Wednesday, June 6, 2018

Nature Communications - 6 June 2018

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  Latest Editorial    
The future of plastic OPEN
05 June 2018 | doi: 10.1038/s41467-018-04565-2
  Latest Comment    
Making head or tail of cnidarian hox gene function OPEN
Fabian Rentzsch & Thomas W. Holstein

Hox genes are known to regulate head-tail axis patterning but their molecular role in animals diverged from the bilaterian lineage is unclear. Here, Fabian Rentzsch and Thomas W. Holstein comment on a paper by Mark Martindale and colleagues on the functional role of two Hox genes in axial patterning of the sea anemone.

05 June 2018 | doi: 10.1038/s41467-018-04585-y
Embryonic induction  Evolution  Evolutionary developmental biology 
  Latest Review View all Articles  
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  Latest Articles View all Articles  
Manipulating type-I and type-II Dirac polaritons in cavity-embedded honeycomb metasurfaces OPEN
Charlie-Ray Mann, Thomas J. Sturges, Guillaume Weick, William L. Barnes & Eros Mariani

Manipulating the properties of artificial graphene systems without changing the lattice has proven difficult. Here, Mann et al. theoretically show that changing the photonic environment alone can modify the fundamental properties of emergent massless Dirac polaritons in honeycomb metasurfaces.

06 June 2018 | doi: 10.1038/s41467-018-03982-7
Graphene  Metamaterials  Microwave photonics  Nanophotonics and plasmonics  Polaritons 

In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs OPEN
Mo Li, Mengxi Zheng, Siyu Wu, Cheng Tian, Di Liu, Yossi Weizmann, Wen Jiang, Guansong Wang & Chengde Mao

RNA nanostructures have been demonstrated in a range of biological applications, but their assembly and delivery to cells is difficult. Here the authors demonstrate the in vivo assembly of a RNA nanostructure from a single transcript inside the cellular environment.

06 June 2018 | doi: 10.1038/s41467-018-04652-4
RNA nanotechnology  Self-assembly 

Polysulfurating reagent design for unsymmetrical polysulfide construction OPEN
Xiao Xiao, Jiahui Xue & Xuefeng Jiang

Synthetic methods to access unsymmetrical polysulfides are limited despite their high biological relevance. Here, the authors disclose a polysulfurating reagent affording unsymmetrical di- and tri-sulfides under mild conditions, and suitable for late-stage modification of natural products.

06 June 2018 | doi: 10.1038/s41467-018-04306-5
Homogeneous catalysis  Synthetic chemistry methodology  Natural product synthesis 

Precise temporal regulation of alternative splicing during neural development OPEN
Sebastien M. Weyn-Vanhentenryck, Huijuan Feng, Dmytro Ustianenko, Rachel Duffié, Qinghong Yan, Martin Jacko, Jose C. Martinez, Marianne Goodwin, Xuegong Zhang, Ulrich Hengst, Stavros Lomvardas, Maurice S. Swanson & Chaolin Zhang

The precise timing of neurodevelopmental splicing switches and the underlying regulatory mechanisms remain poorly understood. This study identifies two major waves of developmental switches under the control of distinct combinations of RNA-binding proteins in central and peripheral nervous systems.

06 June 2018 | doi: 10.1038/s41467-018-04559-0
Alternative splicing  Neuronal development  Regulatory networks 

SETBP1 induces transcription of a network of development genes by acting as an epigenetic hub OPEN
Rocco Piazza , Vera Magistroni, Sara Redaelli, Mario Mauri, Luca Massimino, Alessandro Sessa, Marco Peronaci, Maciej Lalowski, Rabah Soliymani, Caterina Mezzatesta, Alessandra Pirola, Federica Banfi, Alicia Rubio, Delphine Rea, Fabio Stagno, Emilio Usala, Bruno Martino, Leonardo Campiotti, Michele Merli, Francesco Passamonti et al.

SETBP1 variants occur as somatic mutations in several malignancies and as de novo germline mutations in developmental disorders. Here the authors provide evidence that SETBP1 binds to gDNA in AT-rich promoter regions to promote target gene upregulation, indicating SETBP1 functions directly to regulate transcription.

06 June 2018 | doi: 10.1038/s41467-018-04462-8
Cancer genetics  Cancer models  Transcription 

A revised road map for the commitment of human cord blood CD34-negative hematopoietic stem cells OPEN
Keisuke Sumide, Yoshikazu Matsuoka, Hiroshi Kawamura, Ryusuke Nakatsuka, Tatsuya Fujioka, Hiroaki Asano, Yoshihiro Takihara & Yoshiaki Sonoda

Single CD34 negative haematopoietic stem cells (HSCs) can fully reconstitute lympho-myeloid hematopoiesis in mice. Here, using single cell transplantation and gene expression analyses, the authors show that CD34 negative HSCs lie at the apex of haematopoiesis in human cord blood and that they can give rise to erythroid megakaryocytic progenitors.

