanism using linearly polarised laser interaction with foil targets and its future implication in using high power lasers.

20 February 2018 | doi: 10.1038/s41467-018-03063-9
Laser-produced plasmas  Plasma-based accelerators 

Committed sea-level rise under the Paris Agreement and the legacy of delayed mitigation action OPEN
Matthias Mengel, Alexander Nauels, Joeri Rogelj & Carl-Friedrich Schleussner

Rising seas are a legacy of present and future climate change. Here the authors show that under the Paris Agreement, emissions in the next decades have a strong influence on the amount of sea level rise in the centuries to come, with the uncertainty dominated by ice-sheet contributions.

20 February 2018 | doi: 10.1038/s41467-018-02985-8
Climate-change impacts  Cryospheric science  Projection and prediction 

The mark of vegetation change on Earth’s surface energy balance OPEN
Gregory Duveiller, Josh Hooker & Alessandro Cescatti

Depending on where and when it occurs, vegetation cover change can affect local climate by altering the surface energy balance. Based on satellite data, this study provides the first data-driven assessment of such effects for multiple vegetation transitions at global scale.

20 February 2018 | doi: 10.1038/s41467-017-02810-8
Climate-change mitigation  Ecosystem ecology  Forestry 

Oxidation-stable amine-containing adsorbents for carbon dioxide capture OPEN
Kyungmin Min, Woosung Choi, Chaehoon Kim & Minkee Choi

Amine-containing solids are promising adsorbents for CO2 capture, but their low oxidative stability has hindered their application. Here, Choi and colleagues develop a strategy to poison the metal impurities present in poly(ethyleneimine)/silica adsorbents, significantly improving their stability towards oxidation.

20 February 2018 | doi: 10.1038/s41467-018-03123-0
Carbon capture and storage  Materials chemistry  Porous materials 

LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during late mitosis OPEN
Ye Hong, Remi Sonneville, Bin Wang, Viktor Scheidt, Bettina Meier, Alexander Woglar, Sarah Demetriou, Karim Labib, Verena Jantsch & Anton Gartner

Chromosome segregation and genome maintenance require the removal of DNA bridges that link chromosomes just before cells divide. Here the authors show that the LEM-3/Ankle1 nuclease processes DNA bridges before cells divide and define a previously undescribed genome integrity mechanism.

20 February 2018 | doi: 10.1038/s41467-018-03135-w
Chromosome segregation  Cytokinesis 

Clonal dynamics towards the development of venetoclax resistance in chronic lymphocytic leukemia OPEN
Carmen D. Herling, Nima Abedpour, Jonathan Weiss, Anna Schmitt, Ron Daniel Jachimowicz, Olaf Merkel, Maria Cartolano, Sebastian Oberbeck, Petra Mayer, Valeska Berg, Daniel Thomalla, Nadine Kutsch, Marius Stiefelhagen, Paula Cramer, Clemens-Martin Wendtner, Thorsten Persigehl, Andreas Saleh, Janine Altmüller, Peter Nürnberg, Christian Pallasch et al.

BCL2-inhibitor venetoclax is used to treat relapsed/refractory chronic lymphocytic leukemia (CLL). Here, the authors show the clonal dynamics towards venetoclax resistance by performing whole-exome sequencing of 8 CLL patients undergoing venetoclax treatment.

20 February 2018 | doi: 10.1038/s41467-018-03170-7
Chronic lymphocytic leukaemia  Computational biology and bioinformatics 

Diverse genetic error modes constrain large-scale bio-based production OPEN
Peter Rugbjerg, Nils Myling-Petersen, Andreas Porse, Kira Sarup-Lytzen & Morten O. A. Sommer

The declining performance of scale-up bioreactor cultures is commonly attributed to phenotypic and physical heterogeneities. Here, the authors reveal multiple recurring intra-pathway error modes that limit engineered E. coli mevalonic acid production over time- and industrial-scale fermentations.

