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woensdag 26 september 2018

Nature Communications - 26 September 2018

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26 September 2018 
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Nature Index 2018 Rising Stars

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USCAP's 2019 Annual Meeting at National Harbor, Maryland, is the magnet for global pathologists to come together to think out loud about what's new, exciting and relevant in translational research and anatomic/molecular diagnostics. It's the forum for intellectual stimulation, information exchange, and social interaction. The 2019 program is designed to exceed your expectations and expose you to contemporary and vibrant pathology education at its best. 

Submit your abstract now! (Deadline September 27th)

Nature Outline: Retinal repair

The retina is crucial for vision, but damage to this light-sensing part of the eye cannot yet be repaired. Growing and then transplanting healthy retinal cells, or building entire retinas from stem cells, might offer a solution for the millions of people worldwide who are affected by retinal degeneration. 

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Genome-wide association study of 23,500 individuals identifies 7 loci associated with brain ventricular volume OPEN
Dina Vojinovic, Hieab H. Adams, Xueqiu Jian, Qiong Yang, Albert Vernon Smith, Joshua C. Bis, Alexander Teumer, Markus Scholz, Nicola J. Armstrong, Edith Hofer, Yasaman Saba, Michelle Luciano, Manon Bernard, Stella Trompet, Jingyun Yang, Nathan A. Gillespie, Sven J. van der Lee, Alexander Neumann, Shahzad Ahmad, Ole A. Andreassen et al.

An increase in the volume of the brain lateral ventricles is a sign of normal aging, but can also be associated with neurological and psychiatric disorders. Here, Vojinovic et al. identify seven genetic loci in a GWA study for ventricular volume in 23,500 individuals and find correlation with thalamus volume.

26 September 2018 | doi: 10.1038/s41467-018-06234-w
Genetics of the nervous system  Genome-wide association studies  Heritable quantitative trait 

A distal centriolar protein network controls organelle maturation and asymmetry OPEN
Lei Wang, Marion Failler, Wenxiang Fu & Brian D. Dynlacht

Removal of daughter centriole-specific/enriched proteins (DCPs) and assembly of distal appendages (DA) are important for centrosome asymmetry. Here, the authors report that a centriolar distal end protein network regulates DCP removal, DA assembly, and ciliary vesicle docking.

26 September 2018 | doi: 10.1038/s41467-018-06286-y
Neurodevelopmental disorders  Organelles 

Chiral self-sorted multifunctional supramolecular biocoordination polymers and their applications in sensors OPEN
Xiaobo Shang, Inho Song, Gwan Yeong Jung, Wanuk Choi, Hiroyoshi Ohtsu, Jeong Hyeon Lee, Jin Young Koo, Bo Liu, Jaeyong Ahn, Masaki Kawano, Sang Kyu Kwak & Joon Hak Oh

Chiral supramolecules may be used in chiral recognition, sensing and catalysis. Here the authors selectively synthesized homochiral and heterochiral supramolecular biocoordination polymers of naphthalene diimide ligands with alanine termini and Zn ions.

26 September 2018 | doi: 10.1038/s41467-018-06147-8
Polymer synthesis  Polymers  Supramolecular polymers 

Mitochondrial uncoupling reveals a novel therapeutic opportunity for p53-defective cancers OPEN
R. Kumar, L. Coronel, B. Somalanka, A. Raju, O. A. Aning, O. An, Y. S. Ho, S. Chen, S. Y. Mak, P. Y. Hor, H. Yang, M. Lakshmanan, H. Itoh, S. Y. Tan, Y. K. Lim, A. P. C. Wong, S. H. Chew, T. H. Huynh, B. C. Goh, C. Y. Lim et al.

Several challenges are involved in direct targeting of mutant p53, while targeting altered fitness of cells with loss of wild type p53 is an alternative approach. Here they identify niclosamide to be selectively toxic to p53 deficient cells through a previously unknown mitochondrial uncoupling mechanism.

26 September 2018 | doi: 10.1038/s41467-018-05805-1
Cancer metabolism  Cancer screening  Chemotherapy  Drug development  Oncology 

Magnetized fast isochoric laser heating for efficient creation of ultra-high-energy-density states OPEN
Shohei Sakata, Seungho Lee, Hiroki Morita, Tomoyuki Johzaki, Hiroshi Sawada, Yuki Iwasa, Kazuki Matsuo, King Fai Farley Law, Akira Yao, Masayasu Hata, Atsushi Sunahara, Sadaoki Kojima, Yuki Abe, Hidetaka Kishimoto, Aneez Syuhada, Takashi Shiroto, Alessio Morace, Akifumi Yogo, Natsumi Iwata, Mitsuo Nakai et al.

It is desirable to deposit more energy in the dense plasma core to trigger the fusion ignition. Here the authors demonstrate enhanced energy coupling from laser to plasma core by using solid targets and guiding the transport of relativistic electron beam with external magnetic field.

26 September 2018 | doi: 10.1038/s41467-018-06173-6
Laser-produced plasmas  Plasma physics 

Probing ultrafast spin-relaxation and precession dynamics in a cuprate Mott insulator with seven-femtosecond optical pulses OPEN
T. Miyamoto, Y. Matsui, T. Terashige, T. Morimoto, N. Sono, H. Yada, S. Ishihara, Y. Watanabe, S. Adachi, T. Ito, K. Oka, A. Sawa & H. Okamoto

Understanding the dynamics of cuprates following photoexcitation can provide insights into the complex coupling mechanisms that underlie their exotic equilibrium behaviour. Here the authors use pump-probe reflection spectroscopy to investigate the nonequilibrium spin dynamics of Mott-insulating Nd2CuO4.

26 September 2018 | doi: 10.1038/s41467-018-06312-z
Electronic properties and materials  Magnetic properties and materials 

UBL3 modification influences protein sorting to small extracellular vesicles OPEN
Hiroshi Ageta, Natsumi Ageta-Ishihara, Keisuke Hitachi, Ozge Karayel, Takanori Onouchi, Hisateru Yamaguchi, Tomoaki Kahyo, Ken Hatanaka, Koji Ikegami, Yusuke Yoshioka, Kenji Nakamura, Nobuyoshi Kosaka, Masashi Nakatani, Akiyoshi Uezumi, Tomihiko Ide, Yutaka Tsutsumi, Haruhiko Sugimura, Makoto Kinoshita, Takahiro Ochiya, Matthias Mann et al.

Exosomes mediate cell-to-cell communication by transporting proteins, mRNAs, and miRNAs but the mechanisms of protein sorting to exosomes are poorly understood. Here, the authors uncover that ubiquitin-like 3 (UBL3) regulates protein sorting to exosomes by acting as a posttranslational modification.

26 September 2018 | doi: 10.1038/s41467-018-06197-y
Multivesicular bodies  Post-translational modifications 

A bioinspired multilegged soft millirobot that functions in both dry and wet conditions OPEN
Haojian Lu, Mei Zhang, Yuanyuan Yang, Qiang Huang, Toshio Fukuda, Zuankai Wang & Yajing Shen

Despite the enormous potential of magnetically-guided soft robots for various applications, challenges related to inefficient locomotion in harsh environments hinder its development. Here, the authors demonstrate a multi-legged millirobot with excellent locomotion capability in harsh environments.

26 September 2018 | doi: 10.1038/s41467-018-06491-9
Actuators  Bioinspired materials  Mechanical engineering 

Two-component latency distributions indicate two-step vesicular release at simple glutamatergic synapses OPEN
Takafumi Miki, Yukihiro Nakamura, Gerardo Malagon, Erwin Neher & Alain Marty

Traditionally, synaptic release latency has been viewed as constant. Here, at parallel fiber-interneuron  synapses, authors see that with sustained release emerges a slow component of increased latencies, which can be simulated with a 2-step model comprised of vesicle docking followed by release.

26 September 2018 | doi: 10.1038/s41467-018-06336-5
Biophysics  Neuroscience 

The MinDE system is a generic spatial cue for membrane protein distribution in vitro OPEN
Beatrice Ramm, Philipp Glock, Jonas Mücksch, Philipp Blumhardt, Daniela A. García-Soriano, Michael Heymann & Petra Schwille

The E. coli MinCDE system oscillates between cell poles to position the main division protein FtsZ. Here authors use in vitro reconstitution to show that MinDE oscillations also regulate unrelated membrane proteins spatiotemporally into patterns and gradients by forming a moving physical barrier.

26 September 2018 | doi: 10.1038/s41467-018-06310-1
Molecular biophysics  Synthetic biology 

Physics-based forecasting of man-made earthquake hazards in Oklahoma and Kansas OPEN
Cornelius Langenbruch, Matthew Weingarten & Mark D. Zoback

Reinjection of saltwater, co-produced with oil, has the potential to trigger damaging earthquakes. Here, using Oklahoma and Kansas as an example, the authors present a new physics-based methodology to forecast future probabilities of potentially damaging induced-earthquakes in space and time.

26 September 2018 | doi: 10.1038/s41467-018-06167-4
Energy and society  Hydrology  Seismology 

Strobilurin biosynthesis in Basidiomycete fungi OPEN
Risa Nofiani, Kate de Mattos-Shipley, Karen E. Lebe, Li-Chen Han, Zafar Iqbal, Andrew M. Bailey, Christine L. Willis, Thomas J. Simpson & Russell J. Cox

Strobilurins are fungal metabolites that inspired the creation of β-methoxyacrylate agricultural fungicides. Here, Nofiani et al. identify the strobilurin biosynthesis gene cluster, encoding a polyketide synthase as well as an FAD-dependent oxygenase for an oxidative rearrangement leading to β-methoxyacrylate formation.

26 September 2018 | doi: 10.1038/s41467-018-06202-4
Biosynthesis  Natural product synthesis  Reaction mechanisms  Structure elucidation 

A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes OPEN
Martina Foglizzo, Adam J. Middleton, Abigail E. Burgess, Jennifer M. Crowther, Renwick C. J. Dobson, James M. Murphy, Catherine L. Day & Peter D. Mace

The Polycomb Repressive-Deubiquitinase (PR-DUB) complex is responsible for the removal of the ubiquitin epigenetic modification from Histone 2A. Here the authors describe the structure of the Drosophila PR-DUB complex, providing new insight into its regulation and how cancer-associated mutations disrupt PR-DUB activity.

26 September 2018 | doi: 10.1038/s41467-018-06186-1
Deubiquitylating enzymes  Epigenetics  Structural biology 

Structural analysis of HTL and D14 proteins reveals the basis for ligand selectivity in Striga OPEN
Yuqun Xu, Takuya Miyakawa, Shohei Nosaki, Akira Nakamura, Ying Lyu, Hidemitsu Nakamura, Umeharu Ohto, Hanako Ishida, Toshiyuki Shimizu, Tadao Asami & Masaru Tanokura

HTL and D14 receptors perceive the structurally similar signaling compounds karrikin and strigolactone. Here, the authors show that ShD14 and a divergent clade of ShHTLs from Strigae capable of recognizing strigolact are capable of recognizing strigolactone and provide structural insights into the evolution of ligand specificity.