06 June 2018 | doi: 10.1038/s41467-018-04441-z
Cell growth  Haematopoietic stem cells 

Vms1p is a release factor for the ribosome-associated quality control complex OPEN
Olga Zurita Rendón, Eric K. Fredrickson, Conor J. Howard, Jonathan Van Vranken, Sarah Fogarty, Neal D. Tolley, Raghav Kalia, Beatriz A. Osuna, Peter S. Shen, Christopher P. Hill, Adam Frost & Jared Rutter

The ribosome-associated quality control complex (RQC) functions to disassemble stalled ribosomes. Here the authors find that the tRNA hydrolase Vms1 is involved in the release of nascent peptide from stalled ribosomes.

06 June 2018 | doi: 10.1038/s41467-018-04564-3
Mitochondria  Protein quality control 

The evolution of the temporal program of genome replication OPEN
Nicolas Agier, Stéphane Delmas, Qing Zhang, Aubin Fleiss, Yan Jaszczyszyn, Erwin van Dijk, Claude Thermes, Martin Weigt, Marco Cosentino-Lagomarsino & Gilles Fischer

Temporal programs of genome replication show different levels of conservation between closely or distantly related species. Here, the authors generate genome-wide replication timing profiles for ten yeast species, and analyze their evolutionary dynamics.

06 June 2018 | doi: 10.1038/s41467-018-04628-4
Evolutionary genetics  Functional genomics  Genome informatics 

Living functional hydrogels generated by bioorthogonal cross-linking reactions of azide-modified cells with alkyne-modified polymers OPEN
Koji Nagahama, Yuuka Kimura & Ayaka Takemoto

Cells are often passively encapsulated in hydrogels for a wide range of applications. Here, the authors report on a method of incorporating the cells into the hydrogel using bioorthogonal click reactions to link azide-modified cells with biocompatible polymers to create cell-based materials.

06 June 2018 | doi: 10.1038/s41467-018-04699-3
Biomaterials – cells  Cell biology  Gels and hydrogels 

Broken translational symmetry at edges of high-temperature superconductors OPEN
P. Holmvall, A. B. Vorontsov, M. Fogelström & T. Löfwander

Zero-energy flat bands indicate topological origin but their presence is usually energetically unfavorable. Here, Holmvall et al. propose an order parameter to quantify a phase transition associated with exotic topological properties in high-temperature superconductors hosting such flat bands.

06 June 2018 | doi: 10.1038/s41467-018-04531-y
Electronic properties and materials  Superconducting properties and materials 

Energy-temperature uncertainty relation in quantum thermodynamics OPEN
H. J. D. Miller & J. Anders

The energy-temperature uncertainty relation bounds the precision of simultaneously estimating energy and temperature of a system in equilibrium. In this article, the authors provide a generalised version which is valid for both classical and quantum systems, and at arbitrary coupling to the environment.

06 June 2018 | doi: 10.1038/s41467-018-04536-7
Quantum information  Quantum metrology  Statistical physics  Thermodynamics 

Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme OPEN
Noriyuki Nishimura, Wataru Tsuchiya, James J. Moresco, Yuki Hayashi, Kouji Satoh, Nahomi Kaiwa, Tomoko Irisa, Toshinori Kinoshita, Julian I. Schroeder, John R. Yates III, Takashi Hirayama & Toshimasa Yamazaki

The hormone abscisic acid (ABA) prevents seeds from germination when conditions are not suitable. Here the authors show that DOG1, a positive regulator of germination, impairs ABA signaling via genetic and physical interactions with the AHG1 phosphatase and that DOG1 binding to heme is required for this activity.

06 June 2018 | doi: 10.1038/s41467-018-04437-9
Plant hormones  Plant signalling 

Mapping higher-order relations between brain structure and function with embedded vector representations of connectomes OPEN
Gideon Rosenthal, František Váša, Alessandra Griffa, Patric Hagmann, Enrico Amico, Joaquín Goñi, Galia Avidan & Olaf Sporns

The function of a brain region is determined by the network it is embedded in. Here the authors implement the word2vec algorithm for connectomes generating a vector embedding of the connectivity structure for each node allowing inference about functional relationships between brain regions.

05 June 2018 | doi: 10.1038/s41467-018-04614-w
Network models  Visual system 

Spatial self-organization resolves conflicts between individuality and collective migration OPEN
X. Fu, S. Kato, J. Long, H. H. Mattingly, C. He, D. C. Vural, S. W. Zucker & T. Emonet

How bacteria migrate collectively despite individual phenotypic variation is not understood. Here, the authors show that cells spontaneously sort themselves within moving bands such that variations in individual tumble bias, a determinant of gradient climbing speed, are compensated by the local gradient steepness experienced by individuals.

