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Nature Communications - 16 May 2018

 
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Nominations are now open for the $1Million 2018 Health Category of Al-Sumait Prize for African Development. Nominations are accepted for Institutions or Individuals advancing Health in Africa. The nominations period closes on June 30 2018. Conditions, requirements and a link to the nomination form can be found below. 

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  Latest Editorial    
 
Let there be laser light OPEN

Today, on the 16th May, we celebrate the first International Day of Light, which UNESCO proclaimed late last year. We celebrate the central role light and light-based technologies play in our lives and consider how they can be beneficial to humanity through sustainable lighting, renewable energy and improved health care.

16 May 2018 | doi: 10.1038/s41467-018-04302-9
 
  Latest Perspective    
 
Quantifying climate feedbacks in polar regions OPEN
Hugues Goosse, Jennifer E. Kay, Kyle C. Armour, Alejandro Bodas-Salcedo, Helene Chepfer, David Docquier, Alexandra Jonko, Paul J. Kushner, Olivier Lecomte, François Massonnet, Hyo-Seok Park, Felix Pithan, Gunilla Svensson & Martin Vancoppenolle

Estimating the magnitude of radiative and non-radiative feedbacks is key for understanding the climate dynamics of polar regions. Here the authors propose an inclusive methodology to quantify the influence of all those feedbacks, stimulating more systematic analyses in observational and model ensembles.

15 May 2018 | doi: 10.1038/s41467-018-04173-0
Atmospheric science  Climate and Earth system modelling  Cryospheric science  Physical oceanography 
 
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The CRISPR tool kit for genome editing and beyond OPEN
Mazhar Adli

CRISPR has rapidly become an indispensable tool for biological research. Here Mazhar Adli reviews the current toolbox for editing and manipulating the genome and looks toward future developments in this fast moving field.

15 May 2018 | doi: 10.1038/s41467-018-04252-2
CRISPR-Cas systems  Genomic engineering 
 
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  Latest Articles View all Articles  
 
Myosin1D is an evolutionarily conserved regulator of animal left–right asymmetry OPEN
Thomas Juan, Charles Géminard, Jean-Baptiste Coutelis, Delphine Cerezo, Sophie Polès, Stéphane Noselli & Maximilian Fürthauer

Left-right (LR) axis specification is essential for embryonic patterning but a unifying mechanism across organisms has not been identified. Here, the authors show that Myosin1D, known to regulate Drosophila LR asymmetry, controls zebrafish LR Organizer function, and is therefore a conserved regulator of animal laterality.

16 May 2018 | doi: 10.1038/s41467-018-04284-8
Body patterning  Pattern formation 

Thirty loci identified for heart rate response to exercise and recovery implicate autonomic nervous system OPEN
Julia Ramírez, Stefan van Duijvenboden, Ioanna Ntalla, Borbala Mifsud, Helen R Warren, Evan Tzanis, Michele Orini, Andrew Tinker, Pier D. Lambiase & Patricia B. Munroe

Genome-wide association studies have identified multiple loci for resting heart rate (HR) but the genetic factors associated with HR increase during and HR recovery after exercise are less well studied. Here, the authors examine both traits in a two-stage GWAS design in up to 67,257 individuals from UK Biobank.

16 May 2018 | doi: 10.1038/s41467-018-04148-1
Cardiovascular genetics  Genetics of the nervous system  Genome-wide association studies  Physiology 

A joint view on genetic variants for adiposity differentiates subtypes with distinct metabolic implications OPEN
Thomas W Winkler, Felix Günther, Simon Höllerer, Martina Zimmermann, Ruth JF Loos, Zoltán Kutalik & Iris M Heid

In GWAS, waist-to-hip ratio (WHR) is often adjusted for body mass index (BMI) to account for their correlation (WHRadjBMI). Here, Winkler et al. classify 159 genetic variants for BMI, WHR, or WHRadjBMI based on their effect directions for BMI and WHR to differentiate subtypes of adiposity genetics.

16 May 2018 | doi: 10.1038/s41467-018-04124-9
Genome-wide association studies  Metabolic diseases  Quantitative trait 

A cell-penetrating artificial metalloenzyme regulates a gene switch in a designer mammalian cell OPEN
Yasunori Okamoto, Ryosuke Kojima, Fabian Schwizer, Eline Bartolami, Tillmann Heinisch, Stefan Matile, Martin Fussenegger & Thomas R. Ward

Artificial enzymes can be used to elicit reactions in cells. Here, the authors developed such an artificial catalyst combined with a genetic switch, and showed that it was readily taken up by human cells and able to kick off a reaction cascade resulting in the biosynthesis of the desired product.

16 May 2018 | doi: 10.1038/s41467-018-04440-0
Biocatalysis  Gene regulation  Synthetic biology 

Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width OPEN
Ziwei Dai, Samantha J. Mentch, Xia Gao, Sailendra N. Nichenametla & Jason W. Locasale

Methionine availability is known to affect the global levels of histone methylation. Here the authors investigate the metabolically driven dynamics of H3K4me3 and find that methionine availability influences peak width, which is linked to changes in expression of genes associated with cell fate and cancer.

16 May 2018 | doi: 10.1038/s41467-018-04426-y
Computational biology and bioinformatics  Epigenetics  Epigenomics  Gene expression 

Molecular solar thermal energy storage in photoswitch oligomers increases energy densities and storage times OPEN
Mads Mansø, Anne Ugleholdt Petersen, Zhihang Wang, Paul Erhart, Mogens Brøndsted Nielsen & Kasper Moth-Poulsen

Molecular solar thermal systems are promising for storing solar energy but achieving high energy storage densities and absorption characteristics matching the solar spectrum is challenging. Here the authors present a design strategy for electronically coupled photoswitches which allow for high energy density storage for solar energy storage applications.

16 May 2018 | doi: 10.1038/s41467-018-04230-8
Energy transfer  Reaction kinetics and dynamics  Light harvesting 

Enantioselective reduction of sulfur-containing cyclic imines through biocatalysis OPEN
Nadine Zumbrägel, Christian Merten, Stefan M. Huber & Harald Gröger

The 3-thiazolidine ring, a pharmaceutically interesting cyclic structural element found e.g. in some antibiotics, is hard to obtain via currently used approaches. Here, the authors developed a straightforward method to efficiently synthesize a variety of defined, pure 3-thiazolidines.

16 May 2018 | doi: 10.1038/s41467-018-03841-5
Asymmetric synthesis  Biocatalysis  Synthetic chemistry methodology 

AID/APOBEC-like cytidine deaminases are ancient innate immune mediators in invertebrates OPEN
Mei-Chen Liu, Wen-Yun Liao, Katherine M. Buckley, Shu Yuan Yang, Jonathan P. Rast & Sebastian D. Fugmann

The AID/APOBEC cytidine deaminase family are nucleic acid editors, important for antigen receptor expression and thought to have evolved along with vertebrate adaptive immunity. Here the authors show this family may have evolved prior to adaptive immunity as members with cytidine deaminase activity are present and functional in invertebrate sea urchins and brachiopods.

16 May 2018 | doi: 10.1038/s41467-018-04273-x
Evolutionary developmental biology  Immunogenetics 

A whole-genome sequence study identifies genetic risk factors for neuromyelitis optica OPEN
Karol Estrada, Christopher W. Whelan, Fengmei Zhao, Paola Bronson, Robert E. Handsaker, Chao Sun, John P. Carulli, Tim Harris, Richard M. Ransohoff, Steven A. McCarroll, Aaron G. Day-Williams, Benjamin M. Greenberg & Daniel G. MacArthur

Neuromyelitis optica (NMO) is a rare autoimmune condition characterized by inflammation and demyelination of the optic nerve and the spinal cord. Here, Estrada et al. identify NMO susceptibility variants in the MHC region and find that autoantibody-positive NMO genetically overlaps with lupus.