26 September 2018 | doi: 10.1038/s41467-018-06452-2
Evolution  Plant sciences  Structural biology 

Crystal structure of the red light-activated channelrhodopsin Chrimson OPEN
Kazumasa Oda, Johannes Vierock, Satomi Oishi, Silvia Rodriguez-Rozada, Reiya Taniguchi, Keitaro Yamashita, J. Simon Wiegert, Tomohiro Nishizawa, Peter Hegemann & Osamu Nureki

Channelrhodopsins are light-activated ion channels that mediate cation permeation across cell membranes upon light absorption. Here, the authors report the crystal structure of the most red-shifted channelrhodopsin from the algae Chlamydomonas noctigama at 2.6 Å resolution.

26 September 2018 | doi: 10.1038/s41467-018-06421-9
Neuroscience  X-ray crystallography 

Structural basis for broad neutralization of ebolaviruses by an antibody targeting the glycoprotein fusion loop OPEN
Benjamin M. Janus, Nydia van Dyk, Xuelian Zhao, Katie A. Howell, Cinque Soto, M. Javad Aman, Yuxing Li, Thomas R. Fuerst & Gilad Ofek

The Ebola virus glycoprotein is a target for cross-protective antibodies. Here, Janus et al. report the crystal structure of the antigen-binding fragment of a pan-reactive antibody bound to a conserved epitope of the glycoprotein, facilitating rational design of cross-protective vaccines and therapeutics.

26 September 2018 | doi: 10.1038/s41467-018-06113-4
Ebola virus  X-ray crystallography 

Asymmetric remote C-H borylation of internal alkenes via alkene isomerization OPEN
Xu Chen, Zhaoyang Cheng, Jun Guo & Zhan Lu

Sequential alkene isomerization/functionalization enables enantioselective transformations of remote C–H bonds. Here, the authors report a chiral cobalt catalytic system for the highly enantioselective, remote C–H borylation of internal alkenes via an isomerization/hydroboration sequence.

26 September 2018 | doi: 10.1038/s41467-018-06240-y
Asymmetric synthesis  Homogeneous catalysis  Stereochemistry 

Mapping protein selectivity landscapes using multi-target selective screening and next-generation sequencing of combinatorial libraries OPEN
Si Naftaly, Itay Cohen, Anat Shahar, Alexandra Hockla, Evette S. Radisky & Niv Papo

Characterizing the binding selectivity landscape of interacting proteins is crucial in protein engineering. Here the authors use multi-target selective library screening and in silico next-generation sequencing to map the binding landscape of proteins and produce improved proteases inhibitors.

26 September 2018 | doi: 10.1038/s41467-018-06403-x
High-throughput screening  Next-generation sequencing  Proteases  Protein design 

A scalable online tool for quantitative social network assessment reveals potentially modifiable social environmental risks OPEN
Amar Dhand, Charles C. White, Catherine Johnson, Zongqi Xia & Philip L. De Jager

An individual’s social network—their friends, family, and acquaintances—is important for their health, but existing tools for assessing social networks have limitations. Here, the authors introduce a quantitative social network assessment tool on a secure open-source web platform and show its utility in a nation-wide study.

26 September 2018 | doi: 10.1038/s41467-018-06408-6
Human behaviour  Interdisciplinary studies  Multiple sclerosis  Social behaviour 

Identification of small-molecule ion channel modulators in C. elegans channelopathy models OPEN
Qiang Jiang, Kai Li, Wen-Jing Lu, Shuang Li, Xin Chen, Xi-Juan Liu, Jie Yuan, Qiurong Ding, Feng Lan & Shi-Qing Cai

Mutations in the voltage-gated K+ channel human ether-a-go-go-related gene (hERG) lead to Long-QT syndrome, causing life-threatening cardiac arrhythmia. Here the authors use C. elegans as a platform to run a channelopathy drug screen, identifying drugs to target hERG mutants.

26 September 2018 | doi: 10.1038/s41467-018-06514-5
Arrhythmias  Drug discovery  Ion channels in the nervous system 

Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity OPEN
Andreas Heindl, Adnan Mujahid Khan, Daniel Nava Rodrigues, Katherine Eason, Anguraj Sadanandam, Cecilia Orbegoso, Marco Punta, Andrea Sottoriva, Stefano Lise, Susana Banerjee & Yinyin Yuan

Cancer cells can actively engage in overcoming microenvironmental constraints such as tissue stiffness through adapting their shapes; however it is unclear how microenvironmental cells shape cancer nuclear morphology in human tumors in situ. Here the authors merge machine learning, digital pathology and spatial statistics to study this issue; furthermore the authors identify decreased immune infiltration in the surrounding of diversified cancer cells in a subset of ovarian tumors.

25 September 2018 | doi: 10.1038/s41467-018-06130-3
Ecology  Ovarian cancer 

Predicting nutrient content of ray-finned fishes using phylogenetic information OPEN
Bapu Vaitla, David Collar, Matthew R. Smith, Samuel S. Myers, Benjamin L. Rice & Christopher D. Golden

Humans increasingly depend on seafood for nutrition, but nutrient content is unknown for the vast majority of fish species. Here, the authors use phylogenetic analyses and data imputation to predict the nutrient content of fish that are under-studied but that could be of future dietary importance.

25 September 2018 | doi: 10.1038/s41467-018-06199-w
Evolutionary biology  Nutrition disorders  Phylogenetics 

Lnk/Sh2b3 deficiency restores hematopoietic stem cell function and genome integrity in Fancd2 deficient Fanconi anemia OPEN
Joanna Balcerek, Jing Jiang, Yang Li, Qinqin Jiang, Nicholas Holdreith, Brijendra Singh, Vemika Chandra, Kaosheng Lv, Jian-gang Ren, Krasimira Rozenova, Weihua Li, Roger A. Greenberg & Wei Tong

Loss of Fancd2 leads to replication stress intolerance and Fanconi Anemia, where haematopoietic stem cell (HSC) function is compromised. Here, the authors show that Lnk/Sh2b3 loss restores HSC proliferation and survival in Fancd2 knockout mice and ameliorates replication stress in a cytokine/JAK2 signaling dependent manner.

25 September 2018 | doi: 10.1038/s41467-018-06380-1
Haematopoietic stem cells  Stalled forks 

Analysis of extracellular mRNA in human urine reveals splice variant biomarkers of muscular dystrophies OPEN
Layal Antoury, Ningyan Hu, Leonora Balaj, Sudeshna Das, Sofia Georghiou, Basil Darras, Tim Clark, Xandra O. Breakefield & Thurman M. Wheeler

Patients with myotonic dystrophy need to undergo invasive muscle biopsies to monitor disease progression and response to therapy. Here, the authors show that extracellular RNAs in human urine can be used as biomarkers to differentiate patients from unaffected controls, and to monitor exon skipping in patients with Duchenne muscular dystrophy taking the drug eteplirsen.

25 September 2018 | doi: 10.1038/s41467-018-06206-0
Biomarkers  Neuromuscular disease 

A germanium hole spin qubit OPEN
Hannes Watzinger, Josip Kukučka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian-Jun Zhang & Georgios Katsaros

Germanium’s electronic structure and large, tunable spin-orbit coupling makes it a good material for constructing hole-based quantum devices. Here the authors demonstrate the fabrication and two-axis control of a hole spin qubit in a germanium double quantum dot.

25 September 2018 | doi: 10.1038/s41467-018-06418-4
Nanowires  Quantum dots  Qubits 

Human hippocampal replay during rest prioritizes weakly learned information and predicts memory performance OPEN
Anna C. Schapiro, Elizabeth A. McDevitt, Timothy T. Rogers, Sara C. Mednick & Kenneth A. Norman

The hippocampus is known to 'replay' experiences and memories during rest periods, but it is unclear how particular memories are prioritized for replay. Here, the authors show that information that is remembered less well is replayed more often, suggesting that weaker memories are selected for replay.

25 September 2018 | doi: 10.1038/s41467-018-06213-1
Cognitive neuroscience  Consolidation  Hippocampus  Replay 

Plasmodium co-infection protects against chikungunya virus-induced pathologies OPEN
Teck-Hui Teo, Fok-Moon Lum, Khairunnisa Ghaffar, Yi-Hao Chan, Siti Naqiah Amrun, Jeslin J. L. Tan, Cheryl Y. P. Lee, Tze-Kwang Chua, Guillaume Carissimo, Wendy W. L. Lee, Carla Claser, Ravisankar Rajarethinam, Laurent Rénia & Lisa F. P. Ng

Chikungunya virus (CHIKV) and Plasmodium co-infections have been reported in humans, but effects of the two pathogens on each other are unclear. Here, Teo et al. show in mice that Plasmodium infection affects CHIKV-specific T and B cell responses, leading to reduced joint inflammation.

25 September 2018 | doi: 10.1038/s41467-018-06227-9
Interferons  Malaria  Viral host response  Viral infection 

One-step generation of multiple gene knock-outs in the diatom Phaeodactylum tricornutum by DNA-free genome editing OPEN
Manuel Serif, Gwendoline Dubois, Anne-Laure Finoux, Marie-Ange Teste, Denis Jallet & Fayza Daboussi

The manipulation of diatom genomes is essential for industrial applications based on their metabolic abilities. Here the authors present an efficient multiplex DNA-free gene editing method using CRISPR-Cas9 and counter-selectable markers.

25 September 2018 | doi: 10.1038/s41467-018-06378-9
Biotechnology  CRISPR-Cas systems  Genetics  Plant sciences 

Vibrio parahaemolyticus RhsP represents a widespread group of pro-effectors for type VI secretion systems OPEN
Nan Jiang, Le Tang, Ruiqiang Xie, Zhi Li, Brianne Burkinshaw, Xiaoye Liang, Dylan Sosa, L. Aravind, Tao Dong, Dapeng Zhang & Jun Zheng

It is unclear how Rhs toxins lacking a PAAR motif are secreted by Type VI secretion systems. Here, the authors show for one of these proteins that the mechanism requires removal of an N-terminal fragment by auto-proteolysis, followed by interaction with a PAAR protein and then secretion.

25 September 2018 | doi: 10.1038/s41467-018-06201-5
Bacteriology  Pathogens 

Caspase-1 inhibition alleviates cognitive impairment and neuropathology in an Alzheimer’s disease mouse model OPEN
Joseph Flores, Anastasia Noël, Bénédicte Foveau, Jeffrey Lynham, Clotilde Lecrux & Andréa C. LeBlanc

Caspase-1, activated by stress in immune cells and in CNS human neurons, may contribute to neuronal degeneration. Here, the authors investigate the therapeutic potential of a Caspase-1 inhibitor in a mouse model of Alzheimer’s disease.

25 September 2018 | doi: 10.1038/s41467-018-06449-x
Alzheimer's disease  Microglia 

The evolution of multiple active site configurations in a designed enzyme OPEN
Nan-Sook Hong, Dušan Petrović, Richmond Lee, Ganna Gryn’ova, Miha Purg, Jake Saunders, Paul Bauer, Paul D. Carr, Ching-Yeh Lin, Peter D. Mabbitt, William Zhang, Timothy Altamore, Chris Easton, Michelle L. Coote, Shina C. L. Kamerlin & Colin J. Jackson

Generation and iterative optimization of designed enzymes can provide valuable insights for a more efficient catalysis. Here the authors have followed the iterative improvement of a designed Kemp eliminase and show that remote point mutations could remodel the designed active site via substantial conformational reorganization.