05 June 2018 | doi: 10.1038/s41467-018-04539-4
Bacterial systems biology  Cellular noise  Chemotaxis  Collective cell migration 

Composite regulation of ERK activity dynamics underlying tumour-specific traits in the intestine OPEN
Yu Muta, Yoshihisa Fujita, Kenta Sumiyama, Atsuro Sakurai, M. Mark Taketo, Tsutomu Chiba, Hiroshi Seno, Kazuhiro Aoki, Michiyuki Matsuda & Masamichi Imajo

The ERK signalling pathway regulates homeostasis of the intestinal epithelium. Here the authors identify two modes of ERK activity generated independently from EGFR and ErbB2 receptor and whose balance in cancer is shifted by Wnt pathway activation, resulting in enhanced sensitivity to EGFR inhibitors.

05 June 2018 | doi: 10.1038/s41467-018-04527-8
Colorectal cancer  Fluorescence imaging  Growth factor signalling 

Variable number of TMC1-dependent mechanotransducer channels underlie tonotopic conductance gradients in the cochlea OPEN
Maryline Beurg, Runjia Cui, Adam C. Goldring, Seham Ebrahim, Robert Fettiplace & Bechara Kachar

Mechanoelectrical transduction channel (MET) current found in stereocilia of hair cells matures over the first postnatal week. Here the authors look at the contribution of transmembrane channel-like protein 1 and 2 (TMC1 and TMC2) to MET current during development of tonotopic gradients.

05 June 2018 | doi: 10.1038/s41467-018-04589-8
Hair cell  Neuroscience 

Observation of an anti-PT-symmetric exceptional point and energy-difference conserving dynamics in electrical circuit resonators OPEN
Youngsun Choi, Choloong Hahn, Jae Woong Yoon & Seok Ho Song

The study of parity-time (PT) symmetric optical systems has recently attracted much attention. Here, the authors experimentally study an anti-PT symmetric circuit system and observe an exceptional point with an inverse PT symmetry breaking transition and energy-difference conserving dynamics.

05 June 2018 | doi: 10.1038/s41467-018-04690-y
Electronic and spintronic devices  Microwave photonics  Optical physics 

Gut vagal sensory signaling regulates hippocampus function through multi-order pathways OPEN
Andrea N. Suarez, Ted M. Hsu, Clarissa M. Liu, Emily E. Noble, Alyssa M. Cortella, Emily M. Nakamoto, Joel D. Hahn, Guillaume de Lartigue & Scott E. Kanoski

Feeding-relevant vagal signaling occurs between the gastrointestinal tract and the brain, but it is unclear if this pathway influences cognitive processes. This study shows that endogenous gastrointestinal derived vagal sensory signaling promotes hippocampal-dependent memory function via a multi-order brainstem–septal pathway.

05 June 2018 | doi: 10.1038/s41467-018-04639-1
Feeding behaviour  Hippocampus  Learning and memory  Neural circuits  Neuroscience 

Amplitude mode in the planar triangular antiferromagnet Na0.9MnO2 OPEN
Rebecca L. Dally, Yang Zhao, Zhijun Xu, Robin Chisnell, M. B. Stone, Jeffrey W. Lynn, Leon Balents & Stephen D. Wilson

Oscillations of the order parameter amplitude in magnetically ordered materials provide condensed matter analogues of the Higgs boson but in most cases they are unstable. Dally et al. show that the quasi-one-dimensional magnet α-Na0.9MnO2 supports stable amplitude excitations.

05 June 2018 | doi: 10.1038/s41467-018-04601-1
Condensed-matter physics  Magnetic properties and materials 

Vapor transport deposition of antimony selenide thin film solar cells with 7.6% efficiency OPEN
Xixing Wen, Chao Chen, Shuaicheng Lu, Kanghua Li, Rokas Kondrotas, Yang Zhao, Wenhao Chen, Liang Gao, Chong Wang, Jun Zhang, Guangda Niu & Jiang Tang

Antimony selenide possess several advantages for solar cell applications but state-of-the-art vapor transport deposition methods suffer from poor film quality. Here Wen et al. develop a fast and cheap method to reduce the defect density by 10 times and achieve a certified power conversion efficiency of 7.6%.

05 June 2018 | doi: 10.1038/s41467-018-04634-6
Electronics, photonics and device physics  Solar cells 

In vivo base editing of post-mitotic sensory cells OPEN
Wei-Hsi Yeh, Hao Chiang, Holly A. Rees, Albert S. B. Edge & David R. Liu

Base editing allows the precise introduction of point mutations into cellular DNA without requiring double-stranded DNA breaks or homology-directed repair, which is inefficient in postmitotic cells. Here the authors demonstrate in vivo base editing of post-mitotic somatic cells in the postnatal mouse inner ear with physiological outcomes.

05 June 2018 | doi: 10.1038/s41467-018-04580-3
CRISPR-Cas9 genome editing  Gene targeting  Genetic engineering 

Mapping uncharted territory in ice from zeolite networks to ice structures OPEN
Edgar A. Engel, Andrea Anelli, Michele Ceriotti, Chris J. Pickard & Richard J. Needs

Ice is one of the most well-studied condensed matter systems, yet new phases are still being discovered. Here the authors report a large-scale computational study of the configuration space of water ice, creating a navigable “sketch-map” including new predicted phases as well as relationships between different structures.