20 February 2018 | doi: 10.1038/s41467-018-03232-w
Metabolic engineering  Population genetics  Transposition 

Photonic-crystal exciton-polaritons in monolayer semiconductors OPEN
Long Zhang, Rahul Gogna, Will Burg, Emanuel Tutuc & Hui Deng

Semiconductor microcavities can host polaritons formed by strong exciton-photon coupling, yet they may be plagued by scalability issues. Here, the authors demonstrate a sub-wavelength-thick, one-dimensional photonic crystal platform for strong coupling with atomically thin van der Waals crystals.

19 February 2018 | doi: 10.1038/s41467-018-03188-x
Photonic crystals  Polaritons  Two-dimensional materials 

Systematic generation of biophysically detailed models for diverse cortical neuron types OPEN
Nathan W. Gouwens, Jim Berg, David Feng, Staci A. Sorensen, Hongkui Zeng, Michael J. Hawrylycz, Christof Koch & Anton Arkhipov

Neocortical circuits exhibit diverse cell types that can be difficult to build into computational models. Here the authors employ a genetic algorithm-based parameter optimization to generate multi-compartment Hodgkin-Huxley models for diverse cell types in the Allen Cell Types Database.

19 February 2018 | doi: 10.1038/s41467-017-02718-3
Biophysical models  Cellular neuroscience  Striate cortex 

Ultrafast quantum control of ionization dynamics in krypton OPEN
Konrad Hütten, Michael Mittermair, Sebastian O. Stock, Randolf Beerwerth, Vahe Shirvanyan, Johann Riemensberger, Andreas Duensing, Rupert Heider, Martin S. Wagner, Alexander Guggenmos, Stephan Fritzsche, Nikolay M. Kabachnik, Reinhard Kienberger & Birgitta Bernhardt

Photoionization of atoms and molecules is a complex process and requires sensitive probes to explore the ultrafast dynamics. Here the authors combine transient absorption and photo-ion spectroscopy methods to explore and control the attosecond pulse initiated excitation, ionization and Auger decay in Kr atoms.

19 February 2018 | doi: 10.1038/s41467-018-03122-1
Attosecond science  High-harmonic generation  Nonlinear optics  Optical spectroscopy 

A single NaK channel conformation is not enough for non-selective ion conduction OPEN
Chaowei Shi, Yao He, Kitty Hendriks, Bert L. de Groot, Xiaoying Cai, Changlin Tian, Adam Lange & Han Sun

NaK is a non-selective cation channel that conducts sodium (Na+) and potassium (K+) equally well. Here authors use ssNMR and MD simulations to show that the selectivity filter of NaK adopts two conformations in the absence of ions, one of which is preferred by Na+ and the other by K+.

19 February 2018 | doi: 10.1038/s41467-018-03179-y
Computational biophysics  Solid-state NMR 

Route to high-energy density polymeric nitrogen t-N via He−N compounds OPEN
Yinwei Li, Xiaolei Feng, Hanyu Liu, Jian Hao, Simon A. T. Redfern, Weiwei Lei, Dan Liu & Yanming Ma

Polymeric nitrogen has yet to be recovered to ambient conditions, precluding its practical application as high-energy density material. Here, the authors highlight a possible route to the formation of a tetragonal polymeric nitrogen via helium-nitrogen compounds at high pressures.

19 February 2018 | doi: 10.1038/s41467-018-03200-4
Atomistic models  Materials chemistry  Structure of solids and liquids 

Expedient syntheses of N-heterocycles via intermolecular amphoteric diamination of allenes OPEN
Zhishi Ye, Sarju Adhikari, Yu Xia & Mingji Dai

Saturated N-heterocycle rings are common structural motifs of many FDA-approved drugs. Here, the authors show that a metal-free amphoteric diamination of allenes produces valuable six-, seven- and eight-membered N-heterocycles with high diversity and tolerance of functional groups on the ring.

19 February 2018 | doi: 10.1038/s41467-018-03085-3
Synthetic chemistry methodology  Natural product synthesis  Reaction mechanisms 

An unusual type of polymorphism in a liquid crystal OPEN
Lin Li, Mirosław Salamończyk, Sasan Shadpour, Chenhui Zhu, Antal Jákli & Torsten Hegmann

Polymorphism is a property that allows a material to exist in two or more crystal structures. Here the authors observe thermal-induced structural polymorphism in a bent-core liquid crystal compound and show that by choosing the cooling rate, different structures with distinct structural colours are obtained.