16 May 2018 | doi: 10.1038/s41467-018-04332-3
Autoimmune diseases  Demyelinating diseases  Genome-wide association studies  Neuroimmunology 

Organic matter loading by hippopotami causes subsidy overload resulting in downstream hypoxia and fish kills OPEN
Christopher L. Dutton, Amanda L. Subalusky, Stephen K. Hamilton, Emma J. Rosi & David M. Post

Hypoxic (low oxygen) water conditions are generally thought to be uncommon in rivers and result from human impacts. However, Dutton and colleagues show here that waste from hippos in the Mara River contributes to frequent hypoxic events, suggesting hypoxia is a natural aspect of this system.

16 May 2018 | doi: 10.1038/s41467-018-04391-6
Ecosystem ecology  Freshwater ecology  Limnology 

Asynchronous suppression of visual cortex during absence seizures in stargazer mice OPEN
Jochen Meyer, Atul Maheshwari, Jeffrey Noebels & Stelios Smirnakis

Absence epilepsy is associated with frequent generalized spike-wave seizures and loss of awareness. Here the authors use 2-photon calcium imaging of primary visual cortex in a genetic mouse model of absence epilepsy and find that cortical neurons are less active and more loosely coupled to the seizure EEG signature than previously believed.

16 May 2018 | doi: 10.1038/s41467-018-04349-8
Cortex  Epilepsy 

A multistage rotational speed changing molecular rotor regulated by pH and metal cations OPEN
Yingying Wu, Guangxia Wang, Qiaolian Li, Junfeng Xiang, Hua Jiang & Ying Wang

Molecular rotors with rotational speed modulation have not yet been well established. Here, the authors report a pH and metal cation triggered molecular rotor, which allows for a four stage speed modulation in the slow-to-fast frequency range.

16 May 2018 | doi: 10.1038/s41467-018-04323-4
Interlocked molecules  Molecular machines and motors  Solution-state NMR 

Optical functionalization of human Class A orphan G-protein-coupled receptors OPEN
Maurizio Morri, Inmaculada Sanchez-Romero, Alexandra-Madelaine Tichy, Stephanie Kainrath, Elliot J. Gerrard, Priscila P. Hirschfeld, Jan Schwarz & Harald Janovjak

G-protein coupled receptors (GPCRs) represent the largest receptor family and are prime drug targets, but many orphan GPCRs are poorly characterized. Here authors engineer human orphan GPCRs to be activated by light which allows studying the receptors ligand identity and downstream signaling.

16 May 2018 | doi: 10.1038/s41467-018-04342-1
Cell signalling  Optogenetics  Target identification 

Hollow organic capsules assemble into cellular semiconductors OPEN
Boyuan Zhang, Raúl Hernández Sánchez, Yu Zhong, Melissa Ball, Maxwell W. Terban, Daniel Paley, Simon J. L. Billinge, Fay Ng, Michael L. Steigerwald & Colin Nuckolls

Perylene diimide-bithiophene macrocycles are electroactive and shape-persistent hosts. Here, the authors describe their self-assembly into a cellular organic semiconducting film whose voids are electrically sensitive to different guests, and which can function as the active layer in a field-effect transistor device.

16 May 2018 | doi: 10.1038/s41467-018-04246-0
Electronic materials  Molecular capsules  Organic chemistry  Self-assembly 

Discretization of the total magnetic field by the nuclear spin bath in fluorine-doped ZnSe OPEN
E. A. Zhukov, E. Kirstein, N. E. Kopteva, F. Heisterkamp, I. A. Yugova, V. L. Korenev, D. R. Yakovlev, A. Pawlis, M. Bayer & A. Greilich

Understanding the electron and nuclear spin interactions is essential to the application of quantum information devices. Here the authors report a step-like electron Larmor frequency versus external magnetic field due to the discretization of the total magnetic field by the nuclear spin bath in ZnSe:F.

16 May 2018 | doi: 10.1038/s41467-018-04359-6
Qubits  Spintronics 

Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer OPEN
Anita Sarkar, Shridhar Bale, Anna-Janina Behrens, Sonu Kumar, Shailendra Kumar Sharma, Natalia de Val, Jesper Pallesen, Adriana Irimia, Devan C. Diwanji, Robyn L. Stanfield, Andrew B. Ward, Max Crispin, Richard T. Wyatt & Ian A. Wilson

Native-like soluble HIV envelope (Env) trimers are potential vaccine immunogens, and elimination of furin-dependence could provide a DNA-based alternative. Here, Sarkar et al. show that a cleavage-independent Env construct recapitulates the architecture and glycosylation of the native cleaved trimer.

16 May 2018 | doi: 10.1038/s41467-018-04272-y
Glycosylation  HIV infections  Vaccines  X-ray crystallography 

Ambient ammonia synthesis via palladium-catalyzed electrohydrogenation of dinitrogen at low overpotential OPEN
Jun Wang, Liang Yu, Lin Hu, Gang Chen, Hongliang Xin & Xiaofeng Feng

The Haber-Bosch process, producing NH3 from N2, is a crucial yet energetically demanding reaction, inspiring interest in the exploration of ambient-condition alternatives. Here, authors develop a palladium electrocatalyst that shows a high selectivity and activity for N2 reduction to NH3.

15 May 2018 | doi: 10.1038/s41467-018-04213-9
Electrocatalysis  Nanoparticles 

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9 OPEN
Lun Cui, Antoine Vigouroux, François Rousset, Hugo Varet, Varun Khanna & David Bikard

CRISPR interference (CRISPRi) is a method for targeted silencing of transcription that requires the coexpression of protein dCas9 and a customized guide RNA. Here, Cui et al. show that certain guide RNAs induce toxicity in E. coli, and provide design rules to minimize off-target effects.

15 May 2018 | doi: 10.1038/s41467-018-04209-5
CRISPR-Cas9 genome editing  CRISPR-Cas systems 

Efficacy of a respiratory syncytial virus vaccine candidate in a maternal immunization model OPEN
Jorge C. G. Blanco, Lioubov M. Pletneva, Lori McGinnes-Cullen, Raymonde O. Otoa, Mira C. Patel, Lurds R. Fernando, Marina S. Boukhvalova & Trudy G. Morrison

RSV infection is a major cause of bronchiolitis in infants and maternal vaccination is a potential preventive option. Here, Blanco et al. show efficacy of a Newcastle disease virus-based virus-like particle vaccine candidate in naive and pre-exposed cotton rat dams and their offspring.

15 May 2018 | doi: 10.1038/s41467-018-04216-6
Animal disease models  Protein vaccines  Viral infection  Virus–host interactions 

Diffusion markers of dendritic density and arborization in gray matter predict differences in intelligence OPEN
Erhan Genç, Christoph Fraenz, Caroline Schlüter, Patrick Friedrich, Rüdiger Hossiep, Manuel C. Voelkle, Josef M. Ling, Onur Güntürkün & Rex E. Jung

Previous studies suggest that individual differences in intelligence correlate with circuit complexity and dendritic arborization in the brain. Here the authors use NODDI, a diffusion MRI technique, to confirm that neurite density and arborization are inversely related to measures of intelligence.