05 June 2018 | doi: 10.1038/s41467-018-04618-6
Chemical physics  Computational methods  Structure of solids and liquids 

Upconversion nanocomposite for programming combination cancer therapy by precise control of microscopic temperature OPEN
Xingjun Zhu, Jiachang Li, Xiaochen Qiu, Yi Liu, Wei Feng & Fuyou Li

The combination of chemo and photothermal therapy is widely used to treat cancer but control of chemo and thermal effects is needed for optimized treatment. Here, the authors describe an upconversion nanoparticle which can be used for controlled sequential treatment by controlling laser power.

05 June 2018 | doi: 10.1038/s41467-018-04571-4
Chemotherapy  Nanoparticles  Targeted therapies 

The homeobox protein VentX reverts immune suppression in the tumor microenvironment OPEN
Yi Le, Hong Gao, Ronald Bleday & Zhenglun Zhu

Tumour associated macrophages (TAMs) polarize into either pro-tumor or anti-tumor phenotypes. Here the authors show that the homeobox protein VentX is downregulated in clinical samples of colorectal cancer and regulates TAMs plasticity with its forced re-expression converting TAMs into an anti-tumor phenotype.

05 June 2018 | doi: 10.1038/s41467-018-04567-0
Cancer immunotherapy  Colon cancer 

Overpumping leads to California groundwater arsenic threat OPEN
Ryan Smith, Rosemary Knight & Scott Fendorf

Groundwater resources are coming under increasing pressure leading to water quality loss. Here, the authors find that recent groundwater pumping has led to increasing arsenic concentrations in the San Joaquin Valley, California aquifers from arsenic residing in the pore water of clay strata released by overpumping.

05 June 2018 | doi: 10.1038/s41467-018-04475-3
Geochemistry  Hydrology  Water resources 

Combined Rho-kinase inhibition and immunogenic cell death triggers and propagates immunity against cancer OPEN
Gi-Hoon Nam, Eun Jung Lee, Yoon Kyoung Kim, Yeonsun Hong, Yoonjeong Choi, Myung-Jeom Ryu, Jiwan Woo, Yakdol Cho, Dong June Ahn, Yoosoo Yang, Ick-Chan Kwon, Seung-Yoon Park & In-San Kim

Activation of an immune response is critical for the efficacy of cancer therapies. Here, the authors show that combination of ROCK inhibitor with chemotherapeutics that induce immunogenic cell death of cancer cells leads to increased dendritic cells’ maturation and synergistic CD8+ cytotoxic T cell priming and infiltration into the tumours, leading to suppressed tumour growth and improved overall survival in syngeneic and genetically engineered tumour models.

04 June 2018 | doi: 10.1038/s41467-018-04607-9
Cancer  Oncology 

Laminin heparin-binding peptides bind to several growth factors and enhance diabetic wound healing OPEN
Jun Ishihara, Ako Ishihara, Kazuto Fukunaga, Koichi Sasaki, Michael J. V. White, Priscilla S. Briquez & Jeffrey A. Hubbell

Laminins are important regulators of epidermal wound healing. Here, the authors show that laminins bind to multiple growth factors via their heparin-binding domains, and that incorporation of these domains into fibrin matrices increases growth factor retention, promoting wound healing in type 2 diabetic mouse models.

04 June 2018 | doi: 10.1038/s41467-018-04525-w
Diabetes complications  Extracellular matrix  Regenerative medicine 

Artificial strain of human prions created in vitro OPEN
Chae Kim, Xiangzhu Xiao, Shugui Chen, Tracy Haldiman, Vitautas Smirnovas, Diane Kofskey, Miriam Warren, Krystyna Surewicz, Nicholas R. Maurer, Qingzhong Kong, Witold Surewicz & Jiri G. Safar

Synthetic prions have previously been generated from recombinant rodent PrP. Here the authors generate synthetic human prions, by seeding human PrP with CJD prions, and characterize its infectivity in mice.

04 June 2018 | doi: 10.1038/s41467-018-04584-z
Neurodegeneration  Prion diseases  Prions 

Dynamics of self-reorganization explains passivation of silicate glasses OPEN
Stéphane Gin, Marie Collin, Patrick Jollivet, Maxime Fournier, Yves Minet, Laurent Dupuy, Thiruvilla Mahadevan, Sebastien Kerisit & Jincheng Du

Deciphering the dissolution process of silicate glasses and minerals from atomic to macroscopic scales is a major challenge. Here, the authors explain the passivating properties of the gel layer by its reorganization, which is a key mechanism accounting for very low apparent water diffusivity.

04 June 2018 | doi: 10.1038/s41467-018-04511-2
Gels and hydrogels  Glasses 

Seamlessly fused digital-analogue reconfigurable computing using memristors OPEN
Alexantrou Serb, Ali Khiat & Themistoklis Prodromakis

Conventional analogue and digital circuits are mixed at signal level yet remain technologically separate, adding complexity and cost. This work introduces a new design paradigm where the analogue and digital worlds are seamlessly fused via memristors, enabling electronics with reconfigurability.