25 September 2018 | doi: 10.1038/s41467-018-06305-y
Computational models  Synthetic chemistry methodology  Molecular conformation 

Quantifying climate sensitivity and climate-driven change in North American amphibian communities OPEN
David A. W. Miller, Evan H. Campbell Grant, Erin Muths, Staci M. Amburgey, Michael J. Adams, Maxwell B. Joseph, J. Hardin Waddle, Pieter T. J. Johnson, Maureen E. Ryan, Benedikt R. Schmidt, Daniel L. Calhoun, Courtney L. Davis, Robert N. Fisher, David M. Green, Blake R. Hossack, Tracy A. G. Rittenhouse, Susan C. Walls, Larissa L. Bailey, Sam S. Cruickshank, Gary M. Fellers et al.

Amphibians have seen large population declines, but the key drivers are hard to establish. Here, Miller et al. investigate trends of occupancy for 81 species of amphibians across North America and find greater sensitivity to water availability during breeding and winter conditions than mean climate.

25 September 2018 | doi: 10.1038/s41467-018-06157-6
Climate-change ecology  Community ecology  Conservation biology  Population dynamics 

Lineage dynamics of murine pancreatic development at single-cell resolution OPEN
Lauren E. Byrnes, Daniel M. Wong, Meena Subramaniam, Nathaniel P. Meyer, Caroline L. Gilchrist, Sarah M. Knox, Aaron D. Tward, Chun J. Ye & Julie B. Sneddon

Coordinated proliferation and differentiation of diverse cell populations drive pancreatic epithelial and mesenchymal development. Here, the authors profile cell type dynamics in the developing mouse pancreas using single-cell RNA sequencing, identifying mesenchymal subtypes and undescribed endocrine progenitors.

25 September 2018 | doi: 10.1038/s41467-018-06176-3
Differentiation  Gene expression  Pancreas 

Sex and species specific hearing mechanisms in mosquito flagellar ears OPEN
Matthew P. Su, Marta Andrés, Nicholas Boyd-Gibbins, Jason Somers & Joerg T. Albert

Auditory processing is an important component of mosquito behaviour including mating. Here the authors demonstrate substantial sex- and also species-specific variation in mosquito auditory transduction, amplification and gain control.

25 September 2018 | doi: 10.1038/s41467-018-06388-7
Auditory system  Evolutionary ecology  Sexual dimorphism 

Systemic signaling contributes to the unfolded protein response of the plant endoplasmic reticulum OPEN
Ya-Shiuan Lai, Giovanni Stefano, Starla Zemelis-Durfee, Cristina Ruberti, Lizzie Gibbons & Federica Brandizzi

The unfolded protein response (UPR) maintains cellular function under ER stress. While typically considered cell autonomous, here Lai et al. show that in Arabidopsis the UPR also has a systemic component triggered by intercellular movement of at least one bZIP transcription factor.

25 September 2018 | doi: 10.1038/s41467-018-06289-9
Protein trafficking in plants  Stress signalling 

Fine mapping of MHC region in lung cancer highlights independent susceptibility loci by ethnicity OPEN
Aida Ferreiro-Iglesias, Corina Lesseur, James McKay, Rayjean J. Hung, Younghun Han, Xuchen Zong, David Christiani, Mattias Johansson, Xiangjun Xiao, Yafang Li, David C. Qian, Xuemei Ji, Geoffrey Liu, Neil Caporaso, Ghislaine Scelo, David Zaridze, Anush Mukeriya, Milica Kontic, Simona Ognjanovic, Jolanta Lissowska et al.

The basis for associations between lung cancer and major histocompatibility complex genes is not completely understood. Here the authors further consider genetic variation within the MHC region in lung cancer patients and identify independent associations within HLA genes that explain MHC lung cancer associations in Europeans and Asian populations.

25 September 2018 | doi: 10.1038/s41467-018-05890-2
Epidemiology  Genetics research 

Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes OPEN
Joern Pezoldt, Maria Pasztoi, Mangge Zou, Carolin Wiechers, Michael Beckstette, Guilhem R. Thierry, Ehsan Vafadarnejad, Stefan Floess, Panagiota Arampatzi, Manuela Buettner, Janina Schweer, Diana Fleissner, Marius Vital, Dietmar H. Pieper, Marijana Basic, Petra Dersch, Till Strowig, Mathias Hornef, André Bleich, Ulrike Bode et al.

Induction of tolerance in the gut relies on immunomodulatory functions of mesenteric lymph nodes (mLN). Here the authors show that mLN stromal cells receive early microbiota imprinting in the neonatal phase to exhibit long-term, location-specific transcriptional programs for the induction of regulatory T cells and peripheral tolerance.

25 September 2018 | doi: 10.1038/s41467-018-06423-7
Immunology  Lymph node  Mucosal immunology  Peripheral tolerance  Regulatory T cells 

Simulation of slip transients and earthquakes in finite thickness shear zones with a plastic formulation OPEN
Xinyue Tong & Luc L. Lavier

Differences in energy partitioning between fast earthquakes and slow slip events (SSEs) remain unclear. Here, the authors present a new numerical technique and plastic formulation to model and provide a first-order attempt at quantifying the partitioning elastic energy release in fault zones.

25 September 2018 | doi: 10.1038/s41467-018-06390-z
Geodynamics  Geophysics  Tectonics 

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica OPEN
Timothy Paape, Roman V. Briskine, Gwyneth Halstead-Nussloch, Heidi E. L. Lischer, Rie Shimizu-Inatsugi, Masaomi Hatakeyama, Kenta Tanaka, Tomoaki Nishiyama, Renat Sabirov, Jun Sese & Kentaro K. Shimizu

Despite the prevalence of genome duplication in plants, little is known about the evolutionary patterns of entire subgenomes. Here the authors resequence allopolyploid Arabidopsis kamchatica genome to estimate diversity, linkage disequilibrium and strengths of both positive and purifying selection.

25 September 2018 | doi: 10.1038/s41467-018-06108-1
Evolutionary genetics  Genome evolution  Natural variation in plants 

An OB-fold complex controls the repair pathways for DNA double-strand breaks OPEN
Shengxian Gao, Sumin Feng, Shaokai Ning, Jingyan Liu, Huayu Zhao, Yixi Xu, Jinfeng Shang, Kejiao Li, Qing Li, Rong Guo & Dongyi Xu

How repair pathway selection occurs is still a matter of debate and many factors have been associated to this function. Here the authors provide insight into the role of FAM35A and C20ORF196, two REV7-interacting proteins, which are recruited at double-strand breaks to promote non-homologous end joining repair.

25 September 2018 | doi: 10.1038/s41467-018-06407-7
Double-strand DNA breaks  Non-homologous-end joining 

Persistent repair intermediates induce senescence OPEN
F. M. Feringa, J. A. Raaijmakers, M. A. Hadders, C. Vaarting, L. Macurek, L. Heitink, L. Krenning & R. H. Medema

Cells with damaged DNA can permanently exit the cell cycle during the G2 phase or recover spontaneously entering mitosis. Here the authors reveal that the decision to exit from the cell cycle in G2 is dependent on the presence of repair intermediates associated with homologous recombination.

25 September 2018 | doi: 10.1038/s41467-018-06308-9
Cell-cycle exit  DNA damage and repair  DNA damage checkpoints 

Chirality amplification by desymmetrization of chiral ligand-capped nanoparticles to nanorods quantified in soft condensed matter OPEN
Ahlam Nemati, Sasan Shadpour, Lara Querciagrossa, Lin Li, Taizo Mori, Min Gao, Claudio Zannoni & Torsten Hegmann

The mechanisms by which molecular chirality is amplified through space and across length scales is of great interest. Here the authors show how gold nanorods covered in chiral dopants are more efficient in transducing chiral information compared to other gold nanoparticles decorated with chiral ligands.

25 September 2018 | doi: 10.1038/s41467-018-06400-0
Liquid crystals  Nanoparticles 

LUBAC prevents lethal dermatitis by inhibiting cell death induced by TNF, TRAIL and CD95L OPEN

TNF mediated inflammation is critical in autoimmune mediated pathology, however many patients are refractory to current anti-TNF therapeutics. Here the authors show induction of several death ligands, in addition to TNF is sufficient to cause fatal dermatitis in a LUBAC deficient murine model of disease.

25 September 2018 | doi: 10.1038/s41467-018-06155-8
Apoptosis  Chronic inflammation  Necroptosis  Tumour-necrosis factors  Ubiquitylation 

Skin color-specific and spectrally-selective naked-eye dosimetry of UVA, B and C radiations OPEN
Wenyue Zou, Ana González, Deshetti Jampaiah, Rajesh Ramanathan, Mohammad Taha, Sumeet Walia, Sharath Sriram, Madhu Bhaskaran, José M. Dominguez-Vera & Vipul Bansal

Current ultraviolet (UV) sensors cannot differentiate between UVA, B and C, each of which has a remarkably different impact on human health. Here the authors show spectrally-selective colorimetric monitoring of ultraviolet radiations by developing a photoelectrochromic ink that consists of a multiredox polyoxometalate and an e donor.

25 September 2018 | doi: 10.1038/s41467-018-06273-3
Light harvesting  Natural hazards  Optical sensors 

Gender differences in individual variation in academic grades fail to fit expected patterns for STEM OPEN
R. E. O’Dea, M. Lagisz, M. D. Jennions & S. Nakagawa

Men are over-represented in the STEM (science, technology, engineering and mathematics) workforce even though girls outperform boys in these subjects at school. Here, the authors cast doubt on one leading explanation for this paradox, the ‘variability hypothesis’.

25 September 2018 | doi: 10.1038/s41467-018-06292-0
Education  Intelligence  Psychology  Social sciences 

Loss of PRC1 induces higher-order opening of Hox loci independently of transcription during Drosophila embryogenesis OPEN
Thierry Cheutin & Giacomo Cavalli

Loss of Polycomb repressive complex 1 (PRC1) proteins usually results in both chromatin unfolding and ectopic transcription. Here, the authors analyze the temporal function of two PRC1 proteins during Drosophila embryogenesis and provide evidence that PRC1 maintains gene silencing by folding chromatin domains.

25 September 2018 | doi: 10.1038/s41467-018-05945-4
Chromatin  Epigenetic memory  Gene expression  Gene silencing 

RARα supports the development of Langerhans cells and langerin-expressing conventional dendritic cells OPEN
Seika Hashimoto-Hill, Leon Friesen, Sungtae Park, Suji Im, Mark H. Kaplan & Chang H. Kim

Langerhans cells (LC) and langerin-expressing conventional dendritic cells are made from distinct progenitors and enriched in the distinct microenvironments of the skin. Here the authors show that these immune cells are regulated by retinoic acid receptor alpha (RARα) via simultaneous induction of LC-promoting Runx3 and repression of LC-inhibiting C/EBPβ.