15 May 2018 | doi: 10.1038/s41467-018-04268-8
Human behaviour  Intelligence 

Hematopoietic stem cells can differentiate into restricted myeloid progenitors before cell division in mice OPEN
Tatyana Grinenko, Anne Eugster, Lars Thielecke, Beáta Ramasz, Anja Krüger, Sevina Dietz, Ingmar Glauche, Alexander Gerbaulet, Malte von Bonin, Onur Basak, Hans Clevers, Triantafyllos Chavakis & Ben Wielockx

Dependence of hematopoietic stem cell (HSC) fate on the phase of the cell cycle has not been demonstrated in vivo. Here, the authors find that HSCs can differentiate into a downstream progenitor without physical division, even before progressing into the S phase of the cell cycle.

15 May 2018 | doi: 10.1038/s41467-018-04188-7
Adult stem cells  Haematopoietic stem cells  Stem-cell differentiation 

Resolution of superluminal signalling in non-perturbative cavity quantum electrodynamics OPEN
Carlos Sánchez Muñoz, Franco Nori & Simone De Liberato

Quantum Rabi model is a standard tool for describing cavity quantum electrodynamics, but the potential shortcomings of its single-mode version are usually neglected. Here, the authors show that, in the ultrastrong coupling regime, a multimode Rabi model is mandatory in order to avoid unphysical results.

15 May 2018 | doi: 10.1038/s41467-018-04339-w
Nanocavities  Polaritons  Quantum optics  Single photons and quantum effects 

Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells OPEN

The International Stem Cell Initiative tests methods in a multisite study to detect pluripotency and teratoma formation (PluriTest, Embryoid Body and Teratoma methods) in human pluripotent stem cells. Here, the authors provide guidelines for their application: only the teratoma assay offers evidence of malignant potential.

15 May 2018 | doi: 10.1038/s41467-018-04011-3
Cancer stem cells  Pluripotent stem cells 

Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes OPEN
Rizi Ai, Teresina Laragione, Deepa Hammaker, David L. Boyle, Andre Wildberg, Keisuke Maeshima, Emanuele Palescandolo, Vinod Krishna, David Pocalyko, John W. Whitaker, Yuchen Bai, Sunil Nagpal, Kurtis E. Bachman, Richard I. Ainsworth, Mengchi Wang, Bo Ding, Percio S. Gulko, Wei Wang & Gary S. Firestein

Fibroblast-like synoviocytes (FLS) in the intimal layer of the synovium can become invasive and destroy cartilage in patients with rheumatoid arthritis (RA). Here the authors integrate a variety of epigenomic data to map the epigenome of FLS in RA and identify potential therapeutic targets.

15 May 2018 | doi: 10.1038/s41467-018-04310-9
Epigenomics  Immunology  Rheumatoid arthritis 

Functionalized boron nitride membranes with ultrafast solvent transport performance for molecular separation OPEN
Cheng Chen, Jiemin Wang, Dan Liu, Chen Yang, Yuchen Liu, Rodney S. Ruoff & Weiwei Lei

2D materials show promise for membrane filtration technologies, but their permeance to organic solvents is typically poor. Here, the authors prepare functionalized boron nitride membranes with high flux and high molecular separation performances in both aqueous solutions and organic solvents.

15 May 2018 | doi: 10.1038/s41467-018-04294-6
Nanopores  Structural properties  Two-dimensional materials 

Ratchet-free solid-state inertial rotation of a guest ball in a tight tubular host OPEN
Taisuke Matsuno, Yusuke Nakai, Sota Sato, Yutaka Maniwa & Hiroyuki Isobe

Though dynamics of molecules are generally restricted by intermolecular contacts, C60 fullerene is able to rotate freely despite being tightly bound inside a molecular host. Here, the authors study the solid-state dynamics of this host-guest system to understand the anomalous relationship between tight association and low friction.

15 May 2018 | doi: 10.1038/s41467-018-04325-2
Molecular machines and motors  Supramolecular chemistry 

STT3-dependent PD-L1 accumulation on cancer stem cells promotes immune evasion OPEN
Jung-Mao Hsu, Weiya Xia, Yi-Hsin Hsu, Li-Chuan Chan, Wen-Hsuan Yu, Jong-Ho Cha, Chun-Te Chen, Hsin-Wei Liao, Chu-Wei Kuo, Kay-Hooi Khoo, Jennifer L. Hsu, Chia-Wei Li, Seung-Oe Lim, Shih-Shin Chang, Yi-Chun Chen, Guo-xin Ren & Mien-Chie Hung

PD-L1 accumulates on cancer stem cells and favours immune evasion but the mechanism underlying this accumulation are unknown. Here the authors show that epithelial-mesenchymal transition induces glycosylation and stabilisation of PD-L1; antagonising this process renders cancer cells sensitive to anti-Tim3-therapy.

15 May 2018 | doi: 10.1038/s41467-018-04313-6
Cancer  Glycosylation 

Ambipolar ferromagnetism by electrostatic doping of a manganite OPEN

An ambipolar ferromagnet with both electron- and hole-doped ferromagnetism in a single material would facilitate understanding of ferromagnetic semiconductors for spintronic applications. Here the authors demonstrate ambipolar ferromagnetism in LaMnO3, using ionic liquid gating enabled electrostatic doping to produce electron–hole asymmetry.

15 May 2018 | doi: 10.1038/s41467-018-04233-5
Electronic properties and materials  Ferromagnetism  Magnetic properties and materials 

Hybrid nanostructured particles via surfactant-free double miniemulsion polymerization OPEN
Yongliang Zhao, Junli Liu, Zhi Chen, Xiaomin Zhu & Martin Möller

Double emulsions show significant advantages for microencapsulation but are thermodynamically unstable. Here the authors show, that silica nanocapsules with nanorattles or Janus-like nanomushroom structures can be prepared by stabilizing double emulsions with a silica precursor polymer and subsequent polymerization of the oil phase.

15 May 2018 | doi: 10.1038/s41467-018-04320-7
Nanoparticles  Organic–inorganic nanostructures  Self-assembly 

Solvent-assisted programming of flat polymer sheets into reconfigurable and self-healing 3D structures OPEN
Yang Yang, Eugene M. Terentjev, Yen Wei & Yan Ji

It is desirable to programme 2D plastic films into 3D structures without any assisting equipment. Here the authors show this programming can be achieved with a pipette, a hair dryer, and a bottle of solvent by using a commercial epoxy with a small percentage of a specific catalyst to facilitate bond exchange.

15 May 2018 | doi: 10.1038/s41467-018-04257-x
Polymer chemistry  Polymers 

Programmable sequential mutagenesis by inducible Cpf1 crRNA array inversion OPEN
Ryan D. Chow, Hyunu Ray Kim & Sidi Chen

Few models recapitulate the stepwise nature of cancer evolution. Here the authors introduce Cpf1-Flip, a system to introduce mutations sequentially through inducible inversion of a crRNA array.

15 May 2018 | doi: 10.1038/s41467-018-04158-z
CRISPR-Cas systems  Genetic engineering 

Dynamics of a qubit while simultaneously monitoring its relaxation and dephasing OPEN
Q. Ficheux, S. Jezouin, Z. Leghtas & B. Huard

Information leaked by a quantum system into its environment causes decoherence but if it is recorded then it can be used to infer the quantum state. Ficheux et al. monitor the relaxation and dephasing of a qubit and show that this allows all three components of the qubit to be probed simultaneously.