04 June 2018 | doi: 10.1038/s41467-018-04624-8
Electrical and electronic engineering  Electronic devices 

Pancharatnam–Berry phase in condensate of indirect excitons OPEN
J. R. Leonard, A. A. High, A. T. Hammack, M. M. Fogler, L. V. Butov, K. L. Campman & A. C. Gossard

Geometric phases in matter are of fundamental interest. Here the authors observe the Pancharatnam–Berry phase in matter waves by imaging light interference patterns from cold gases of indirect excitons and find long-range coherent spin transport in the system.

04 June 2018 | doi: 10.1038/s41467-018-04667-x
Condensed-matter physics  Polaritons 

Planar cell polarity signalling coordinates heart tube remodelling through tissue-scale polarisation of actomyosin activity OPEN
Anne Margarete Merks, Marie Swinarski, Alexander Matthias Meyer, Nicola Victoria Müller, Ismail Özcan, Stefan Donat, Alexa Burger, Stephen Gilbert, Christian Mosimann, Salim Abdelilah-Seyfried & Daniela Panáková

The molecular mechanisms underlying cardiac chamber formation are not well understood. Here, the authors show that planar cell polarity signalling through Wnt5b and Wnt11 coordinates localised and tissue-scale polarised actomyosin contractility in the zebrafish heart, regulating cardiac chamber formation and looping.

04 June 2018 | doi: 10.1038/s41467-018-04566-1
Developmental biology  Morphogenesis 

Resolving molecule-specific information in dynamic lipid membrane processes with multi-resonant infrared metasurfaces OPEN
Daniel Rodrigo, Andreas Tittl, Nadine Ait-Bouziad, Aurelian John-Herpin, Odeta Limaj, Christopher Kelly, Daehan Yoo, Nathan J. Wittenberg, Sang-Hyun Oh, Hilal A. Lashuel & Hatice Altug

Complex protein-lipid interactions are difficult to study in real-time without labels. Here, Rodrigo et al. introduce a multimodal plasmonic infrared biosensor to simultaneously distinguish multiple analytes with high sensitivity.

04 June 2018 | doi: 10.1038/s41467-018-04594-x
Applied optics  Biosensors  Metamaterials  Nanophotonics and plasmonics 

Double quantum criticality in superconducting tin arrays-graphene hybrid OPEN
Yinbo Sun, Hong Xiao, Miao Zhang, Zhongying Xue, Yongfeng Mei, Xiaoming Xie, Tao Hu, Zengfeng Di & Xi Wang

Two quantum critical behaviors appear in a two dimensional electron gas (2DEG) but its origin remains to be attested. Here, Sun et al. construct superconducting puddles-2DEG hybrid system by depositing tin nano-islands array on monolayer graphene where the two quantum critical behaviors are reproduced, suggesting the formation of inhomogeneous superconducting 2DEG.

04 June 2018 | doi: 10.1038/s41467-018-04606-w
Electronic properties and devices  Superconducting properties and materials 

Live cyanobacteria produce photocurrent and hydrogen using both the respiratory and photosynthetic systems OPEN
Gadiel Saper, Dan Kallmann, Felipe Conzuelo, Fangyuan Zhao, Tünde N. Tóth, Varda Liveanu, Sagit Meir, Jedrzej Szymanski, Asaph Aharoni, Wolfgang Schuhmann, Avner Rothschild, Gadi Schuster & Noam Adir

Biologically ### produced electrical currents and hydrogen are new energy sources. Here, the authors find that low presser microfluidizer treatment produced cyanobacterium that can utilize electrons from respiratory and photosynthesis to promote current and hydrogen generation, without the addition of exogenous electron mediators.

04 June 2018 | doi: 10.1038/s41467-018-04613-x
Bioenergetics  Bioenergy 

Model structures amplify uncertainty in predicted soil carbon responses to climate change OPEN
Zheng Shi, Sean Crowell, Yiqi Luo & Berrien Moore III

A substantial portion of model uncertainty arises from model parameters and structures. Here, the authors show that alternative model structures with data-driven parameters project greater uncertainty in soil carbon responses to climate change than the conventional soil carbon model.

04 June 2018 | doi: 10.1038/s41467-018-04526-9
Carbon cycle  Climate-change ecology 

Cotransporter-mediated water transport underlying cerebrospinal fluid formation OPEN
Annette B. Steffensen, Eva K. Oernbo, Anca Stoica, Niklas J. Gerkau, Dagne Barbuskaite, Katerina Tritsaris, Christine R. Rose & Nanna MacAulay

Osmotic forces do not suffice to explain the rate of cerebrospinal fluid (CSF) production. Here, the authors show that the Na+/K+/2Cl cotransporter in the choroid plexus contributes substantially to CSF production via its inherent ability to cotransport water.

04 June 2018 | doi: 10.1038/s41467-018-04677-9
Blood–brain barrier  Molecular neuroscience  Neurophysiology 

Targeting repair pathways with small molecules increases precise genome editing in pluripotent stem cells OPEN
Stephan Riesenberg & Tomislav Maricic

Small molecule inhibitors can influence the choice of repair pathways, enhancing nucleotide substitution and gene integration in CRISPR-mediated genome editing. Here the authors introduce CRISPY, a mix of small molecules that can enhance precise editing with Cpf1 and Cas9D10A in hiPSCs.