19 February 2018 | doi: 10.1038/s41467-018-03160-9
Liquid crystals  Self-assembly  Stereochemistry 

Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard–Jones potential OPEN
Isidro Lorenzo Geada, Hadi Ramezani-Dakhel, Tariq Jamil, Marialore Sulpizi & Hendrik Heinz

Molecular dynamics models for predicting the behavior of metallic nanostructures typically do not take into account polarization effects in metals. Here, the authors introduce a polarizable Lennard–Jones potential that provides quantitative insight into the role of induced charges at metal surfaces and related complex material interfaces.

19 February 2018 | doi: 10.1038/s41467-018-03137-8
Computational chemistry  Computational nanotechnology  Surface assembly  Surfaces, interfaces and thin films 

Split spawning realigns coral reproduction with optimal environmental windows OPEN
Taryn Foster, Andrew J. Heyward & James P. Gilmour

Corals usually undergo single mass spawning events, however, occasionally they split reproductive effort across two months. Here, Foster et al. use 10 years of data to determine the drivers and timing of split spawning, showing that these events realign spawning with optimal environmental conditions.

19 February 2018 | doi: 10.1038/s41467-018-03175-2
Ecology  Marine biology 

C-terminal calcium binding of α-synuclein modulates synaptic vesicle interaction OPEN

Alpha-synuclein is associated with neuronal dysfunction in Parkinson’s disease. This study shows that alpha-synuclein interacts with neuronal synaptic vesicles in a calcium-dependent fashion, and this interaction is important for synaptic vesicle clustering.

19 February 2018 | doi: 10.1038/s41467-018-03111-4
Molecular neuroscience  Neuroscience 

Generalized leaky integrate-and-fire models classify multiple neuron types OPEN
Corinne Teeter, Ramakrishnan Iyer, Vilas Menon, Nathan Gouwens, David Feng, Jim Berg, Aaron Szafer, Nicholas Cain, Hongkui Zeng, Michael Hawrylycz, Christof Koch & Stefan Mihalas

Simplified neuron models, such as generalized leaky integrate-and-fire (GLIF) models, are extensively used in network modeling. Here the authors systematically generate and compare GLIF models of varying complexity for their ability to classify cell types in the Allen Cell Types Database and faithfully reproduce spike trains.

19 February 2018 | doi: 10.1038/s41467-017-02717-4
Computational neuroscience  Computational science 

Selection of GalNAc-conjugated siRNAs with limited off-target-driven rat hepatotoxicity OPEN
Maja M. Janas, Mark K. Schlegel, Carole E. Harbison, Vedat O. Yilmaz, Yongfeng Jiang, Rubina Parmar, Ivan Zlatev, Adam Castoreno, Huilei Xu, Svetlana Shulga-Morskaya, Kallanthottathil G. Rajeev, Muthiah Manoharan, Natalie D. Keirstead, Martin A. Maier & Vasant Jadhav

A subset of chemically-modified siRNAs conjugated to trivalent GalNAc may fail during nonclinical development due to rat hepatotoxicity. Here, the authors show that hepatotoxicity may be accounted for by microRNA-like off-target effects of siRNA and can be mitigated by a thermally destabilizing modification in the siRNA seed region.

19 February 2018 | doi: 10.1038/s41467-018-02989-4
Drug safety  Hepatotoxicity  RNAi therapy 

Submarine slope failures due to pipe structure formation OPEN
Judith Elger, Christian Berndt, Lars Rüpke, Sebastian Krastel, Felix Gross & Wolfram H. Geissler

There is a strong correlation between submarine slope failures and the occurrence of gas hydrates. Here, the authors use a combination of seismic data and numerical modelling to show that overpressure at the gas hydrate stability zone leads to potential destabilization of the slope and submarine landslides.