15 May 2018 | doi: 10.1038/s41467-018-04372-9
Quantum information  Quantum mechanics  Superconducting devices 

Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection OPEN
Hongshuo Song , Elena E. Giorgi, Vitaly V. Ganusov, Fangping Cai, Gayathri Athreya, Hyejin Yoon, Oana Carja, Bhavna Hora, Peter Hraber, Ethan Romero-Severson, Chunlai Jiang, Xiaojun Li, Shuyi Wang, Hui Li, Jesus F. Salazar-Gonzalez, Maria G. Salazar, Nilu Goonetilleke, Brandon F. Keele, David C. Montefiori, Myron S. Cohen et al.

Recombination contributes to HIV evolution in patients, but its identification can be difficult. Here, the authors develop a computational tool called RAPR to track recombination in patients, identify recombination hot spots, and show contribution of recombination to antibody escape.

15 May 2018 | doi: 10.1038/s41467-018-04217-5
Computational platforms and environments  Experimental evolution  HIV infections  Viral genetics 

Tip60-mediated lipin 1 acetylation and ER translocation determine triacylglycerol synthesis rate OPEN
Terytty Yang Li, Lintao Song, Yu Sun, Jingyi Li, Cong Yi, Sin Man Lam, Dijin Xu, Linkang Zhou, Xiaotong Li, Ying Yang, Chen-Song Zhang, Changchuan Xie, Xi Huang, Guanghou Shui, Shu-Yong Lin, Karen Reue & Sheng-Cai Lin

The acetyltransferase Tip60 mediates signaling pathways by acetylating non-histone proteins. Here the authors show that fatty acids induce Tip60–dependent acetylation of phosphatidic acid phosphatase lipin1 which, then, translocates to the ER and generates diacylglycerols for triglyceride synthesis.

15 May 2018 | doi: 10.1038/s41467-018-04363-w
Acetylation  Fat metabolism 

Tissue and cellular rigidity and mechanosensitive signaling activation in Alexander disease OPEN
Liqun Wang, Jing Xia, Jonathan Li, Tracy L. Hagemann, Jeffrey R. Jones, Ernest Fraenkel, David A. Weitz, Su-Chun Zhang, Albee Messing & Mel B. Feany

Alexander disease is a rare neurodegeneration caused by mutations in a glial gene GFAP. Here, Wang and colleagues show in animal models of Alexander disease that GFAP mutant brain and cells have greater tissue and cellular stiffness and greater activation of mechanosensitive signaling cascade.

15 May 2018 | doi: 10.1038/s41467-018-04269-7
Astrocyte  Neurodegeneration 

Symmetry mismatch-driven perpendicular magnetic anisotropy for perovskite/brownmillerite heterostructures OPEN
Jing Zhang, Zhicheng Zhong, Xiangxiang Guan, Xi Shen, Jine Zhang, Furong Han, Hui Zhang, Hongrui Zhang, Xi Yan, Qinghua Zhang, Lin Gu, Fengxia Hu, Richeng Yu, Baogen Shen & Jirong Sun

Complex oxide heterostructures exhibit multifunctional behaviour that could be used in a range of device applications. Here, the authors observe that reconstruction at oxide perovskite/brownmillerite interfaces leads to perpendicular magnetic spin orientation, with potential use in spintronic devices.

15 May 2018 | doi: 10.1038/s41467-018-04304-7
Applied physics  Surfaces, interfaces and thin films 

DOT1L inhibition attenuates graft-versus-host disease by allogeneic T cells in adoptive immunotherapy models OPEN
Yuki Kagoya, Munehide Nakatsugawa, Kayoko Saso, Tingxi Guo, Mark Anczurowski, Chung-Hsi Wang, Marcus O. Butler, Cheryl H. Arrowsmith & Naoto Hirano

Adoptive T cell therapy using an allogeneic T cell graft is an encouraging therapeutic approach in cancer, but issues such as graft-versus-host disease can hinder applicability. Here, the authors show that DOT1L inhibition or DUSP6 overexpression in T cells attenuates graft-versus-host disease but retains anti-tumour activity in mouse models.

15 May 2018 | doi: 10.1038/s41467-018-04262-0
Epigenetics  Immunotherapy  Tumour immunology 

Abnormal band bowing effects in phase instability crossover region of GaSe1-xTe x nanomaterials OPEN
Hui Cai, Bin Chen, Mark Blei, Shery L. Y. Chang, Kedi Wu, Houlong Zhuang & Sefaattin Tongay

Alloys of two-dimensional materials normally occur when two components crystallize in the same phase. Here, the authors observe an anomalous phase instability, accompanied by a band bowing effect, in GaSe1-xTe x alloys on GaAs(111).

15 May 2018 | doi: 10.1038/s41467-018-04328-z
Materials science  Two-dimensional materials 

Early Cambrian origin of the shelf sediment mixed layer OPEN
Romain C. Gougeon, M. Gabriela Mángano, Luis A. Buatois, Guy M. Narbonne & Brittany A. Laing

The timing of origin of the mixed layer, the zone of fully homogenized sediment resulting from bioturbation in modern oceans, is controversial, with estimates ranging from Cambrian to Silurian. Here, the authors show that a well-developed mixed layer was established in shallow marine settings by the early Cambrian.

15 May 2018 | doi: 10.1038/s41467-018-04311-8
Geology  Palaeontology 

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages OPEN
Evelien M. Bunnik, Kate B. Cook, Nelle Varoquaux, Gayani Batugedara, Jacques Prudhomme, Anthony Cort, Lirong Shi, Chiara Andolina, Leila S. Ross, Declan Brady, David A. Fidock, Francois Nosten, Rita Tewari, Photini Sinnis, Ferhat Ay, Jean-Philippe Vert, William Stafford Noble & Karine G. Le Roch

The development of malaria parasites is controlled by coordinated changes in gene expression. Here, the authors show that the three-dimensional genome structure of human malaria parasites is strongly connected with transcriptional activity of specific gene families throughout the life cycles of Plasmodium falciparum and Plasmodium vivax parasites.

15 May 2018 | doi: 10.1038/s41467-018-04295-5
Epigenomics  Malaria  Nuclear organization  Parasitology 

Coherent X-rays reveal the influence of cage effects on ultrafast water dynamics OPEN
Fivos Perakis , Gaia Camisasca, Thomas J. Lane, Alexander Späh, Kjartan Thor Wikfeldt, Jonas A. Sellberg, Felix Lehmkühler, Harshad Pathak, Kyung Hwan Kim, Katrin Amann-Winkel, Simon Schreck, Sanghoon Song, Takahiro Sato, Marcin Sikorski, Andre Eilert, Trevor McQueen, Hirohito Ogasawara, Dennis Nordlund, Wojciech Roseker, Jake Koralek et al.

The dynamics of liquid water is rich due to its complex, highly disordered hydrogen-bond network, which hasn’t been fully understood. Perakis et al. measure water dynamics at sub-100 fs and show that it cannot be described by simple thermal motion due to the build-up of tetrahedral structures upon supercooling.

15 May 2018 | doi: 10.1038/s41467-018-04330-5
Chemical physics  Imaging techniques 

Sensible heat has significantly affected the global hydrological cycle over the historical period OPEN

Precipitation changes are strongly linked to the Earth’s energy budget. Here the authors show that changes in sensible heat are the dominant contributor to the present global-mean precipitation change since pre-industrial time.

15 May 2018 | doi: 10.1038/s41467-018-04307-4
Atmospheric science  Climate and Earth system modelling 

Emergent superconductivity in an iron-based honeycomb lattice initiated by pressure-driven spin-crossover OPEN
Yonggang Wang, Jianjun Ying, Zhengyang Zhou, Junliang Sun, Ting Wen, Yannan Zhou, Nana Li, Qian Zhang, Fei Han, Yuming Xiao, Paul Chow, Wenge Yang, Viktor V. Struzhkin, Yusheng Zhao & Ho-kwang Mao

Up to now, all iron-based high-Tc superconductors contain a square iron lattice. Here, Wang et al. report the observation of superconductivity in an iron honeycomb lattice accompanied with pressure-driven spin-crossover, in-plane lattice collapse and insulator-metal transition.