04 June 2018 | doi: 10.1038/s41467-018-04609-7
CRISPR-Cas systems  Small molecules  Stem-cell biotechnology 

Crosslinking of fibrous hydrogels OPEN
Daniël C. Schoenmakers, Alan E. Rowan & Paul H. J. Kouwer

Unlike synthetic hydrogels, biological gels are made of fibrous networks which give rise to unique properties, such as high porosity and mechanical responsiveness. Here the authors use polyisocyanide-based gels and selectively crosslink inside the bundles to lock the fibrous network and thus control the architecture and the mechanics.

04 June 2018 | doi: 10.1038/s41467-018-04508-x
Bioinspired materials  Biomedical materials  Materials chemistry  Polymer chemistry  Soft materials 

Variability in the location of high frequency oscillations during prolonged intracranial EEG recordings OPEN
Stephen V. Gliske, Zachary T. Irwin, Cynthia Chestek, Garnett L. Hegeman, Benjamin Brinkmann, Oren Sagher, Hugh J. L. Garton, Greg A. Worrell & William C. Stacey

High frequency oscillations (HFO) are a promising biomarker for identifying epileptogenic zones without the need to monitor spontaneous seizure episodes. Here the authors report that there is much variability in the location of HFOs offering a note of caution toward using HFO locations from short recordings as a guide for surgery.

01 June 2018 | doi: 10.1038/s41467-018-04549-2
Diagnostic markers  Epilepsy 

Total synthesis of cyrneines A–B and glaucopine C OPEN
Guo-Jie Wu, Yuan-He Zhang, Dong-Xing Tan & Fu-She Han

Cyrneine diterpenoids represent a biologically important subfamily of cyathane-type diterpenoids. Here, the authors show new key steps to access their 5-6-7-tricyclic core and establish a more step-economic synthesis of cyrneine A and the first synthesis of cyrneine B and glaucopine C in a divergent manner.

01 June 2018 | doi: 10.1038/s41467-018-04480-6
Homogeneous catalysis  Synthetic chemistry methodology  Natural product synthesis 

Tet1 and Tet2 maintain mesenchymal stem cell homeostasis via demethylation of the P2rX7 promoter OPEN
Ruili Yang, Tingting Yu, Xiaoxing Kou, Xiang Gao, Chider Chen, Dawei Liu, Yanheng Zhou & Songtao Shi

Tet-mediated DNA oxidation converts 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), which is essential to regulate different biological processes. Here the authors show that Tet1 and Tet2 regulate mesenchymal stem cell and bone homeostasis through demethylation of P2rX7 promoter.

01 June 2018 | doi: 10.1038/s41467-018-04464-6
Bone development  DNA methylation  Mesenchymal stem cells  miRNAs 

Dynamic structural states of ClpB involved in its disaggregation function OPEN
Takayuki Uchihashi, Yo-hei Watanabe, Yosuke Nakazaki, Takashi Yamasaki, Hiroki Watanabe, Takahiro Maruno, Kentaro Ishii, Susumu Uchiyama, Chihong Song, Kazuyoshi Murata, Ryota Iino & Toshio Ando

The bacterial protein disaggregation machine ClpB uses ATP to generate mechanical force to unfold and thread its protein substrates. Here authors visualize the ClpB ring using high-speed atomic force microscopy and capture conformational changes of the hexameric ring during the ATPase reaction.

01 June 2018 | doi: 10.1038/s41467-018-04587-w
Atomic force microscopy  Enzyme mechanisms  Single-molecule biophysics 

Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis OPEN
Ryota Yamagami, Jamie L. Bingaman, Erica A. Frankel & Philip C. Bevilacqua

The concentration of divalent cations is well-known to influence molecular processes such as enzymatic activity and RNA folding. Here the authors attempt to reproduce physiological conditions for RNA folding in vitro and establish an important contribution of chelated magnesium ions in enhancing RNA function.

01 June 2018 | doi: 10.1038/s41467-018-04415-1
Biophysical chemistry  RNA 

Recurrent rearrangements of FOS and FOSB define osteoblastoma OPEN
Matthew W. Fittall , William Mifsud, Nischalan Pillay, Hongtao Ye, Anna-Christina Strobl, Annelien Verfaillie, Jonas Demeulemeester, Lei Zhang, Fitim Berisha, Maxime Tarabichi, Matthew D. Young, Elena Miranda, Patrick S. Tarpey, Roberto Tirabosco, Fernanda Amary, Agamemnon E. Grigoriadis, Michael R. Stratton, Peter Van Loo, Cristina R. Antonescu, Peter J. Campbell et al.

FOS has been linked to bone tumour pathogenesis, and viral homologue v-fos causes osteosarcoma in mice. Here, the authors report rearrangement of FOS and its paralogue FOSB in osteoblastoma and osteoid osteoma, revealing human bone tumours that are defined by mutations of FOS and FOSB.