25 September 2018 | doi: 10.1038/s41467-018-06341-8
Antigen-presenting cells  Gene regulation in immune cells  Langerhans cells  Conventional dendritic cells 

An orbitally derived single-atom magnetic memory OPEN
Brian Kiraly, Alexander N. Rudenko, Werner M. J. van Weerdenburg, Daniel Wegner, Mikhail I. Katsnelson & Alexander A. Khajetoorians

Single-atom storage can dramatically exceed the limit of traditional high-density memory devices but is challenging. Here the authors show the bistability in the orbital configuration of a single Co atom on black phosphorus which can be accessed, manipulated and has potential for high-temperature single-atom information storage.

25 September 2018 | doi: 10.1038/s41467-018-06337-4
Magnetic properties and materials  Spintronics 

RNA editing derived epitopes function as cancer antigens to elicit immune responses OPEN
Minying Zhang, Jens Fritsche, Jason Roszik, Leila J. Williams, Xinxin Peng, Yulun Chiu, Chih-Chiang Tsou, Franziska Hoffgaard, Valentina Goldfinger, Oliver Schoor, Amjad Talukder, Marie A. Forget, Cara Haymaker, Chantale Bernatchez, Leng Han, Yiu-Huen Tsang, Kathleen Kong, Xiaoyan Xu, Kenneth L. Scott, Harpreet Singh-Jasuja et al.

RNA editing is a biological process that creates sequence variation. Here the authors show that peptides generated as a consequence of RNA editing are naturally presented by human leukocyte antigen (HLA) and serve as antigens to elicit anti-tumour immune responses.

25 September 2018 | doi: 10.1038/s41467-018-06405-9
Antigen processing and presentation  Cancer immunotherapy  Tumour immunology 

Functional modulation of primary visual cortex by the superior colliculus in the mouse OPEN
Mehran Ahmadlou, Larry S. Zweifel & J. Alexander Heimel

The role of the superior colliculus (SC) in modulating V1 cortical activity is not clear. Here, the authors demonstrate the functional role of SC in modulating V1 responses through an excitatory pathway via the dorsal lateral geniculate nucleus.

25 September 2018 | doi: 10.1038/s41467-018-06389-6
Neural circuits  Visual system 

Microglial dopamine receptor elimination defines sex-specific nucleus accumbens development and social behavior in adolescent rats OPEN
Ashley M. Kopec, Caroline J. Smith, Nathan R. Ayre, Sean C. Sweat & Staci D. Bilbo

Dopaminergic circuits in the nucleus accumbens regulate reward, including social play behavior in adolescent rodents. Here, the authors show that in male but not female rats, dopamine receptors are tagged by complement for microglial phagocytosis, thus mediating changes in social behavior.

25 September 2018 | doi: 10.1038/s41467-018-06118-z
Developmental biology  Neuroscience 

Cortical modulation of sensory flow during active touch in the rat whisker system OPEN
Shubhodeep Chakrabarti & Cornelius Schwarz

During active touch, sensory responses to object touch are gated at the level of thalamus and cortex. Here, the authors report gating at the level of the brainstem and show that an intact somatosensory cortex is essential for this response modulation.

25 September 2018 | doi: 10.1038/s41467-018-06200-6
Neural circuits  Whisker system 

Estimating sources and sinks of malaria parasites in Madagascar OPEN
Felana Angella Ihantamalala, Vincent Herbreteau, Feno M. J. Rakotoarimanana, Jean Marius Rakotondramanga, Simon Cauchemez, Bienvenue Rahoilijaona, Gwenaëlle Pennober, Caroline O. Buckee, Christophe Rogier, C. J. E. Metcalf & Amy Wesolowski

Understanding the source of malaria outbreaks in low-transmission areas is important for controlling the disease. Here, the authors use mobile phone data to map malaria transmission in Madagascar, and are able to show that primary sources of infection in the capital city are found along populated coastal areas.

25 September 2018 | doi: 10.1038/s41467-018-06290-2
Ecological modelling  Geography  Infectious diseases 

Single cell molecular alterations reveal target cells and pathways of concussive brain injury OPEN
Douglas Arneson, Guanglin Zhang, Zhe Ying, Yumei Zhuang, Hyae Ran Byun, In Sook Ahn, Fernando Gomez-Pinilla & Xia Yang

Traumatic brain injury (TBI) affects the hippocampus and can lead to neurological and psychiatric disorders. Here, the authors perform single-cell RNA sequencing to reveal molecular pathways across a range of cell types affected during TBI.

25 September 2018 | doi: 10.1038/s41467-018-06222-0
Brain injuries  Computational biology and bioinformatics  Gene expression analysis  Systems biology 

Using both qualitative and quantitative data in parameter identification for systems biology models OPEN
Eshan D. Mitra, Raquel Dias, Richard G. Posner & William S. Hlavacek

Much of the data generated in biology is qualitative, but exploiting such data to inform models of biological systems remains a challenge. Here, the authors demonstrate an approach that allows use of both quantitative and qualitative data for parameterising dynamical models.

25 September 2018 | doi: 10.1038/s41467-018-06439-z
Computational models  Statistical methods 

Mapping of histone-binding sites in histone replacement-completed spermatozoa OPEN
Keisuke Yoshida, Masafumi Muratani, Hiromitsu Araki, Fumihito Miura, Takehiro Suzuki, Naoshi Dohmae, Yuki Katou, Katsuhiko Shirahige, Takashi Ito & Shunsuke Ishii

While a majority of histones are replaced by protamines during spermatogenesis, a small amount is retained in mammalian spermatozoa. Here the authors develop a method to purify histones from replacement-completed sperm (HRCS), completely solubilize histones from cross-linked HRCS without MNase digestion, and map histone-binding sites in these cells.

24 September 2018 | doi: 10.1038/s41467-018-06243-9
Biological techniques  Gene silencing  Nucleosomes 

Solution-processed perovskite light emitting diodes with efficiency exceeding 15% through additive-controlled nanostructure tailoring OPEN
Muyang Ban, Yatao Zou, Jasmine P. H. Rivett, Yingguo Yang, Tudor H. Thomas, Yeshu Tan, Tao Song, Xingyu Gao, Dan Credington, Felix Deschler, Henning Sirringhaus & Baoquan Sun

Crystal sizes play a vital role in pushing up the efficiency of organometal halide perovskites based LEDs. Here Ban et al. incorporate a molecular additive to control the crystallite distribution and phase separation in the perovskite devices, resulting in high external quantum efficiency of 15.5%.

24 September 2018 | doi: 10.1038/s41467-018-06425-5
Electronic devices  Lasers, LEDs and light sources 

Microfluidic deposition for resolving single-molecule protein architecture and heterogeneity OPEN
Francesco Simone Ruggeri, Jerome Charmet, Tadas Kartanas, Quentin Peter, Sean Chia, Johnny Habchi, Christopher M. Dobson, Michele Vendruscolo & Tuomas P. J. Knowles

Manual sample deposition on a substrate can introduce artifacts in quantitative AFM measurements. Here the authors present a microfluidic spray device for reliable deposition of subpicoliter droplets which dry out in milliseconds after landing on the surface, thereby avoiding protein self-assembly.

24 September 2018 | doi: 10.1038/s41467-018-06345-4
Applications of AFM  Atomic force microscopy  Microfluidics  Protein aggregation  Single-molecule biophysics 

Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA OPEN
K. G. Paulson, V. Voillet, M. S. McAfee, D. S. Hunter, F. D. Wagener, M. Perdicchio, W. J. Valente, S. J. Koelle, C. D. Church, N. Vandeven, H. Thomas, A. G. Colunga, J. G. Iyer, C. Yee, R. Kulikauskas, D. M. Koelle, R. H. Pierce, J. H. Bielas, P. D. Greenberg, S. Bhatia et al.

Acquired resistance is a major problem in cancer immunotherapy. Here the authors report a study of two patients with Merkel cell carcinoma under immunotherapy treatment who develop resistance after deep responses for >1 year and identified a novel mechanism of acquired, gene-specific transcriptional suppression of HLAs.

24 September 2018 | doi: 10.1038/s41467-018-06300-3
MHC  Skin cancer  Tumour immunology 

Electrical conductivity and magnetic dynamos in magma oceans of Super-Earths OPEN
François Soubiran & Burkhard Militzer

With the discovery of large rocky exoplanets called Super-Earths, questions have arisen regarding the properties of their interiors and their ability to produce a magnetic field. Here, the authors show that under high pressure, molten silicates are semi-metallic and that magma oceans would host a dynamo process.

24 September 2018 | doi: 10.1038/s41467-018-06432-6
Electronic properties and materials  Exoplanets  Geomagnetism 

Towards exact molecular dynamics simulations with machine-learned force fields OPEN
Stefan Chmiela, Huziel E. Sauceda, Klaus-Robert Müller & Alexandre Tkatchenko

Simultaneous accurate and efficient prediction of molecular properties relies on combined quantum mechanics and machine learning approaches. Here the authors develop a flexible machine-learning force-field with high-level accuracy for molecular dynamics simulations.

24 September 2018 | doi: 10.1038/s41467-018-06169-2
Atomic and molecular physics  Chemical physics  Theoretical chemistry 

Gas-solid reaction based over one-micrometer thick stable perovskite films for efficient solar cells and modules OPEN
Zonghao Liu, Longbin Qiu, Emilio J. Juarez-Perez, Zafer Hawash, Taehoon Kim, Yan Jiang, Zhifang Wu, Sonia R. Raga, Luis K. Ono, Shengzhong (Frank) Liu & Yabing Qi

Perovskite solar cells often suffer from poor uniformity and reproducibility especially in case of large area devices. Here Liu et al. developed a gas−solid reaction method that enables facile fabrication of over 1 µm thick perovskite films for solar modules with high efficiency, stability and reproducibility.

24 September 2018 | doi: 10.1038/s41467-018-06317-8
Devices for energy harvesting  Solar cells 

Spatiotemporal dynamics of homologous recombination repair at single collapsed replication forks OPEN
Donna R. Whelan, Wei Ting C. Lee, Yandong Yin, Dylan M. Ofri, Keria Bermudez-Hernandez, Sarah Keegan, David Fenyo & Eli Rothenberg

How factors involved in homologous recombination interact and function is a matter of interest. Here the authors use super-resolution imaging to describe the spatiotemporal dynamics of proteins associated with homologous recombination DNA repair in response to replication stress.

24 September 2018 | doi: 10.1038/s41467-018-06435-3
DNA  DNA replication  Double-strand DNA breaks  Homologous recombination 

OCP–FRP protein complex topologies suggest a mechanism for controlling high light tolerance in cyanobacteria OPEN
Nikolai N. Sluchanko, Yury B. Slonimskiy, Evgeny A. Shirshin, Marcus Moldenhauer, Thomas Friedrich & Eugene G. Maksimov

Cyanobacterial photoprotection is controlled by OCP and FRP proteins, but their dynamic interplay is not fully understood. Here, the authors combine protein engineering, disulfide trapping and structural analyses to provide mechanistic insights into the transient OCP-FRP interaction.

24 September 2018 | doi: 10.1038/s41467-018-06195-0
Light responses  Non-photochemical quenching  Proteins  SAXS 

Identifying the missing link in catalyst transfer polymerization OPEN
Weiying He, Brian O. Patrick & Pierre Kennepohl

The mechanism for nickel-catalyzed catalyst transfer polycondensation of thiophenes to polythiophenes. Here the authors show experimental and computational evidence of structurally characterized square planar η2-Ni(0)–thiophene species and their relevance to the mechanism of catalyst transfer polycondensation.