15 May 2018 | doi: 10.1038/s41467-018-04326-1
Superconducting properties and materials  Superconductors 

PCGF5 is required for neural differentiation of embryonic stem cells OPEN
Mingze Yao, Xueke Zhou, Jiajian Zhou, Shixin Gong, Gongcheng Hu, Jiao Li, Kaimeng Huang, Ping Lai, Guang Shi, Andrew P. Hutchins, Hao Sun, Huating Wang & Hongjie Yao

Polycomb-group proteins are key regulators of transcriptional programs that maintain cell identity. Here the authors provide evidence that PCGF5, a subunit of Polycomb Repressor Complex 1, is important for the differentiation of mouse embryonic stem cells towards a neural cell fate.

15 May 2018 | doi: 10.1038/s41467-018-03781-0
Embryonic stem cells  Gene silencing  Histone post-translational modifications 

Concurrent and orthogonal gold(I) and ruthenium(II) catalysis inside living cells OPEN
Cristian Vidal, María Tomás-Gamasa, Paolo Destito, Fernando López & José L. Mascareñas

Transition-metal catalysis in living cells poses numerous challenges in terms of biocompatibility, and complex stability and reactivity. Here, the authors report a bioorthogonal gold-catalyzed C-C coupling reaction, occurring in living mammalian cells, even in parallel with a ruthenium-catalyzed deallylation reaction.

15 May 2018 | doi: 10.1038/s41467-018-04314-5
Chemical biology  Homogeneous catalysis  Organometallic chemistry 

B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation OPEN
Benjamin G. Barwick, Christopher D. Scharer, Ryan J. Martinez, Madeline J. Price, Alexander N. Wein, Robert R. Haines, Alexander P. R. Bally, Jacob E. Kohlmeier & Jeremy M. Boss

DNA methylation is known to contribute to B cell differentiation, but de novo methylation has not been studied in this context. Here the authors use a conditional Dnmt3a/b knockout mouse to map the function of de novo DNA methylation in B cell differentiation and the development of humoral immunity.

15 May 2018 | doi: 10.1038/s41467-018-04234-4
B cells  Epigenetics in immune cells  Epigenomics  Immunogenetics 

Nanographenes as electron-deficient cores of donor-acceptor systems OPEN
Yu-Min Liu, Hao Hou, Yan-Zhen Zhou, Xin-Jing Zhao, Chun Tang, Yuan-Zhi Tan & Klaus Müllen

Nanographenes in donor-acceptor π-systems generally serve as electron-donating moieties but the reversed structures are hardly reported. Here, the authors present a facile synthetic protocol towards reversed donor-acceptor nanographenes by amination and demonstrate fine property tuning by varying the donating ability of the aniline groups.

15 May 2018 | doi: 10.1038/s41467-018-04321-6
Graphene  Light harvesting  Optical materials  Self-assembly 

Estrogen-related receptor gamma functions as a tumor suppressor in gastric cancer OPEN
Myoung-Hee Kang, Hyunji Choi, Masanobu Oshima, Jae-Ho Cheong, Seokho Kim, Jung Hoon Lee, Young Soo Park, Hueng-Sik Choi, Mi-Na Kweon, Chan-Gi Pack, Ju-Seog Lee, Gordon B. Mills, Seung-Jae Myung & Yun-Yong Park

Very little is known regarding the molecular mechanisms involved in gastric cancer development. Here the authors show estrogen-related receptor gamma (ESRRG) is a tumor suppressor in gastric cancer and suggest the mechanism of this tumor suppression function involves the inhibition of Wnt signaling.

15 May 2018 | doi: 10.1038/s41467-018-04244-2
Gastric cancer  Transcription  Transcriptional regulatory elements 

Instability of the Northeast Greenland Ice Stream over the last 45,000 years OPEN
Nicolaj K. Larsen, Laura B. Levy, Anders E. Carlson, Christo Buizert, Jesper Olsen, Astrid Strunk, Anders A. Bjørk & Daniel S. Skov

The outlet glaciers that comprise the Northeast Greenland Ice Stream (NEGIS) have experienced accelerated retreat in recent years, yet their longterm stability remains unclear. Here, via cosmogenic surface exposure and radiocarbon ages, the authors investigate the stability of the NEGIS for the past 45 kyr.

14 May 2018 | doi: 10.1038/s41467-018-04312-7
Cryospheric science  Palaeoclimate 

Stepwise heating in Stille polycondensation toward no batch-to-batch variations in polymer solar cell performance OPEN
Sang Myeon Lee, Kwang Hyun Park, Seungon Jung, Hyesung Park & Changduk Yang

Polymer electronics may have a bright future but the poor reproducibility limits the scaled-up manufacturing. Here Lee et al. employ a stepwise-heating protocol in the Stille polycondensation and fabricate polymer solar cells with improved performance and ignorable device-to-device variations.

14 May 2018 | doi: 10.1038/s41467-018-03718-7
Conjugated polymers  Solar cells 

Silicon-chip-based mid-infrared dual-comb spectroscopy OPEN
Mengjie Yu, Yoshitomo Okawachi, Austin G. Griffith, Nathalie Picqué, Michal Lipson & Alexander L. Gaeta

Dual-comb spectroscopy is a powerful tool for realizing rapid spectroscopic measurements with high sensitivity and selectivity. Here, Yu et al. demonstrate silicon microresonator-based dual comb spectroscopy in the mid-infrared region, where strong vibrational resonances of many liquids exist.

14 May 2018 | doi: 10.1038/s41467-018-04350-1
Frequency combs  Infrared spectroscopy  Microresonators 

Self-organizing layers from complex molecular anions OPEN
Jonas Warneke, Martin E. McBriarty, Shawn L. Riechers, Swarup China, Mark H. Engelhard, Edoardo Aprà, Robert P. Young, Nancy M. Washton, Carsten Jenne, Grant E. Johnson & Julia Laskin

Using ions of one polarity to form functional layers on surfaces is usually challenging because of counter ions which are inevitably present in the condensed phase. Here the authors demonstrate accumulation of mass-selected anions and neutral molecules from the gas phase to form a self-organizing liquid-like layer on a surface.

14 May 2018 | doi: 10.1038/s41467-018-04228-2
Mass spectrometry  Soft materials  Wetting 

Neural encoding and production of functional morphemes in the posterior temporal lobe OPEN
Daniel K. Lee, Evelina Fedorenko, Mirela V. Simon, William T. Curry, Brian V. Nahed, Dan P. Cahill & Ziv M. Williams

Functional morphemes allow us to express details about objects, events, and their relationships. Here, authors show that inhibiting a small cortical area within left posterior superior temporal lobe selectively impairs the ability to produce functional morphemes but does not impair other linguistic abilities.

14 May 2018 | doi: 10.1038/s41467-018-04235-3
Cortex  Language 

Sculpting and fusing biomimetic vesicle networks using optical tweezers OPEN
Guido Bolognesi, Mark S. Friddin, Ali Salehi-Reyhani, Nathan E. Barlow, Nicholas J. Brooks, Oscar Ces & Yuval Elani

Assembly of higher-order artificial vesicles can unlock new applications. Here, the authors use optical tweezers to construct user-defined 2D and 3D architectures of chemically distinct vesicles and demonstrate inter-vesicle communication and light-enabled compartment merging.