01 June 2018 | doi: 10.1038/s41467-018-04530-z
Bone cancer  Cancer genomics  Diagnostic markers 

Mucosal-associated invariant T cells are a profibrogenic immune cell population in the liver OPEN
Pushpa Hegde, Emmanuel Weiss, Valérie Paradis, Jinghong Wan, Morgane Mabire, Sukriti Sukriti, Pierre-Emmanuel Rautou, Miguel Albuquerque, Olivia Picq, Abhishak Chandra Gupta, Gladys Ferrere, Hélène Gilgenkrantz, Badr Kiaf, Amine Toubal, Lucie Beaudoin, Philippe Lettéron, Richard Moreau, Agnès Lehuen & Sophie Lotersztajn

Hepatic fibrosis represents the liver response to chronic injury and can lead to cirrhosis. Here the authors show that mucosal-associated invariant T cells mediate chronic inflammation and fibrogenesis in the liver by inducing a proinflammatory phenotype in macrophages and myofibroblasts and proliferation of the latter.

01 June 2018 | doi: 10.1038/s41467-018-04450-y
Immunology  Physiology 

Operando monitoring the lithium spatial distribution of lithium metal anodes OPEN
Shasha Lv, Tomas Verhallen, Alexandros Vasileiadis, Frans Ooms, Yaolin Xu, Zhaolong Li, Zhengcao Li & Marnix Wagemaker

Rechargeable lithium metal batteries could offer a major leap in energy capacity but suffer from the electrolyte reactivity and dendrite growth. Here the authors apply neutron depth profiling to provide quantitative insight into the evolution of the Li-metal morphology during plating and stripping.

01 June 2018 | doi: 10.1038/s41467-018-04394-3
Chemistry  Energy science and technology  Materials science 

Protein disorder–order interplay to guide the growth of hierarchical mineralized structures OPEN

There is evidence that disordered proteins play a role in the mineralization process. Here, the authors report on the development of elastin-like recombinant protein membranes using disordered-ordered interplay to investigate and guide mineralization.

01 June 2018 | doi: 10.1038/s41467-018-04319-0
Bioinspired materials  Biomimetic synthesis  Biomineralization 

Reward probability and timing uncertainty alter the effect of dorsal raphe serotonin neurons on patience OPEN
Katsuhiko Miyazaki, Kayoko W. Miyazaki, Akihiro Yamanaka, Tomoki Tokuda, Kenji F. Tanaka & Kenji Doya

Activation of serotonin neurons in the dorsal raphe nucleus promotes patience in waiting for future rewards. Here the authors show that this effect is maximal for high probability reward or high temporal reward uncertainty suggesting that it boosts the prior probability of reward.

01 June 2018 | doi: 10.1038/s41467-018-04496-y
Decision  Motivation  Operant learning  Reward 

Species traits and network structure predict the success and impacts of pollinator invasions OPEN
Fernanda S. Valdovinos, Eric L. Berlow, Pablo Moisset de Espanés, Rodrigo Ramos-Jiliberto, Diego P. Vázquez & Neo D. Martinez

The role of adaptive foraging in the threat of invasive pollinators to plant-pollinator systems is difficult to characterise. Here, Valdavinos et al. use network modelling to show the importance of foraging efficiency, diet overlap, plant species visitation, and degree of specialism in native pollinators.

31 May 2018 | doi: 10.1038/s41467-018-04593-y
Ecological modelling  Ecological networks  Food webs  Invasive species 

ADAR1-mediated regulation of melanoma invasion OPEN
Yael Nemlich, Erez Nissim Baruch, Michal Judith Besser, Einav Shoshan, Menashe Bar-Eli, Liat Anafi, Iris Barshack, Jacob Schachter, Rona Ortenberg & Gal Markel

In metastatic melanoma, ADAR1 is downregulated, facilitating proliferation. Here, the authors show an ADAR1-dependent and RNA-editing-independent regulation of melanoma invasion mediated by ITGB3 expression, which can be reversed when ITGB3 is blocked.

31 May 2018 | doi: 10.1038/s41467-018-04600-2
Cell invasion  Melanoma 

Uncertainty about social interactions leads to the evolution of social heuristics OPEN
Pieter van den Berg & Tom Wenseleers

Humans are known to use social heuristics to make intuitive decisions on whether to cooperate. Here, the authors show with evolutionary simulations that social heuristics can be an adaptive solution to uncertainties about the consequences of cooperation and can greatly increase cooperation levels.