19 February 2018 | doi: 10.1038/s41467-018-03176-1
Geophysics  Natural hazards  Stratigraphy 

Localization of adaptive variants in human genomes using averaged one-dependence estimation OPEN
Lauren Alpert Sugden, Elizabeth G. Atkinson, Annie P. Fischer, Stephen Rong, Brenna M. Henn & Sohini Ramachandran

Selective sweeps are events in which beneficial mutations spread rapidly through a population. Here, Sugden et al. develop SWIF(r), a probabilistic classification framework for detecting and localizing selective sweeps, and apply it to genomic data from the ‡Khomani San.

19 February 2018 | doi: 10.1038/s41467-018-03100-7
Evolution  Population genetics  Statistical methods 

Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration OPEN
Wei Huang, Yuliang Feng, Jialiang Liang, Hao Yu, Cheng Wang, Boyu Wang, Mingyang Wang, Lin Jiang, Wei Meng, Wenfeng Cai, Mario Medvedovic, Jenny Chen, Christian Paul, W. Sean Davidson, Sakthivel Sadayappan, Peter J. Stambrook, Xi-Yong Yu & Yigang Wang

During early postnatal development in mammals, cardiomyocytes exit the cell cycle, losing their regenerative capacity. Here the authors show that, following myocardial infarction, loss of microRNA-128 promotes cardiomyocyte proliferation and cardiac regeneration in adult mice partly via enhancing the expression of the chromatin modifier SUZ12.

16 February 2018 | doi: 10.1038/s41467-018-03019-z
Cardiac regeneration  Cell proliferation  Heart development  miRNAs 

Chemisorption of polysulfides through redox reactions with organic molecules for lithium–sulfur batteries OPEN
Ge Li, Xiaolei Wang, Min Ho Seo, Matthew Li, Lu Ma, Yifei Yuan, Tianpin Wu, Aiping Yu, Shun Wang, Jun Lu & Zhongwei Chen

Novel cathode design holds the key to enabling high performance lithium-sulfur batteries. Here the authors utilize anthraquinone to chemically stabilize polysulfides, revealing that the keto groups of anthraquinone play a critical role in forming strong Lewis acid-based chemical bonding.

16 February 2018 | doi: 10.1038/s41467-018-03116-z

Host defense against oral microbiota by bone-damaging T cells OPEN
Masayuki Tsukasaki, Noriko Komatsu, Kazuki Nagashima, Takeshi Nitta, Warunee Pluemsakunthai, Chisa Shukunami, Yoichiro Iwakura, Tomoki Nakashima, Kazuo Okamoto & Hiroshi Takayanagi

IL-17-producing T cells are protective against infection, but the authors of this article previously showed that these cells also contribute to inflammatory bone destruction. Here they show in the context of periodontitis that microbiota-driven Th17-mediated bone destruction may actually be a physiological rather than a pathological process, as associated tooth loss prevents dissemination of oral bacteria.

16 February 2018 | doi: 10.1038/s41467-018-03147-6
Bacterial infection  Bone  Mucosal immunology  Osteoimmunology 

Identifying noncoding risk variants using disease-relevant gene regulatory networks OPEN
Long Gao, Yasin Uzun, Peng Gao, Bing He, Xiaoke Ma, Jiahui Wang, Shizhong Han & Kai Tan

Current methods for prioritization of non-coding genetic risk variants are based on sequence and chromatin features. Here, Gao et al. develop ARVIN, which predicts causal regulatory variants using disease-relevant gene-regulatory networks, and validate this approach in reporter gene assays.

16 February 2018 | doi: 10.1038/s41467-018-03133-y
Bioinformatics  Gene regulation  Gene regulatory networks  Systems biology 

Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation OPEN
Juliana Durack, Nikole E. Kimes, Din L. Lin, Marcus Rauch, Michelle McKean, Kathryn McCauley, Ariane R. Panzer, Jordan S. Mar, Michael D. Cabana & Susan V. Lynch

Gut microbial dysbiosis in infancy is associated with childhood atopy and the development of asthma. Here, the authors show that gut microbiota perturbation is evident in the very earliest stages of postnatal life, continues throughout infancy, and can be partially rescued by Lactobacillus supplementation in high-risk for asthma infants.