14 May 2018 | doi: 10.1038/s41467-018-04282-w
Membrane structure and assembly  Membranes  Soft materials  Synthetic biology 

Aurora A-dependent CENP-A phosphorylation at inner centromeres protects bioriented chromosomes against cohesion fatigue OPEN
Grégory Eot-Houllier, Laura Magnaghi-Jaulin, Géraldine Fulcrand, François-Xavier Moyroud, Solange Monier & Christian Jaulin

Sustained spindle tension applied to sister centromeres during mitosis leads to loss of sister chromatid cohesion which is known as cohesion fatigue. Here the authors show that Aurora A-dependent phosphorylation of CENP-A at the inner centromeres protects bioriented chromosomes against cohesion fatigue.

14 May 2018 | doi: 10.1038/s41467-018-04089-9
Centromeres  Chromosome segregation 

Outlier response to anti-PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors OPEN
Manuel Rodrigues , Lenha Mobuchon, Alexandre Houy, Alice Fiévet, Sophie Gardrat, Raymond L. Barnhill, Tatiana Popova, Vincent Servois, Aurore Rampanou, Aurore Mouton, Stéphane Dayot, Virginie Raynal, Michèle Galut, Marc Putterman, Sarah Tick, Nathalie Cassoux, Sergio Roman-Roman, François-Clément Bidard, Olivier Lantz, Pascale Mariani et al.

Hypermutated tumors respond more favorably to checkpoint inhibitor-based immune therapy. Here, the authors describe a new hypermutated phenotype due to germline mutations and subsequent somatic loss of heterozygosity of MBD4, and a dramatic response to the PD-1 inhibitor pembrolizumab in a patient with a MBD4-inactivated hypermutated uveal melanoma.

14 May 2018 | doi: 10.1038/s41467-018-04322-5
Cancer genetics  Eye cancer 

Evolutionary instability of CUG-Leu in the genetic code of budding yeasts OPEN
Tadeusz Krassowski, Aisling Y. Coughlan, Xing-Xing Shen, Xiaofan Zhou, Jacek Kominek, Dana A. Opulente, Robert Riley, Igor V. Grigoriev, Nikunj Maheshwari, Denis C. Shields, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas & Kenneth H. Wolfe

The genetic code for amino acids is nearly universal, and among eukaryotic nuclear genomes the only known reassignments are of codon CUG in yeasts. Here, the authors identify a third independent CUG transition in budding yeasts that is still ongoing with alternative tRNAs present in the genome.

14 May 2018 | doi: 10.1038/s41467-018-04374-7
Evolutionary biology  Molecular evolution  tRNAs 

Quantifying compressive forces between living cell layers and within tissues using elastic round microgels OPEN
Erfan Mohagheghian, Junyu Luo, Junjian Chen, Gaurav Chaudhary, Junwei Chen, Jian Sun, Randy H. Ewoldt & Ning Wang

Increasing importance is placed upon the effect of mechanical forces on cell regulation, fate and disease states. Here, the authors describe a deformable fluorescent nanoparticle labeled elastic microsphere which can be used to calculate strain and traction forces in vitro and in vivo.

14 May 2018 | doi: 10.1038/s41467-018-04245-1
Biophysical methods  Cell biology  Nanoparticles  Sensors and probes 

Minerals in the pre-settled coral Stylophora pistillata crystallize via protein and ion changes OPEN
Anat Akiva, Maayan Neder, Keren Kahil, Rotem Gavriel, Iddo Pinkas, Gil Goobes & Tali Mass

Coral biomineralization is an important example of natural mineralization and understanding the process will aid biomineralization research. Here, the authors identify the precipitation of amorphous calcium carbonate and small aragonite crystals in pre-settled larva of Stylophora pistillata.

14 May 2018 | doi: 10.1038/s41467-018-04285-7
Biomineralization  Marine biology  Solid-state NMR 

Top-down descending facilitation of spinal sensory excitatory transmission from the anterior cingulate cortex OPEN
Tao Chen, Wataru Taniguchi, Qi-Yu Chen, Hidetoshi Tozaki-Saitoh, Qian Song, Ren-Hao Liu, Kohei Koga, Tsuyoshi Matsuda, Yae Kaito-Sugimura, Jian Wang, Zhi-Hua Li, Ya-Cheng Lu, Kazuhide Inoue, Makoto Tsuda, Yun-Qing Li, Terumasa Nakatsuka & Min Zhuo

It is known that descending facilitation of spinal responses may contribute to chronic pain, however many studies have focussed on brainstem mechanisms. Here the authors show that stimulation of the anterior cingulate cortex increases excitatory transmission in the dorsal horn, and that this may be via a direct pathway independent of the brainstem.

14 May 2018 | doi: 10.1038/s41467-018-04309-2
Chronic pain  Sensory processing 

The rise of South–South trade and its effect on global CO2 emissions OPEN
Jing Meng, Zhifu Mi, Dabo Guan, Jiashuo Li, Shu Tao, Yuan Li, Kuishuang Feng, Junfeng Liu, Zhu Liu, Xuejun Wang, Qiang Zhang & Steven J. Davis

The rapid growth of South–South trade reflects a new phase of globalization. Here the authors show that some energy-intensive production activities, particularly raw materials and intermediate goods, and related CO2 emissions are relocating from China and India to other developing countries.

14 May 2018 | doi: 10.1038/s41467-018-04337-y
Climate change  Climate-change policy  Developing world  Environmental economics 

Cross-ancestry genome-wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases OPEN
Adriana I. Iglesias , Aniket Mishra, Veronique Vitart, Yelena Bykhovskaya, René Höhn, Henriët Springelkamp, Gabriel Cuellar-Partida, Puya Gharahkhani, Jessica N. Cooke Bailey, Colin E. Willoughby, Xiaohui Li, Seyhan Yazar, Abhishek Nag, Anthony P. Khawaja, Ozren Polašek, David Siscovick, Paul Mitchell, Yih Chung Tham, Jonathan L. Haines, Lisa S. Kearns et al.

Reduced central corneal thickness (CCT) is observed in common eye diseases as well as in rare Mendelian disorders. Here, in a cross-ancestry GWAS, the authors identify 19 novel genetic loci associated with CCT, a subset of which is involved in rare corneal or connective tissue disorders.

14 May 2018 | doi: 10.1038/s41467-018-03646-6
Genetics of the nervous system  Genetics research  Genome-wide association studies  Hereditary eye disease 

Frequent pauses in Escherichia coli flagella elongation revealed by single cell real-time fluorescence imaging OPEN
Ziyi Zhao, Yifan Zhao, Xiang-Yu Zhuang, Wei-Chang Lo, Matthew A. B. Baker, Chien-Jung Lo & Fan Bai

The bacterial flagellar filament is assembled from tens of thousands of flagellin subunits that are exported by a dedicated secretion system. Here, the authors show that, on average, the growth rate of flagella in E. coli decays as flagella lengthen, with large variations due to frequent pauses.

14 May 2018 | doi: 10.1038/s41467-018-04288-4
Cellular motility  Computational biophysics 

Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses OPEN
Lars E. Clark, Selma Mahmutovic, Donald D. Raymond, Taleen Dilanyan, Takaaki Koma, John T. Manning, Sundaresh Shankar, Silvana C. Levis, Ana M. Briggiler, Delia A. Enria, Kai W. Wucherpfennig, Slobodan Paessler & Jonathan Abraham

The five known New World hemorrhagic fever arenaviruses use the same entry receptor, but their viral glycoproteins are markedly different. Here, the authors isolate monoclonal antibodies from a Junin virus vaccinated person that cross-neutralize Machupo virus and identify a conserved epitope in the receptor-binding domain.