24 September 2018 | doi: 10.1038/s41467-018-06324-9
Catalytic mechanisms  Chemical bonding  Cross-coupling reactions  Homogeneous catalysis 

Modulating the hierarchical fibrous assembly of Au nanoparticles with atomic precision OPEN
Qi Li, Jake C. Russell, Tian-Yi Luo, Xavier Roy, Nathaniel L. Rosi, Yan Zhu & Rongchao Jin

Constructing nanoparticle assemblies with atomic precision remains a major challenge in nanoscience. Here, the authors realize atomic‐level control over the 1D, 2D and hierarchical 3D assembly of Au nanoparticles by modulating the site‐specific surface ligands and associated counterions.

24 September 2018 | doi: 10.1038/s41467-018-06395-8
Materials chemistry  Nanoscale materials  Self-assembly 

Natural variation at XND1 impacts root hydraulics and trade-off for stress responses in Arabidopsis OPEN
Ning Tang, Zaigham Shahzad, Fabien Lonjon, Olivier Loudet, Fabienne Vailleau & Christophe Maurel

Soil water uptake is a major determinant of plant performance and stress tolerance. Here the authors show that, by affecting xylem formation in the root, natural variation at the Arabidopsis XND1 locus has contrasting effects on root hydraulics and drought tolerance versus pathogen resistance.

24 September 2018 | doi: 10.1038/s41467-018-06430-8
Genome-wide association studies  Natural variation in plants  Plant stress responses 

Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination OPEN
Nina M. S. Gustafsson, Katarina Färnegårdh, Nadilly Bonagas, Anna Huguet Ninou, Petra Groth, Elisee Wiita, Mattias Jönsson, Kenth Hallberg, Jemina Lehto, Rosa Pennisi, Jessica Martinsson, Carina Norström, Jessica Hollers, Johan Schultz, Martin Andersson, Natalia Markova, Petra Marttila, Baek Kim, Martin Norin, Thomas Olin et al.

Targeting the glycolytic PFKFB3 enzyme is being studied as a therapeutic strategy against cancer. Here the authors identify PFKFB3 as being involved in homologous recombination (HR) repair of DNA double strand breaks (DSBs) and present a PFKFB3 inhibitor.

24 September 2018 | doi: 10.1038/s41467-018-06287-x
Cancer metabolism  Cancer therapy  DNA damage and repair  DNA replication 

Neurogenetic profiles delineate large-scale connectivity dynamics of the human brain OPEN
Ibai Diez & Jorge Sepulcre

Attractor dynamics have been discovered in neural circuits, but it is not clear if they exist at the level of whole-brain activity. Here, the authors show that certain brain regions act as nodes in which many activity ‘streams’ converge, regardless of brain state. These regions show distinctive gene expression.

24 September 2018 | doi: 10.1038/s41467-018-06346-3
Cognitive neuroscience  Genetics of the nervous system  Network models  Neuroscience 

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements OPEN
Katariina Pärnänen, Antti Karkman, Jenni Hultman, Christina Lyra, Johan Bengtsson-Palme, D. G. Joakim Larsson, Samuli Rautava, Erika Isolauri, Seppo Salminen, Himanshu Kumar, Reetta Satokari & Marko Virta

The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) even in the absence of antibiotic exposure. Here, Pärnänen et al. analyse breast milk as well as infant and maternal gut microbiomes, and show that some of the infant gut ARGs are transferred from the mothers.

24 September 2018 | doi: 10.1038/s41467-018-06393-w
Computational biology and bioinformatics  Microbiology 

Regulation of the terminal maturation of iNKT cells by mediator complex subunit 23 OPEN
Yu Xu, Yang Sun, Hao Shen, Yuling Dai, Haifeng Liu, Ronghong Li, Hongdao Zhang, Ligang Wu, Xiaoyan Zhu & Xiaolong Liu

Invariant Natural Killer T cells (iNKT) rapidly exert effector functions upon activation, but the mechanisms of their functional maturation remain to be determined. Here, Xu and colleagues show that the mediator subunit Med23 is a transcriptional regulator controlling iNKT cell terminal maturation.

24 September 2018 | doi: 10.1038/s41467-018-06372-1
Cell death and immune response  Differentiation  Gene regulation in immune cells  NKT cells 

Circuit quantum electrodynamics of granular aluminum resonators OPEN
N. Maleeva, L. Grünhaupt, T. Klein, F. Levy-Bertrand, O. Dupre, M. Calvo, F. Valenti, P. Winkel, F. Friedrich, W. Wernsdorfer, A. V. Ustinov, H. Rotzinger, A. Monfardini, M. V. Fistul & I. M. Pop

The electrodynamics of superconducting devices make them suitable for applications as detectors, amplifiers, and qubits. Here the authors show that resonators made from granular aluminum, which naturally realizes a network of Josephson junctions, have practically useful impedances and nonlinearities.

24 September 2018 | doi: 10.1038/s41467-018-06386-9
Superconducting devices  Superconducting properties and materials 

PAXX and its paralogs synergistically direct DNA polymerase λ activity in DNA repair OPEN
Andrew Craxton, Deeksha Munnur, Rebekah Jukes-Jones, George Skalka, Claudia Langlais, Kelvin Cain & Michal Malewicz

PAXX functions as part of the nonhomologous end-joining pathway to repair double-strand DNA breaks. Here the authors show PAXX and its paralogs interact with polymerase lambda to promote joining of incompatible ends.

24 September 2018 | doi: 10.1038/s41467-018-06127-y
DNA  DNA-binding proteins  Double-strand DNA breaks  Non-homologous-end joining 

Plant neighbor detection and allelochemical response are driven by root-secreted signaling chemicals OPEN
Chui-Hua Kong, Song-Zhu Zhang, Yong-Hua Li, Zhi-Chao Xia, Xue-Fang Yang, Scott J. Meiners & Peng Wang

Plant growth and physiology respond to the presence of neighboring plants. Here the authors show that the chemicals (-)-loliolide and jasmonic acid, which were present in the root exudates of a range of plant species, can be detected by wheat and induce allelochemical production.

24 September 2018 | doi: 10.1038/s41467-018-06429-1
Agriculture  Ecology  Plant sciences 

Structure of Type-I Mycobacterium tuberculosis fatty acid synthase at 3.3 Å resolution OPEN
Nadav Elad, Szilvia Baron, Yoav Peleg, Shira Albeck, Jacob Grunwald, Gal Raviv, Zippora Shakked, Oren Zimhony & Ron Diskin

The type-I fatty acid synthase (FAS-I) complex is essential for Mycobacterium tuberculosis (Mtb) and mediates the production of C26 fatty acids that are precursors for the synthesis of mycolic acids. Here the authors present the 3.3 Å resolution cryo-EM structure of Mtb FAS-I, which is of interest for tuberculosis drug development.

24 September 2018 | doi: 10.1038/s41467-018-06440-6
Cryoelectron microscopy  Electron microscopy  Pathogens  Structural biology 

Griffithsin carrageenan fast dissolving inserts prevent SHIV HSV-2 and HPV infections in vivo OPEN
Nina Derby, Manjari Lal, Meropi Aravantinou, Larisa Kizima, Patrick Barnable, Aixa Rodriguez, Manshun Lai, Asa Wesenberg, Shweta Ugaonkar, Keith Levendosky, Olga Mizenina, Kyle Kleinbeck, Jeffrey D. Lifson, M. Melissa Peet, Zachary Lloyd, Michael Benson, Walid Heneine, Barry R O’Keefe, Melissa Robbiani, Elena Martinelli et al.

Safety and efficacy remain important challenges for non-antiretroviral-based microbicides. Here, Derby et al. show that a Griffithsin-Carrageenan fast dissolving vaginal insert provides on-demand protection against SHIV infections in macaques, paving the way for the development of pre-exposure prophylaxis on-demand products.

24 September 2018 | doi: 10.1038/s41467-018-06349-0
Antivirals  Experimental models of disease  Human papilloma virus  Preclinical research  Retrovirus 

Contrasting effects on deep convective clouds by different types of aerosols OPEN
Jonathan H. Jiang, Hui Su, Lei Huang, Yuan Wang, Steven Massie, Bin Zhao, Ali Omar & Zhien Wang

Aerosol effects on convection have been debated for decades when all types of aerosols are lumped together in the analyses. Using NASA satellite measurements, the authors find strong evidence that smoke inhibits convection but polluted continental aerosols invigorate convection.

24 September 2018 | doi: 10.1038/s41467-018-06280-4
Atmospheric science  Climate sciences 

A room-temperature sodium–sulfur battery with high capacity and stable cycling performance OPEN
Xiaofu Xu, Dong Zhou, Xianying Qin, Kui Lin, Feiyu Kang, Baohua Li, Devaraj Shanmukaraj, Teofilo Rojo, Michel Armand & Guoxiu Wang

Sodium–sulfur batteries operating at a high temperature between 300 and 350°C have been used commercially, but the safety issue hinders their wider adoption. Here the authors report a “cocktail optimized” electrolyte system that enables higher electrochemical performance and room-temperature operation.

24 September 2018 | doi: 10.1038/s41467-018-06443-3
Batteries  Electrochemistry 

BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis OPEN
Malay Mandal, Mark Maienschein-Cline, Patrick Maffucci, Margaret Veselits, Domenick E. Kennedy, Kaitlin C. McLean, Michael K. Okoreeh, Sophiya Karki, Charlotte Cunningham-Rundles & Marcus R. Clark

B-cell development is tightly regulated by transcription programs that are coordinated by transcription factors (TF) and locus accessibility. Here the authors show that, in mice and humans, the epigenetic reader BRWD1 inhibits and promotes the accessibility of enhancers for early and late B lymphopoiesis, respectively.

24 September 2018 | doi: 10.1038/s41467-018-06165-6
B cells  Epigenetics in immune cells  Lymphocyte differentiation  Systems analysis 

Eosinophil recruitment is dynamically regulated by interplay among lung dendritic cell subsets after allergen challenge OPEN
Shuying Yi, Jing Zhai, Rui Niu, Guangming Zhu, Meixiang Wang, Jianguo Liu, Hua Huang, Yaping Wang, Xiuli Jing, Li Kang, Wengang Song, Yufang Shi & Hua Tang

Eosinophils are important mediators of allergic responses, but how they are recruited to the inflamed site is still unclear. Here the authors show that CD103+ cDC1 cells secrete CCL17 and CCL22 for eosinophil recruitment, with this process promoted by CD24CD11b+ DC2s in the early phase but suppressed by CD24+ cDC2s in the late phase.

24 September 2018 | doi: 10.1038/s41467-018-06316-9
Eosinophils  Inflammatory diseases  Mucosal immunology  Conventional dendritic cells 

Direct electric field imaging of graphene defects OPEN
Ryo Ishikawa, Scott D. Findlay, Takehito Seki, Gabriel Sánchez-Santolino, Yuji Kohno, Yuichi Ikuhara & Naoya Shibata

Imaging chemical bonding states in defective graphene is important to determine its functional properties. Here, the authors report triangular and rectangular atomic electric fields in monolayer graphene induced by silicon as imaged by differential phase contrast STEM.