16 February 2018 | doi: 10.1038/s41467-018-03157-4
Asthma  Microbiome  Microbiota  Paediatric research 

Bone marrow lympho-myeloid malfunction in obesity requires precursor cell-autonomous TLR4 OPEN
Ailing Liu, Minhui Chen, Rashmi Kumar, Maja Stefanovic-Racic, Robert M. O’Doherty, Ying Ding, Willi Jahnen-Dechent & Lisa Borghesi

Obesity can affect bone marrow cell differentiation and the generation of myeloid and lymphoid cells. Here, the authors show that diet and obesity, as well as low-dose lipopolysaccharide, can alter Toll-like receptor 4 signaling bone marrow cells to skew the myeloid-lymphoid homeostasis in mice.

16 February 2018 | doi: 10.1038/s41467-018-03145-8
Inflammatory diseases  Lymphopoiesis  Myelopoiesis  Obesity 

Physical basis of amyloid fibril polymorphism OPEN
William Close, Matthias Neumann, Andreas Schmidt, Manuel Hora, Karthikeyan Annamalai, Matthias Schmidt, Bernd Reif, Volker Schmidt, Nikolaus Grigorieff & Marcus Fändrich

Amyloid fibril structures can display polymorphism. Here the authors reveal the cryo-EM structures of several different fibril morphologies of a peptide derived from an amyloidogenic immunoglobulin light chain and present a mathematical analysis of physical factors that influence fibril polymorphism.

16 February 2018 | doi: 10.1038/s41467-018-03164-5
Cryoelectron microscopy  Protein aggregation  Self-assembly 

Observationally quantified reconnection providing a viable mechanism for active region coronal heating OPEN
Kai E. Yang, Dana W. Longcope, M. D. Ding & Yang Guo

The solar corona heating mechanism is still subject to debate. Here, the authors report that impulsive reconnection can give rise to an active region corona that is compatible with extreme-ultraviolet observations.

15 February 2018 | doi: 10.1038/s41467-018-03056-8
Solar physics 

Inference of field reversed configuration topology and dynamics during Alfvenic transients OPEN
J. A. Romero, S. A. Dettrick, E. Granstedt, T. Roche & Y. Mok

It is important to understand the fast plasma dynamics in the operation of fusion plasma devices. Here the authors demonstrate the inference on the internal field reversed configuration magnetic topology and their occurrence during fast Alfvenic transient phenomena in C-2U device.

15 February 2018 | doi: 10.1038/s41467-018-03110-5
Characterization and analytical techniques  Magnetically confined plasmas  Nuclear fusion and fission 

Discovery of a magnetic conductive interface in PbZr0.2Ti0.8O3 /SrTiO3 heterostructures OPEN

Two-dimensional electron gases that form in some complex oxide heterostructures may have useful functional behavior due to the interaction of the parent materials. Here the authors show that PZT/STO interfaces can host a spin-polarized electron gas, even though the bulk materials are nonmagnetic.

15 February 2018 | doi: 10.1038/s41467-018-02914-9
Ferroelectrics and multiferroics  Ferromagnetism  Surfaces, interfaces and thin films 

Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes OPEN
Alexander P. S. Darlington, Juhyun Kim, José I. Jiménez & Declan G. Bates

Competition between synthetic genetic circuits and host genes for shared resources can complicate circuit design and lead to failure. Here the authors demonstrate, mathematically and experimentally, the use of orthogonal ribosomes to decouple competing genes.

15 February 2018 | doi: 10.1038/s41467-018-02898-6
Metabolic engineering  Ribosome  Synthetic biology 

Systematic analysis of protein turnover in primary cells OPEN
Toby Mathieson, Holger Franken, Jan Kosinski, Nils Kurzawa, Nico Zinn, Gavain Sweetman, Daniel Poeckel, Vikram S. Ratnu, Maike Schramm, Isabelle Becher, Michael Steidel, Kyung-Min Noh, Giovanna Bergamini, Martin Beck, Marcus Bantscheff & Mikhail M. Savitski

The proteome-wide characterization of proteostasis depends on robust approaches to determine protein half-lives. Here, the authors improve the accuracy and precision of mass spectrometry-based quantification, enabling reliable protein half-life determination in several non-dividing cell types.