14 May 2018 | doi: 10.1038/s41467-018-04271-z
Antibodies  Arenaviruses  Immunological memory  Vaccines 

Controlling evanescent waves using silicon photonic all-dielectric metamaterials for dense integration OPEN
Saman Jahani, Sangsik Kim, Jonathan Atkinson, Justin C. Wirth, Farid Kalhor, Abdullah Al Noman, Ward D. Newman, Prashant Shekhar, Kyunghun Han, Vien Van, Raymond G. DeCorby, Lukas Chrostowski, Minghao Qi & Zubin Jacob

Miniaturization of optical components could give way to dense photonic-integrated circuits. Here, the authors demonstrate the control of evanescent waves using all-dielectric metamaterials and show that they can reduce cross-talk and bending loss, which limit the integration density in photonic circuits.

14 May 2018 | doi: 10.1038/s41467-018-04276-8
Metamaterials  Nanophotonics and plasmonics  Sub-wavelength optics 

Global genetic differentiation of complex traits shaped by natural selection in humans OPEN
Jing Guo, Yang Wu, Zhihong Zhu, Zhili Zheng, Maciej Trzaskowski, Jian Zeng, Matthew R. Robinson, Peter M. Visscher & Jian Yang

Human complex traits and disorders often show differentiation among populations. Here, the authors analyze SNPs associated with 10 complex traits using data of large sample size from African, East Asian and European populations, and find significant genetic differentiation among global populations shaped by natural selection.

14 May 2018 | doi: 10.1038/s41467-018-04191-y
Evolutionary genetics  Genetic association study 

Structural basis of actin monomer re-charging by cyclase-associated protein OPEN
Tommi Kotila, Konstantin Kogan, Giray Enkavi, Siyang Guo, Ilpo Vattulainen, Bruce L. Goode & Pekka Lappalainen

Depolymerized ADP-actin monomers must be recharged with ATP for new rounds of filament assembly. Here the authors show that cyclase-associated protein (CAP) catalyzes actin nucleotide exchange in vivo and their CAP–actin complex structure reveals the molecular mechanism of CAP-mediated actin nucleotide exchange.

14 May 2018 | doi: 10.1038/s41467-018-04231-7
Actin  X-ray crystallography 

CO2-sensitive tRNA modification associated with human mitochondrial disease OPEN
Huan Lin, Kenjyo Miyauchi, Tai Harada, Ryo Okita, Eri Takeshita, Hirofumi Komaki, Kaoru Fujioka, Hideki Yagasaki, Yu-ichi Goto, Kaori Yanaka, Shinichi Nakagawa, Yuriko Sakaguchi & Tsutomu Suzuki

Transfer RNA modifications play critical roles in protein synthesis. Here the authors reveal the t6A37 tRNA modification is dynamically regulated by sensing intracellular CO2 concentration in mitochondria, implying metabolic regulation of protein synthesis.

14 May 2018 | doi: 10.1038/s41467-018-04250-4
RNA  RNA modification 

Belief state representation in the dopamine system OPEN
Benedicte M. Babayan, Naoshige Uchida & Samuel. J. Gershman

Dopamine neurons encode reward prediction errors (RPE) that report the mismatch between expected reward and outcome for a given state. Here the authors report that when there is uncertainty about the current state, RPEs are calculated on the probabilistic representation of the current state or belief state.

14 May 2018 | doi: 10.1038/s41467-018-04397-0
Learning algorithms  Reward 

Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells OPEN
Ábel Vértesy, Wibowo Arindrarto, Matthias S. Roost, Björn Reinius, Vanessa Torrens-Juaneda, Monika Bialecka, Ioannis Moustakas, Yavuz Ariyurek, Ewart Kuijk, Hailiang Mei, Rickard Sandberg, Alexander van Oudenaarden & Susana M. Chuva de Sousa Lopes

In mammalian female germ cells, parent-specific epigenetic marks are erased and the X chromosome reactivated before entry into meiosis. Here, by combining parental haplotype reconstruction with single-cell transcriptomics of human female embryonic germ cells, the authors demonstrate that epigenetic reprogramming occurs in a heterogeneous fashion and during a broad time window up to week 14.

14 May 2018 | doi: 10.1038/s41467-018-04215-7
Embryogenesis  Imprinting  Oogenesis 

Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma OPEN
Jeffrey P. North, Justin Golovato, Charles J. Vaske, J. Zachary Sanborn, Andrew Nguyen, Wei Wu, Benjamin Goode, Meredith Stevers, Kevin McMullen, Bethany E. Perez White, Eric A. Collisson, Michele Bloomer, David A. Solomon, Stephen C. Benz & Raymond J. Cho

Sebaceous carcinomas (SeC) are cutaneous malignancies that sometimes metastasize and cause death. Here the authors perform whole-exome sequencing on 32 SeC and report distinct mutational classes that may explain cancer ontogeny and clinical outcome.

14 May 2018 | doi: 10.1038/s41467-018-04008-y
Cancer genomics  Skin cancer 

Two-photon imaging of neuronal activity in motor cortex of marmosets during upper-limb movement tasks OPEN
Teppei Ebina, Yoshito Masamizu, Yasuhiro R. Tanaka, Akiya Watakabe, Reiko Hirakawa, Yuka Hirayama, Riichiro Hira, Shin-Ichiro Terada, Daisuke Koketsu, Kazuo Hikosaka, Hiroaki Mizukami, Atsushi Nambu, Erika Sasaki, Tetsuo Yamamori & Masanori Matsuzaki

Marmosets are an important model organism in neuroscience but there has only been limited success in training them on behavioral tasks. Here the authors report their ability to train marmosets in various motor tasks and simultaneously image neural dynamics in motor cortex with 2-photon imaging.

14 May 2018 | doi: 10.1038/s41467-018-04286-6
Behavioural methods  Ca2+ imaging  Motor cortex 

Cyclin K regulates prereplicative complex assembly to promote mammalian cell proliferation OPEN
Tingjun Lei, Peixuan Zhang, Xudong Zhang, Xue Xiao, Jingli Zhang, Tong Qiu, Qian Dai, Yujun Zhang, Ling Min, Qian Li, Rutie Yin, Ping Ding, Ni Li, Yi Qu, Dezhi Mu, Jun Qin, Xiaofeng Zhu, Zhi-Xiong Xiao & Qintong Li

Prereplicative complex (pre-RC) formation during G1 is fundamental for cell replication. Here the authors report a role for cyclin K in regulating pre-RC formation in mammalian cells by affecting cyclin E1 activity.

14 May 2018 | doi: 10.1038/s41467-018-04258-w
Cancer  Cell division  DNA replication 

Indirect excitons in van der Waals heterostructures at room temperature OPEN
E. V. Calman, M. M. Fogler, L. V. Butov, S. Hu, A. Mishchenko & A. K. Geim

Indirect excitons, composed of a spatially separated electron and hole, could find applications in excitonic devices for signal processing and communication, however they are normally detected at low temperatures. Here, the authors observe room-temperature indirect excitons in van der Waals transition metal dichalcogenide heterostructures.

14 May 2018 | doi: 10.1038/s41467-018-04293-7
Optoelectronic devices and components  Two-dimensional materials 

Asynchronous evolution of interdependent nest characters across the avian phylogeny OPEN
Yi-Ting Fang, Mao-Ning Tuanmu & Chih-Ming Hung

Nearly all bird species build nests; however, there is extensive variation in both how and where their nests are built. Here, Fang and colleagues reconstruct the evolution of nest structure, nest site and nest attachment across all extant bird families.