24 September 2018 | doi: 10.1038/s41467-018-06387-8
Catalysis  Graphene 

Atom-hybridization for synthesis of polymetallic clusters OPEN
Takamasa Tsukamoto, Tetsuya Kambe, Aiko Nakao, Takane Imaoka & Kimihisa Yamamoto

Multimetallic clusters are difficult to synthesize with control over elemental composition and organization. Here, the authors use dendrimers to precisely template the formation of five-element sub-nanoclusters, providing an elegant route to otherwise-inaccessible multinary compounds.

24 September 2018 | doi: 10.1038/s41467-018-06422-8
Inorganic chemistry  Materials chemistry  Nanoparticles 

Beaming random lasers with soliton control OPEN
Sreekanth Perumbilavil, Armando Piccardi, Raouf Barboza, Oleksandr Buchnev, Martti Kauranen, Giuseppe Strangi & Gaetano Assanto

Owing to their lack of a conventional cavity, random lasers typically do not emit a defined beam in a specific direction. Here, the authors combine spatial solitons and collinear pumping to achieve light-confined random lasing with a smooth output profile and a controllable direction of emission.

21 September 2018 | doi: 10.1038/s41467-018-06170-9
Lasers, LEDs and light sources  Liquid crystals  Solitons 

Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin OPEN
J. Hu, L. J. Worrall, C. Hong, M. Vuckovic, C. E. Atkinson, N. Caveney, Z. Yu & N. C. J. Strynadka

The bacterial type III secretion system of Gram-negative bacteria uses its core, the needle complex, to penetrate through the infected host cell membrane. Here authors show a near-atomic resolution structure of a needle complex which sheds light on the assembly and function of this nanomachine.

21 September 2018 | doi: 10.1038/s41467-018-06298-8
Cryoelectron microscopy  Pathogens 

Gallium nitride nanowire as a linker of molybdenum sulfides and silicon for photoelectrocatalytic water splitting OPEN
Baowen Zhou, Xianghua Kong, Srinivas Vanka, Sheng Chu, Pegah Ghamari, Yichen Wang, Nick Pant, Ishiang Shih, Hong Guo & Zetian Mi

Sunlight-harvesting materials require the clean integration of light-absorbing and catalytic components to be efficient. Here, authors link silicon photoelectrodes and molybdenum sulfide catalysts with defect-free gallium nitride nanowire to improve photoelectrochemical hydrogen evolution.

21 September 2018 | doi: 10.1038/s41467-018-06140-1
Light harvesting  Nanowires  Photocatalysis  Solar fuels 

Structures of insect Imp-L2 suggest an alternative strategy for regulating the bioavailability of insulin-like hormones OPEN
Nikolaj Kulahin Roed, Cristina M. Viola, Ole Kristensen, Gerd Schluckebier, Mathias Norrman, Waseem Sajid, John D. Wade, Asser Sloth Andersen, Claus Kristensen, Timothy R. Ganderton, Johan P. Turkenburg, Pierre De Meyts & Andrzej M. Brzozowski

Insulin-like polypeptide binding proteins (IBPs) from insects can bind diverse insulin-like proteins (ILPs) including human insulin and IGFs. Here, the authors present structures of a Drosophila IBP in its free and ILP-bound forms, providing insights into the regulation of ILP bioavailability by insect IBPs.

21 September 2018 | doi: 10.1038/s41467-018-06192-3
Insect hormones  Insulin signalling  X-ray crystallography 

Discovering human diabetes-risk gene function with genetics and physiological assays OPEN
Heshan Peiris, Sangbin Park, Shreya Louis, Xueying Gu, Jonathan Y. Lam, Olof Asplund, Gregory C. Ippolito, Rita Bottino, Leif Groop, Haley Tucker & Seung K. Kim

The function of genes linked to type 2 diabetes is poorly characterized. Here the authors combine Drosophila genetics and physiology with human islet biology to identify new regulators of insulin secretion including BCL11A.

21 September 2018 | doi: 10.1038/s41467-018-06249-3
Biological models  Diabetes  Endocrinology  Genetic techniques  Genetics 

Alpha-enolase regulates the malignant phenotype of pulmonary artery smooth muscle cells via the AMPK-Akt pathway OPEN
Jingbo Dai, Qiyuan Zhou, Jiwang Chen, Megan L. Rexius-Hall, Jalees Rehman & Guofei Zhou

Metabolic reprogramming of smooth muscle cells (SMCs) plays an important role in the pathogenesis of pulmonary arterial hypertension (PAH). Here, Dai et al. show that the glycolytic enzyme alpha-enolase contributes to this reprogramming, and that its inhibition limits SMC proliferation and disease progression in animal models of PAH.

21 September 2018 | doi: 10.1038/s41467-018-06376-x
Hypertension  Metabolism 

A cocoon silk chemistry strategy to ultrathin N-doped carbon nanosheet with metal single-site catalysts OPEN
Youqi Zhu, Wenming Sun, Jun Luo, Wenxing Chen, Tai Cao, Lirong Zheng, Juncai Dong, Jian Zhang, Maolin Zhang, Yunhu Han, Chen Chen, Qing Peng, Dingsheng Wang & Yadong Li

Single-site catalysts supported by ultrathin two-dimensional (2D) porous matrix are desirable for catalytic reactions, yet their synthesis remains a great challenge. Herein the authors report a cocoon silk chemistry strategy to synthesize isolated metal single-site catalysts embedded in ultrathin 2D porous N-doped carbon nanosheets.

21 September 2018 | doi: 10.1038/s41467-018-06296-w
Catalyst synthesis  Heterogeneous catalysis  Two-dimensional materials 

Reconfiguring surface functions using visible-light-controlled metal-ligand coordination OPEN
Chaoming Xie, Wen Sun, Hao Lu, Annika Kretzschmann, Jiahui Liu, Manfred Wagner, Hans-Jürgen Butt, Xu Deng & Si Wu

Configuring surfaces on-demand for desired functionalities is an ongoing challenge. Here, diverse and tailorable modifications of quartz and porous silica surfaces that are rapidly and reversibly switchable by the use of visible light are achieved via ruthenium-thioether coordination.

21 September 2018 | doi: 10.1038/s41467-018-06180-7
Chemical bonding  Organic molecules in materials science  Sensors and biosensors  Surface chemistry 

Spatiotemporal segregation of human marginal zone and memory B cell populations in lymphoid tissue OPEN
Yuan Zhao, Mohamed Uduman, Jacqueline H. Y. Siu, Thomas J. Tull, Jeremy D. Sanderson, Yu-Chang Bryan Wu, Julian Q. Zhou, Nedyalko Petrov, Richard Ellis, Katrina Todd, Konstantia-Maria Chavele, William Guesdon, Anna Vossenkamper, Wayel Jassem, David P. D’Cruz, David J. Fear, Susan John, Dagmar Scheel-Toellner, Claire Hopkins, Estefania Moreno et al.

Human memory and marginal zone B cells share some features including CD27 expression and somatic hypermutation, but their lineage relationship is still unclear. Here the authors use mass cytometry and sequential clustering methods to show that, despite their shared features, memory and marginal zone B cells represent distinct lineage choices.

21 September 2018 | doi: 10.1038/s41467-018-06089-1
Adaptive immunity  B cells  Immunological memory  Lymphocyte differentiation 

Influence of PEDOT:PSS crystallinity and composition on electrochemical transistor performance and long-term stability OPEN
Seong-Min Kim, Chang-Hyun Kim, Youngseok Kim, Nara Kim, Won-June Lee, Eun-Hak Lee, Dokyun Kim, Sungjun Park, Kwanghee Lee, Jonathan Rivnay & Myung-Han Yoon

The lack of understanding of mixed transport in ion-permeable conjugated polymer films hinders the advance of organic electrochemical transistors for bioelectronics. Here, the authors elucidate the structure-property-performance relationships for conventional and crystallized PEDOT:PSS films.

21 September 2018 | doi: 10.1038/s41467-018-06084-6
Electronic devices  Sensors and biosensors 

Ancient and modern anticonvulsants act synergistically in a KCNQ potassium channel binding pocket OPEN
Rían W. Manville & Geoffrey W. Abbott

In some countries, leaves of the shrub Mallotus oppositifolius have been used to treat epilepsy. Here, authors look at the structural and molecular basis for how chemical components of M. oppositifolius have their anticonvulsant effects, via modulation of potassium channel activity.

21 September 2018 | doi: 10.1038/s41467-018-06339-2
Molecular medicine  Physiology 

Cerebello-thalamo-cortical hyperconnectivity as a state-independent functional neural signature for psychosis prediction and characterization OPEN
Hengyi Cao, Oliver Y. Chén, Yoonho Chung, Jennifer K. Forsyth, Sarah C. McEwen, Dylan G. Gee, Carrie E. Bearden, Jean Addington, Bradley Goodyear, Kristin S. Cadenhead, Heline Mirzakhanian, Barbara A. Cornblatt, Ricardo E. Carrión, Daniel H. Mathalon, Thomas H. McGlashan, Diana O. Perkins, Aysenil Belger, Larry J. Seidman, Heidi Thermenos, Ming T. Tsuang et al.

Brain function alterations in schizophrenia and other psychotic disorders remain poorly understood. Here, the authors discover that increased neural connectivity in the cerebello-thalamo-cortical circuitry predicts psychosis in those at high risk, and is present in people with schizophrenia.

21 September 2018 | doi: 10.1038/s41467-018-06350-7
Cognitive neuroscience  Diagnostic markers  Predictive markers  Psychosis 

Complex strain evolution of polar and magnetic order in multiferroic BiFeO3 thin films OPEN
Zuhuang Chen, Zhanghui Chen, Chang-Yang Kuo, Yunlong Tang, Liv R. Dedon, Qian Li, Lei Zhang, Christoph Klewe, Yen-Lin Huang, Bhagwati Prasad, Alan Farhan, Mengmeng Yang, James D. Clarkson, Sujit Das, Sasikanth Manipatruni, A. Tanaka, Padraic Shafer, Elke Arenholz, Andreas Scholl, Ying-Hao Chu et al.

To fully exploit the potential of multiferroic materials the control of their intrinsic degrees of freedom is a prerequisite. Here, the control of spin orientation in strained BiFeO3 films is demonstrated elucidating the microscopic mechanism of the complex interplay of polar and magnetic order.

21 September 2018 | doi: 10.1038/s41467-018-06190-5
Electronic devices  Ferroelectrics and multiferroics  Magnetic properties and materials 

A naturally protective epitope of limited variability as an influenza vaccine target OPEN
Craig P. Thompson, José Lourenço, Adam A. Walters, Uri Obolski, Matthew Edmans, Duncan S. Palmer, Kreepa Kooblall, George W. Carnell, Daniel O’Connor, Thomas A. Bowden, Oliver G. Pybus, Andrew J. Pollard, Nigel J. Temperton, Teresa Lambe, Sarah C. Gilbert & Sunetra Gupta

Current influenza vaccine approaches largely focus on highly variable epitopes with high immunogenicity or epitopes of low variability that often have low immunogenicity. Here, Thompson et al. identify a highly immunogenic epitope of limited variability in the head domain of the H1 haemagglutinin and show protection from diverse H1N1 strains in mice.