31 May 2018 | doi: 10.1038/s41467-018-04493-1
Evolutionary theory  Human behaviour  Social evolution 
  Latest Correspondence    
On the role of STAT1 and STAT6 ADP-ribosylation in the regulation of macrophage activation OPEN
Andreas Begitt, James Cavey, Mathias Droescher & Uwe Vinkemeier
01 June 2018 | doi: 10.1038/s41467-018-04522-z
Cell signalling  Cytokines 
  Latest Author Corrections    
Author Correction: RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia OPEN
Jason X. Cheng, Li Chen, Yuan Li, Adam Cloe, Ming Yue, Jiangbo Wei, Kenneth A. Watanabe, Jamile M. Shammo, John Anastasi, Qingxi J. Shen, Richard A. Larson, Chuan He, Michelle M. Le Beau & James W. Vardiman
06 June 2018 | doi: 10.1038/s41467-018-04518-9
Haematological cancer  Oncology 

Author Correction: ID3 regulates the MDC1-mediated DNA damage response in order to maintain genome stability OPEN
Jung-Hee Lee, Seon-Joo Park, Gurusamy Hariharasudhan, Min-Ji Kim, Sung Mi Jung, Seo-Yeon Jeong, In-Youb Chang, Cheolhee Kim, Eunae Kim, Jihyeon Yu, Sangsu Bae & Ho Jin You
06 June 2018 | doi: 10.1038/s41467-018-04599-6
DNA damage response  Double-strand DNA breaks 

Author Correction: High frequency temperature variability reduces the risk of coral bleaching OPEN
Aryan Safaie, Nyssa J. Silbiger, Timothy R. McClanahan, Geno Pawlak, Daniel J. Barshis, James L. Hench, Justin S. Rogers, Gareth J. Williams & Kristen A. Davis
05 June 2018 | doi: 10.1038/s41467-018-04741-4
Climate-change ecology  Marine biology  Physical oceanography 

Author Correction: HIV-1 counteracts an innate restriction by amyloid precursor protein resulting in neurodegeneration OPEN
Qingqing Chai, Vladimir Jovasevic, Viacheslav Malikov, Yosef Sabo, Scott Morham, Derek Walsh & Mojgan H. Naghavi
05 June 2018 | doi: 10.1038/s41467-018-04750-3
HIV infections  Mechanisms of disease  Neurodegenerative diseases  Virus–host interactions 

Author Correction: Ultra-thin enzymatic liquid membrane for CO2 separation and capture OPEN
Yaqin Fu, Ying-Bing Jiang, Darren Dunphy, Haifeng Xiong, Eric Coker, Stan Chou, Hongxia Zhang, Juan M. Vanegas, Jonas G. Croissant, Joseph L. Cecchi, Susan B. Rempe & C. Jeffrey Brinker
01 June 2018 | doi: 10.1038/s41467-018-04642-6
Bioinspired materials  Carbon capture and storage  Chemical engineering  Materials chemistry 

Author Correction: Spatial fidelity of workers predicts collective response to disturbance in a social insect OPEN
James D. Crall, Nick Gravish, Andrew M. Mountcastle, Sarah D. Kocher, Robert L. Oppenheimer, Naomi E. Pierce & Stacey A. Combes
31 May 2018 | doi: 10.1038/s41467-018-04598-7
Behavioural ecology  Entomology  Social behaviour  Social evolution 

Author Correction: Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting OPEN
Wiebke Manuela Schulze, Frank Stein, Mandy Rettel, Max Nanao & Stephen Cusack
31 May 2018 | doi: 10.1038/s41467-018-04643-5
RNA-binding proteins  RNA metabolism  X-ray crystallography 
  Latest Publisher Corrections    
Publisher Correction: Imaging the square of the correlated two-electron wave function of a hydrogen molecule OPEN
M. Waitz , R. Y. Bello, D. Metz, J. Lower, F. Trinter, C. Schober, M. Keiling, U. Lenz, M. Pitzer, K. Mertens, M. Martins, J. Viefhaus, S. Klumpp, T. Weber, L. Ph. H. Schmidt, J. B. Williams, M. S. Schöffler, V. V. Serov, A. S. Kheifets, L. Argenti et al.
05 June 2018 | doi: 10.1038/s41467-018-04740-5

Publisher Correction: 78,000-year-old record of Middle and Later Stone Age innovation in an East African tropical forest OPEN
Ceri Shipton , Patrick Roberts, Will Archer, Simon J. Armitage, Caesar Bita, James Blinkhorn, Colin Courtney-Mustaphi, Alison Crowther, Richard Curtis, Francesco d’ Errico, Katerina Douka, Patrick Faulkner, Huw S. Groucutt, Richard Helm, Andy I. R. Herries, Severinus Jembe, Nikos Kourampas, Julia Lee-Thorp, Rob Marchant, Julio Mercader et al.
05 June 2018 | doi: 10.1038/s41467-018-04753-0
Archaeology  Palaeoecology 

Publisher Correction: Stabilizing spin spirals and isolated skyrmions at low magnetic field exploiting vanishing magnetic anisotropy OPEN
Marie Hervé, Bertrand Dupé, Rafael Lopes, Marie Böttcher, Maximiliano D. Martins, Timofey Balashov, Lukas Gerhard, Jairo Sinova & Wulf Wulfhekel
01 June 2018 | doi: 10.1038/s41467-018-04680-0
Ferromagnetism  Spintronics  Surfaces, interfaces and thin films 

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