15 February 2018 | doi: 10.1038/s41467-018-03106-1
Cell biology  Nuclear pore complex  Proteasome  Proteomics 

A community approach to mortality prediction in sepsis via gene expression analysis OPEN
Timothy E. Sweeney, Thanneer M. Perumal, Ricardo Henao, Marshall Nichols, Judith A. Howrylak, Augustine M. Choi, Jesús F. Bermejo-Martin, Raquel Almansa, Eduardo Tamayo, Emma E. Davenport, Katie L. Burnham, Charles J. Hinds, Julian C. Knight, Christopher W. Woods, Stephen F. Kingsmore, Geoffrey S. Ginsburg, Hector R. Wong, Grant P. Parnell, Benjamin Tang, Lyle L. Moldawer et al.

Sepsis is characterized by deregulated host response to infection. Efficient therapies are still needed but a limitation for sepsis treatment is the heterogeneity in patients. Here Sweeney et al. generate prognostic models based on gene expression to improve risk stratification classification and prediction for 30-day mortality of patients.

15 February 2018 | doi: 10.1038/s41467-018-03078-2
Computational biology and bioinformatics  Infection  Molecular medicine  Prognosis  Prognostic markers 

Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T-PLL OPEN
A. Schrader, G. Crispatzu, S. Oberbeck, P. Mayer, S. Pützer, J. von Jan, E. Vasyutina, K. Warner, N. Weit, N. Pflug, T. Braun, E. I. Andersson, B. Yadav, A. Riabinska, B. Maurer, M. S. Ventura Ferreira, F. Beier, J. Altmüller, M. Lanasa, C. D. Herling et al.

T-cell prolymphocytic leukemia (T-PLL) is a rare malignancy with a poor prognosis. Here, the authors investigate the genomic landscape, gene expression profiles and functional mechanisms in 111 patients, highlighting TCL1 overexpression and ATM aberrations as core lesions which co-operate to impair DNA damage processing.

15 February 2018 | doi: 10.1038/s41467-017-02688-6
Cancer genomics  Leukaemia 

Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure OPEN
Kieran A. Bates, Frances C. Clare, Simon O’Hanlon, Jaime Bosch, Lola Brookes, Kevin Hopkins, Emilia J. McLaughlin, Olivia Daniel, Trenton W. J. Garner, Matthew C. Fisher & Xavier A. Harrison

Amphibian skin microbe communities have been putatively associated with the severity of chytrid fungal disease. Here, the authors show that different types of disease dynamics (enzootic versus epizootic) are associated with different microbiota in the host populations.

15 February 2018 | doi: 10.1038/s41467-018-02967-w
Ecological epidemiology  Herpetology  Microbial ecology 

USP35 regulates mitotic progression by modulating the stability of Aurora B OPEN
Jinyoung Park, Mi-Sun Kwon, Eunice EunKyeong Kim, Hyunsook Lee & Eun Joo Song

Aurora B kinase is a member of the chromosomal passenger complex, which is an indispensable regulator of mitosis. Here the authors show that the deubiquitinating enzyme USP35 has a role in mitotic progression by inhibiting proteasomal degradation of Aurora B kinase, leading to its activation.

15 February 2018 | doi: 10.1038/s41467-018-03107-0
Mitosis  Ubiquitylation 

Mutations in CFAP43 and CFAP44 cause male infertility and flagellum defects in Trypanosoma and human OPEN
Charles Coutton, Alexandra S. Vargas, Amir Amiri-Yekta, Zine-Eddine Kherraf, Selima Fourati Ben Mustapha, Pauline Le Tanno, Clémentine Wambergue-Legrand, Thomas Karaouzène, Guillaume Martinez, Serge Crouzy, Abbas Daneshipour, Seyedeh Hanieh Hosseini, Valérie Mitchell, Lazhar Halouani, Ouafi Marrakchi, Mounir Makni, Habib Latrous, Mahmoud Kharouf, Jean-François Deleuze, Anne Boland et al.