21 September 2018 | doi: 10.1038/s41467-018-06228-8
Influenza virus  Vaccines  Viral evolution  Viral immune evasion 

Active particles bound by information flows OPEN
Utsab Khadka, Viktor Holubec, Haw Yang & Frank Cichos

Synthetic active particles with inter-particle propulsion have been served as a model system to study the collective animal behaviors. Here, Khadka et al. add complexity to the model by spatially controlling particle motions through a laser feedback loop in response to the collective dynamics of particles.

21 September 2018 | doi: 10.1038/s41467-018-06445-1
Colloids  Optical manipulation and tweezers  Statistical physics, thermodynamics and nonlinear dynamics 

Towards synthetic cells using peptide-based reaction compartments OPEN
Kilian Vogele, Thomas Frank, Lukas Gasser, Marisa A. Goetzfried, Mathias W. Hackl, Stephan A. Sieber, Friedrich C. Simmel & Tobias Pirzer

Lipid-based membranes coupled to biochemical reaction networks can be difficult to implement in vitro. Here the authors use elastin-like peptides to create self-assembled vesicle structures containing transcription-translation systems for autonomous growth.

21 September 2018 | doi: 10.1038/s41467-018-06379-8
Biological physics  Synthetic biology 

A conformational sensor based on genetic code expansion reveals an autocatalytic component in EGFR activation OPEN
Martin Baumdick, Márton Gelléri, Chayasith Uttamapinant, Václav Beránek, Jason W. Chin & Philippe I. H. Bastiaens

Upon ligand binding epidermal growth factor receptor (EGFR) dimerizes and activates its intrinsic kinase to auto-phosphorylate EGFR. Here, the authors engineer and image a FRET-based conformational EGFR indicator which reveals that activation loop phosphorylation induces a catalytically active conformation in EGFR monomers.

21 September 2018 | doi: 10.1038/s41467-018-06299-7
Biological techniques  Chemical biology  Molecular biology 

Forward models demonstrate that repetition suppression is best modelled by local neural scaling OPEN
Arjen Alink, Hunar Abdulrahman & Richard N. Henson

The neural mechanisms underlying the suppression of fMRI responses to repeated stimuli are under debate. Here, the authors compare computational models to show that only a local scaling model can fit univariate and multivariate fMRI repetition effects across two paradigms and multiple brain regions.

21 September 2018 | doi: 10.1038/s41467-018-05957-0
Cognitive neuroscience  Neuroscience  Sensory processing  Visual system 

Positive cardiac inotrope omecamtiv mecarbil activates muscle despite suppressing the myosin working stroke OPEN
Michael S. Woody, Michael J. Greenberg, Bipasha Barua, Donald A. Winkelmann, Yale E. Goldman & E. Michael Ostap

Omecamtiv mecarbil (OM) is a positive cardiac inotrope in clinical trials for the treatment of heart failure whose mechanism of action is incompletely understood. Here the authors show that OM inhibits myosin's working stroke and prolongs actomyosin attachment and propose a model that reconciles the OM-induced increase in cardiac performance in vivo with the inhibitory actions observed in vitro.

21 September 2018 | doi: 10.1038/s41467-018-06193-2
Heart failure  Single-molecule biophysics 

The chromatin remodeler RSF1 controls centromeric histone modifications to coordinate chromosome segregation OPEN
Ho-Soo Lee, Zhonghui Lin, Sunyoung Chae, Young-Suk Yoo, Byung-Gyu Kim, Youngsoo Lee, Jared L. Johnson, You-Sun Kim, Lewis C. Cantley, Chang-Woo Lee, Hongtao Yu & Hyeseong Cho

The chromatin remodeler RSF1 is enriched at mitotic centromeres but its function there is poorly understood. Here, the authors show that RSF1 regulates H2A phosphorylation and acetylation at mitotic centromeres and contributes to chromosome stability.

21 September 2018 | doi: 10.1038/s41467-018-06377-w
Chromosome segregation  Cohesion 

Tunable colloid trajectories in nematic liquid crystals near wavy walls OPEN
Yimin Luo, Daniel A. Beller, Giuseppe Boniello, Francesca Serra & Kathleen J. Stebe

Nematic liquid crystals have a rich energy landscape which can define elastic fields to guide colloidal assembly. Here the authors show controllable trapping of colloidal particles by placing them in a system with wavy walls which are exploited to obtain stable, metastable and unstable equilibria.

21 September 2018 | doi: 10.1038/s41467-018-06054-y
Colloids  Liquid crystals  Self-assembly 

Controlling factor of incoming plate hydration at the north-western Pacific margin OPEN
Gou Fujie, Shuichi Kodaira, Yuka Kaiho, Yojiro Yamamoto, Tsutomu Takahashi, Seiichi Miura & Tomoaki Yamada

Bend faulting prior to subduction is considered to promote hydration, yet the relationship remains ambiguous. Here, via analysis of seismic surveys from the Japan and Kuril trenches junction, the authors show that pre-subduction bend faulting and post-subduction plate hydration are strongly correlated.

21 September 2018 | doi: 10.1038/s41467-018-06320-z
Seismology  Tectonics 

Gap junction protein Connexin-43 is a direct transcriptional regulator of N-cadherin in vivo OPEN
Maria Kotini, Elias H. Barriga, Jonathan Leslie, Marc Gentzel, Verena Rauschenberger, Alexandra Schambon & Roberto Mayor

Connexins are components of gap junctions that link cells and allow intercellular communication. Here, the authors show that the Connexin 43 carboxy tail interacts with basic transcription factor-3, leading to nuclear translocation and direct regulation of N-cadherin expression and neural crest migration.

21 September 2018 | doi: 10.1038/s41467-018-06368-x
Cell adhesion  Cell migration  Morphogenesis 

Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles OPEN

The harlequin ladybird beetle, Harmonia axyridis, has remarkable phenotypic diversity, with over 200 colour patterns. Here, Ando et al. show that this patterning is regulated by the transcription factor gene pannier and has diversified by repeated inversions and cis-regulatory modifications of pannier.

21 September 2018 | doi: 10.1038/s41467-018-06116-1
Evolutionary developmental biology  Evolutionary genetics  Structural variation 

Hierarchical and stage-specific regulation of murine cardiomyocyte maturation by serum response factor OPEN
Yuxuan Guo, Blake D. Jardin, Pingzhu Zhou, Isha Sethi, Brynn N. Akerberg, Christopher N Toepfer, Yulan Ai, Yifei Li, Qing Ma, Silvia Guatimosim, Yongwu Hu, Grigor Varuzhanyan, Nathan J. VanDusen, Donghui Zhang, David C. Chan, Guo-Cheng Yuan, Christine E. Seidman, Jonathan G. Seidman & William T. Pu

The processes regulating cardiomyocyte (CM) maturation are unclear. Here, the authors show that serum response factor regulates CM maturation only in neonatal CMs through stage-specific chromatin occupancy that affects cell size, sarcomere and transverse-tubule organization, and mitochondria

21 September 2018 | doi: 10.1038/s41467-018-06347-2
Differentiation  Heart development  Transcription 

A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions OPEN
Jill M. Brown, Nigel A. Roberts, Bryony Graham, Dominic Waithe, Christoffer Lagerholm, Jelena M. Telenius, Sara De Ornellas, A. Marieke Oudelaar, Caroline Scott, Izabela Szczerbal, Christian Babbs, Mira T. Kassouf, Jim R. Hughes, Douglas R. Higgs & Veronica J. Buckle

Self-interacting chromatin domains encompass genes and their cis-regulatory elements. Here the authors use high-resolution chromosome conformation capture and super-resolution imaging to study a 70 kb domain that includes the mouse α-globin regulatory locus and find that a tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions.

21 September 2018 | doi: 10.1038/s41467-018-06248-4
Gene expression  Gene regulation  Nuclear organization  Super-resolution microscopy 

Notch2 controls non-autonomous Wnt-signalling in chronic lymphocytic leukaemia OPEN
Maurizio Mangolini, Frederik Götte, Andrew Moore, Tim Ammon, Madlen Oelsner, Gloria Lutzny-Geier, Ludger Klein-Hitpass, James C. Williamson, Paul J. Lehner, Jan Dürig, Michael Möllmann, Lívia Rásó-Barnett, Katherine Hughes, Antonella Santoro, Simón Méndez-Ferrer, Robert A. J. Oostendorp, Ursula Zimber-Strobl, Christian Peschel, Daniel J. Hodson, Marc Schmidt-Supprian et al.

The Wnt pathway is one of the core de-regulated pathways in chronic lymphocytic leukaemia (CLL) and is activated in only a subset of patients; however, no universal drivers of the disease have been identified. Here the authors show that Notch2 and β-catenin pathways are the main drivers of the pro-survival bidirectional crosstalk between stromal cells and leukemic cells.

21 September 2018 | doi: 10.1038/s41467-018-06069-5
Cancer microenvironment  Chronic lymphocytic leukaemia 

An interstellar synthesis of phosphorus oxoacids OPEN
Andrew M. Turner, Alexandre Bergantini, Matthew J. Abplanalp, Cheng Zhu, Sándor Góbi, Bing-Jian Sun, Kang-Heng Chao, Agnes H. H. Chang, Cornelia Meinert & Ralf I. Kaiser

Extraterrestrial sources may have provided prebiotic phosphorus to the early Earth. Here, the authors investigate the potential of phosphine-doped astrochemical analog ices to form phosphorus oxoacids as precursors to more complex prebiotic compounds.

21 September 2018 | doi: 10.1038/s41467-018-06415-7
Chemical origin of life  Physical chemistry 

Vegetation response to exceptional global warmth during Oceanic Anoxic Event 2 OPEN
Ulrich Heimhofer, Nina Wucherpfennig, Thierry Adatte, Stefan Schouten, Elke Schneebeli-Hermann, Silvia Gardin, Gerta Keller, Sarah Kentsch & Ariane Kujau

The Cretaceous Oceanic Anoxic Event 2 represents one of the warmest episodes in the last 250 million years. Here, the authors present spore-pollen data and temperature estimates (TEX86) across an expanded stratigraphic section illustrating the dynamic response of vegetation during this exceptionally warm interval.

20 September 2018 | doi: 10.1038/s41467-018-06319-6
Palaeoceanography  Palaeoclimate  Sedimentology  Solid Earth sciences 

Structural basis for recognition of the malaria vaccine candidate Pfs48/45 by a transmission blocking antibody OPEN
Frank Lennartz, Florian Brod, Rebecca Dabbs, Kazutoyo Miura, David Mekhaiel, Arianna Marini, Matthijs M. Jore, Max M. Søgaard, Thomas Jørgensen, Willem A. de Jongh, Robert W. Sauerwein, Carole A. Long, Sumi Biswas & Matthew K. Higgins

Pfs48/45 is a promising component for a transmission-blocking malaria vaccine. Here, the authors develop a system to produce full-length Pfs48/45 for immunisation, characterise a panel of monoclonal antibodies and determine the structure of a potent transmission-blocking epitope.

20 September 2018 | doi: 10.1038/s41467-018-06340-9
Antibodies  Malaria  Vaccines  X-ray crystallography 

Strongly lensed repeating fast radio bursts as precision probes of the universe OPEN
Zheng-Xiang Li, He Gao, Xu-Heng Ding, Guo-Jian Wang & Bing Zhang

Fast radio bursts (FRBs) are likely to be gravitationally lensed by intervening galaxies. Here, the authors propose to make accurate measurements of time delays between images of lensed FRBs as a powerful probe for precision cosmology.

20 September 2018 | doi: 10.1038/s41467-018-06303-0
Cosmology  Transient astrophysical phenomena 

LNMAT1 promotes lymphatic metastasis of bladder cancer via CCL2 dependent macrophage recruitment OPEN
Changhao Chen, Wang He, Jian Huang, Bo Wang, Hui Li, Qingqing Cai, Feng Su, Junming Bi, Hongwei Liu, Bin Zhang, Ning Jiang, Guangzheng Zhong, Yue Zhao, Wen Dong & Tianxin Lin

Mechanism of lymph node (LN) metastasis induced by tumor associated macrophages (TAMs) remains unclear. Here they demonstrate that a long noncoding RNA LNMAT1 promotes LN metastasis of bladder cancer via recruitment of TAMs through epigenetic regulation of CCL2 expression.

20 September 2018 | doi: 10.1038/s41467-018-06152-x
Cancer microenvironment  Metastasis 

Robust single-cell DNA methylome profiling with snmC-seq2 OPEN
Chongyuan Luo, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, Joseph R. Nery, António Pinto-Duarte, Brian Bui, Conor Fitzpatrick, Carolyn O’Connor, Seth Ruga, Marc E. Van Eden, David A. Davis, Deborah C. Mash, M. Margarita Behrens & Joseph R. Ecker

Single-cell DNA methylome profiling allows the study of epigenomic heterogeneity in tissues but has been impeded by library quality. Here the authors demonstrate snmC-seq2 which improves mapping, throughput and library complexity.

20 September 2018 | doi: 10.1038/s41467-018-06355-2
DNA methylation  DNA sequencing  Epigenomics 

Rechargeable potassium-ion batteries with honeycomb-layered tellurates as high voltage cathodes and fast potassium-ion conductors OPEN
Titus Masese, Kazuki Yoshii, Yoichi Yamaguchi, Toyoki Okumura, Zhen-Dong Huang, Minami Kato, Keigo Kubota, Junya Furutani, Yuki Orikasa, Hiroshi Senoh, Hikari Sakaebe & Masahiro Shikano

The development of potassium-ion batteries requires cathode materials that can maintain the structural stability during cycling. Here the authors have developed honeycomb-layered tellurates K2M2TeO6 that afford high ionic conductivity and reversible intercalation of large K ions at high voltages.

20 September 2018 | doi: 10.1038/s41467-018-06343-6
Batteries  Ceramics  Solid-phase synthesis 

Identification of active sites on supported metal catalysts with carbon nanotube hydrogen highways OPEN
Nicholas M. Briggs, Lawrence Barrett, Evan C. Wegener, Leidy V. Herrera, Laura A. Gomez, Jeffrey T. Miller & Steven P. Crossley

Understanding the location and nature of the catalytic active site is critical for controlling a catalyst’s activity and selectivity. Here, the authors separate the metal from the support by a controlled distance while maintaining the ability to promote defects via the use of carbon nanotube hydrogen highways.

20 September 2018 | doi: 10.1038/s41467-018-06100-9
Carbon nanotubes and fullerenes  Catalyst synthesis  Chemical engineering  Heterogeneous catalysis 

Frustrated endocytosis controls contractility-independent mechanotransduction at clathrin-coated structures OPEN
Francesco Baschieri, Stéphane Dayot, Nadia Elkhatib, Nathalie Ly, Anahi Capmany, Kristine Schauer, Timo Betz, Danijela Matic Vignjevic, Renaud Poincloux & Guillaume Montagnac

Cells sense mechanical properties of their environment using various cellular structures including focal adhesions. Here, the authors identify flat clathrin-coated structures (CCSs) as mechanosensitive signaling platforms that form independently of contractility and in response to substrate rigidity.

20 September 2018 | doi: 10.1038/s41467-018-06367-y
Cell adhesion  Cell biology 

Female mice lacking Ftx lncRNA exhibit impaired X-chromosome inactivation and a microphthalmia-like phenotype OPEN
Yusuke Hosoi, Miki Soma, Hirosuke Shiura, Takashi Sado, Hidetoshi Hasuwa, Kuniya Abe, Takashi Kohda, Fumitoshi Ishino & Shin Kobayashi

Although Ftx lncRNA has been linked to X-chromosome inactivation, its physiological roles in vivo remain unclear. Here the authors show that deletion of mouse Ftx causes eye abnormalities similar to human microphthalmia in a subset of female mice but rarely in males and provide evidence that Ftx plays a role in gene silencing on the inactive X chromosome.

20 September 2018 | doi: 10.1038/s41467-018-06327-6
Dosage compensation  Embryology  Epigenetic memory  Epigenetics 

Lung colonization by Aspergillus fumigatus is controlled by ZNF77 OPEN
Sara Gago, Nicola L. D. Overton, Nagwa Ben-Ghazzi, Lilyann Novak-Frazer, Nick D. Read, David W. Denning & Paul Bowyer

Aspergillus fumigatus regularly colonises the lungs but in the context of respiratory disease can be associated with increased pathology. Here the authors show mutations in ZNF77 result in altered bronchial epithelial characteristics and enhanced fungal burden.

20 September 2018 | doi: 10.1038/s41467-018-06148-7
Clinical microbiology  Fungal host response  Fungal infection  Fungi 

Endogenous metabolites of vitamin E limit inflammation by targeting 5-lipoxygenase OPEN
Helmut Pein, Alexia Ville, Simona Pace, Veronika Temml, Ulrike Garscha, Martin Raasch, Khaled Alsabil, Guillaume Viault, Chau-Phi Dinh, David Guilet, Fabiana Troisi, Konstantin Neukirch, Stefanie König, Rosella Bilancia, Birgit Waltenberger, Hermann Stuppner, Maria Wallert, Stefan Lorkowski, Christina Weinigel, Silke Rummler et al.

Vitamin E metabolites are proposed to have signalling capacity, but how they may regulate immune responses is still unclear. Here the authors show that a vitamin E metabolite, α-T-13′-COOH, can inhibit 5-lipoxygenase and thereby suppress the synthesis of lipid mediators of immune activation and inflammatory responses.

20 September 2018 | doi: 10.1038/s41467-018-06158-5
Granulocytes  Inflammatory diseases  Lipids  Pharmacology 

Copper-on-nitride enhances the stable electrosynthesis of multi-carbon products from CO2 OPEN
Zhi-Qin Liang, Tao-Tao Zhuang, Ali Seifitokaldani, Jun Li, Chun-Wei Huang, Chih-Shan Tan, Yi Li, Phil De Luna, Cao Thang Dinh, Yongfeng Hu, Qunfeng Xiao, Pei-Lun Hsieh, Yuhang Wang, Fengwang Li, Rafael Quintero-Bermudez, Yansong Zhou, Peining Chen, Yuanjie Pang, Shen-Chuan Lo, Lih-Juann Chen et al.

While multi-carbon (C2+) products present high-value species attainable from emitted carbon dioxide, it is challenging to prepare stable, C2+ selective catalysts. Here, authors support copper on copper nitride to improve copper’s electrocatalytic stability and selectivity toward C2+ synthesis.

20 September 2018 | doi: 10.1038/s41467-018-06311-0
Carbon capture and storage  Electrocatalysis 
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More science events from
  Latest Author Corrections    
Author Correction: An intercross population study reveals genes associated with body size and plumage color in ducks OPEN
Zhengkui Zhou , Ming Li, Hong Cheng, Wenlei Fan, Zhengrong Yuan, Qiang Gao, Yaxi Xu, Zhanbao Guo, Yunsheng Zhang, Jian Hu, Hehe Liu, Dapeng Liu, Weihuang Chen, Zhuqing Zheng, Yong Jiang, Zhiguo Wen, Yongming Liu, Hua Chen, Ming Xie, Qi Zhang et al.
25 September 2018 | doi: 10.1038/s41467-018-06521-6
Animal breeding  Genome evolution  Population genetics 

Author Correction: Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls OPEN
Cynthia M. Kallenbach, Serita D. Frey & A. Stuart Grandy
24 September 2018 | doi: 10.1038/s41467-018-06427-3

Author Correction: Commensal microflora-induced T cell responses mediate progressive neurodegeneration in glaucoma OPEN
Huihui Chen , Kin-Sang Cho, T. H. Khanh Vu, Ching-Hung Shen, Mandeep Kaur, Guochun Chen, Rose Mathew, M. Lisa McHam, Ahad Fazelat, Kameran Lashkari, Ngan Pan Bennett Au, Joyce Ka Yu Tse, Yingqian Li, Honghua Yu, Lanbo Yang, Joan Stein-Streilein, Chi Him Eddie Ma, Clifford J. Woolf, Mark T. Whary, Martine J. Jager et al.
20 September 2018 | doi: 10.1038/s41467-018-06428-2
Mucosal immunology  Neuroimmunology  Retina  T cells 

Author Correction: MYC-driven epigenetic reprogramming favors the onset of tumorigenesis by inducing a stem cell-like state OPEN
Vittoria Poli, Luca Fagnocchi, Alessandra Fasciani, Alessandro Cherubini, Stefania Mazzoleni, Sara Ferrillo, Annarita Miluzio, Gabriella Gaudioso, Valentina Vaira, Alice Turdo, Miriam Gaggianesi, Aurora Chinnici, Elisa Lipari, Silvio Bicciato, Silvano Bosari, Matilde Todaro & Alessio Zippo
20 September 2018 | doi: 10.1038/s41467-018-06480-y
Breast cancer  Histone post-translational modifications  Reprogramming  Transcriptional regulatory elements 

Author Correction: Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3 OPEN
Luigi Scietti, Antonella Chiapparino, Francesca De Giorgi, Marco Fumagalli, Lela Khoriauli, Solomon Nergadze, Shibom Basu, Vincent Olieric, Lucia Cucca, Blerida Banushi, Antonella Profumo, Elena Giulotto, Paul Gissen & Federico Forneris
20 September 2018 | doi: 10.1038/s41467-018-06481-x
Biochemistry  Enzymes  X-ray crystallography 
  Latest Publisher Corrections    
Publisher Correction: Hypermethylation of gene body CpG islands predicts high dosage of functional oncogenes in liver cancer OPEN
Maria Arechederra, Fabrice Daian, Annie Yim, Sehrish K. Bazai, Sylvie Richelme, Rosanna Dono, Andrew J. Saurin, Bianca H. Habermann & Flavio Maina
25 September 2018 | doi: 10.1038/s41467-018-06482-w
Cancer models  Hepatocellular carcinoma 

Publisher Correction: Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation OPEN
Éadaoin Harney, Hila May, Dina Shalem, Nadin Rohland, Swapan Mallick, Iosif Lazaridis, Rachel Sarig, Kristin Stewardson, Susanne Nordenfelt, Nick Patterson, Israel Hershkovitz & David Reich
20 September 2018 | doi: 10.1038/s41467-018-06484-8
Anthropology  Population genetics 

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