Asthenozoospermia is a major cause of male infertility, and multiple morphological abnormalities of the flagella (MMAF) is a particularly severe form. Here, using whole-exome sequencing of 78 MMAF patients, the authors identify mutations in two WDR proteins, CFAP43 and CFAP44, and confirm that these proteins are required for flagellogenesis in mouse and Trypanosoma brucei.

15 February 2018 | doi: 10.1038/s41467-017-02792-7
Cilia  Genetics  Infertility  Male factor infertility 

Aggregation-fragmentation and individual dynamics of active clusters OPEN
F. Ginot, I. Theurkauff, F. Detcheverry, C. Ybert & C. Cottin-Bizonne

The cluster phase of active particles is one instance of the propensity of active matter to self-organize. Combining high-statistics experiments on Janus colloids and simple modeling, Ginot et al. provide a thorough characterization of cluster’s size and motion.

15 February 2018 | doi: 10.1038/s41467-017-02625-7
Condensed-matter physics  Soft materials  Statistical physics, thermodynamics and nonlinear dynamics 

Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics OPEN
Thibault Lagache, Alexandre Grassart, Stéphane Dallongeville, Orestis Faklaris, Nathalie Sauvonnet, Alexandre Dufour, Lydia Danglot & Jean-Christophe Olivo-Marin

Elucidating molecular organisation requires precise localisation and analysis. Here the authors develop SODA software for automatic and quantitative mapping of statistically coupled molecules, and use it to unravel spatial organisation of thousands of synaptic proteins in SIM and 3DSTORM microscopy.

15 February 2018 | doi: 10.1038/s41467-018-03053-x
Fluorescence imaging  Image processing  Statistical methods  Super-resolution microscopy 

CD1d-dependent immune suppression mediated by regulatory B cells through modulations of iNKT cells OPEN
K. Oleinika, E. C. Rosser, D. E. Matei, K. Nistala, A. Bosma, I. Drozdov & C. Mauri

Regulatory B cells (Breg) are known to suppress immune responses by secreting interleukin-10 (IL-10). Here the authors show that, alternatively, Bregs may also present lipid antigens on surface CD1d to induce IFN-γ production from invariant natural killer cells to ameliorate experimental arthritis via IL-10-independent pathways.

15 February 2018 | doi: 10.1038/s41467-018-02911-y
Autoimmunity  B cells  Cellular immunity  NKT cells 
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Author Correction: Uplift of the central transantarctic mountains OPEN
Phil Wannamaker, Graham Hill, John Stodt, Virginie Maris, Yasuo Ogawa, Kate Selway, Goran Boren, Edward Bertrand, Daniel Uhlmann, Bridget Ayling, A. Marie Green & Daniel Feucht
16 February 2018 | doi: 10.1038/s41467-018-03349-y
Geodynamics  Tectonics 

Author Correction: North Atlantic variability and its links to European climate over the last 3000 years OPEN
Paola Moffa-Sánchez & Ian R. Hall
15 February 2018 | doi: 10.1038/s41467-018-03338-1
Palaeoceanography  Palaeoclimate 

Author Correction: How to probe the spin contribution to momentum relaxation in topological insulators OPEN
Moon-Sun Nam, Benjamin H. Williams, Yulin Chen, Sonia Contera, Shuhua Yao, Minghui Lu, Yan-Feng Chen, Grigore A. Timco, Christopher A. Muryn, Richard E. P. Winpenny & Arzhang Ardavan
15 February 2018 | doi: 10.1038/s41467-018-03331-8
Magnetic properties and materials  Topological insulators 
  Latest Publisher Corrections    
Publisher Correction: Evolutionary adaptations to new environments generally reverse plastic phenotypic changes OPEN
Wei-Chin Ho & Jianzhi Zhang
21 February 2018 | doi: 10.1038/s41467-018-03360-3
Evolutionary genetics  Experimental evolution 

Publisher Correction: Intercalation events visualized in single microcrystals of graphite OPEN
Edward R. White, Jared J. Lodico & B. C. Regan
19 February 2018 | doi: 10.1038/s41467-018-02957-y
Batteries  Transmission electron microscopy 

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