14 May 2018 | doi: 10.1038/s41467-018-04265-x
Evolutionary ecology  Phylogenetics 

Structural basis for the recognition of complex-type N-glycans by Endoglycosidase S OPEN
Beatriz Trastoy, Erik Klontz, Jared Orwenyo, Alberto Marina, Lai-Xi Wang, Eric J. Sundberg & Marcelo E. Guerin

Endoglycosidase S only recognizes one particular type of glycan within IgG antibodies but the molecular basis for this high specificity is not fully understood. Here, the authors present the crystal structure of product-bound Endoglycosidase S, revealing the determinants for its glycan specificity.

14 May 2018 | doi: 10.1038/s41467-018-04300-x
Antibody therapy  Enzymes  Glycobiology  X-ray crystallography 

Engineering modular intracellular protein sensor-actuator devices OPEN
Velia Siciliano, Breanna DiAndreth, Blandine Monel, Jacob Beal, Jin Huh, Kiera L Clayton, Liliana Wroblewska, AnneMarie McKeon, Bruce D. Walker & Ron Weiss

Synthetic biology principles are often used to design circuits that tune gene expression in response to changes in intracellular environments. Here the authors design a modular platform for intracellular protein sensing devices with transcriptional output.

14 May 2018 | doi: 10.1038/s41467-018-03984-5
Protein engineering  Synthetic biology 

Hierarchical mechanism of amino acid sensing by the T-box riboswitch OPEN
Krishna C. Suddala, Javier Cabello-Villegas, Malgorzata Michnicka, Collin Marshall, Edward P. Nikonowicz & Nils G. Walter

Riboswitches on 5′ ends of mRNAs are important for bacterial gene regulation. Here the authors probe the mechanism of a tRNA aminoacylation sensing T-box riboswitch using single-molecule fluorescence microscopy to characterize dynamic solution conformations and heterogeneous tRNA binding kinetics.

14 May 2018 | doi: 10.1038/s41467-018-04305-6
RNA  Single-molecule biophysics 

Rapid labelling and covalent inhibition of intracellular native proteins using ligand-directed N-acyl-N-alkyl sulfonamide OPEN
Tomonori Tamura, Tsuyoshi Ueda, Taiki Goto, Taku Tsukidate, Yonatan Shapira, Yuki Nishikawa, Alma Fujisawa & Itaru Hamachi

Chemically modifying proteins is hard to achieve selectively without purifying the target protein. Here, the authors present a method to modify proteins on lysine residues in living cells quicker than via known approaches and show that it can be used to develop protein covalent inhibitors.

14 May 2018 | doi: 10.1038/s41467-018-04343-0
Chaperones  Chemical modification 

Olfactory bulb acetylcholine release dishabituates odor responses and reinstates odor investigation OPEN
M. Cameron Ogg, Jordan M. Ross, Mounir Bendahmane & Max L. Fletcher

Habituation reduces neural responsiveness to prolonged irrelevant stimuli and dishabituation reverses these effects when a salient stimulus is encountered. Here the authors demonstrate that acetylcholine is involved in dishabituating odor responses in the mouse olfactory bulb.

14 May 2018 | doi: 10.1038/s41467-018-04371-w
Olfactory bulb  Sensory processing 

Multidimensional heuristic process for high-yield production of astaxanthin and fragrance molecules in Escherichia coli OPEN
Congqiang Zhang, Vui Yin Seow, Xixian Chen & Heng-Phon Too

Achieving high titer yield and productivity of target chemicals in industrial organism depends on multidimensional pathway optimization. Here, the authors use a refined modular method called multidimensional heuristic process to improve production of astaxanthin, nerolidol and linalool in E. coli.

11 May 2018 | doi: 10.1038/s41467-018-04211-x
Metabolic engineering 

Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa OPEN
Jiajia You, Li Sun, Xiaojing Yang, Xuewei Pan, Zhiwei Huang, Xixi Zhang, Mengxin Gong, Zheng Fan, Lingyan Li, Xiaoli Cui, Zhaoyuan Jing, Shouguang Jin, Zhiming Rao, Weihui Wu & Hongjiang Yang

You et al. show that SrpA, a small protein widely conserved among bacteria, controls core cellular processes in response to phage infection and environmental signals in Pseudomonas aeruginosa, including cell motility, chemotaxis, biofilm formation, and virulence.

10 May 2018 | doi: 10.1038/s41467-018-04232-6
Bacterial evolution  Bacterial genetics  Phage biology 

Distinct homeostatic modulations stabilize reduced postsynaptic receptivity in response to presynaptic DLK signaling OPEN
Pragya Goel & Dion Dickman

Dual leucine zipper kinase (DLK) activates an intrinsic neuronal response to injury and is also implicated in neurodegeneration. Here, Goel and Dickman characterize how postsynaptic targets adapt to presynaptic DLK signaling through a downregulation of synaptic strength.

10 May 2018 | doi: 10.1038/s41467-018-04270-0
Cellular neuroscience  Regeneration and repair in the nervous system 

Ultrafast probes of electron–hole transitions between two atomic layers OPEN

The investigation into the dynamical transitions of charged quasiparticles on interfaces remains technically challenging. Here, the authors use ultrafast, mid-infrared micro-spectroscopy to unveil the formation of tightly bound interlayer excitons between conducting graphene and semiconducting MoSe2.

10 May 2018 | doi: 10.1038/s41467-018-04291-9
Electron transfer  Surfaces, interfaces and thin films  Two-dimensional materials  Ultrafast photonics 

Diffusion in translucent media OPEN
Zhou Shi & Azriel Z. Genack

Despite the universal nature of diffusion, the behavior of light transport in optically thin media has remained unclear. Here the authors show that the description of this behavior in translucent media has the same form as in opaque media, even at length scales far below the mean free path.

10 May 2018 | doi: 10.1038/s41467-018-04242-4
Other photonics  Sub-wavelength optics 

Explaining the apparent impenetrable barrier to ultra-relativistic electrons in the outer Van Allen belt OPEN
Louis G. Ozeke, Ian R. Mann, Kyle R. Murphy, Alex W. Degeling, Seth G. Claudepierre & Harlan E. Spence

The origin of the apparent impenetrable barrier in the outer Van Allen belt is still uncertain. Here, the authors report that penetration to the barrier can occur by means of ultra-low frequency wave transport, enabling ultra-relativistic electrons to reach the location of the barrier.

10 May 2018 | doi: 10.1038/s41467-018-04162-3
Astrophysical plasmas  Magnetospheric physics 

Direct neurotransmitter activation of voltage-gated potassium channels OPEN
Rían W. Manville, Maria Papanikolaou & Geoffrey W. Abbott

M-current is conveyed by voltage-sensitive KCNQ channels, which are enriched in GABAergic neurons and are activated by anticonvulsants such as retigabine. Here the authors show that GABA directly activates KCNQ3, at the residue required for its anticonvulsant activity.

10 May 2018 | doi: 10.1038/s41467-018-04266-w
Biophysics  Ion channels in the nervous system  Neurophysiology 

Genome-wide and high-density CRISPR-Cas9 screens identify point mutations in PARP1 causing PARP inhibitor resistance OPEN
Stephen J. Pettitt , Dragomir B. Krastev, Inger Brandsma, Amy Dréan, Feifei Song, Radoslav Aleksandrov, Maria I. Harrell, Malini Menon, Rachel Brough, James Campbell, Jessica Frankum, Michael Ranes, Helen N. Pemberton, Rumana Rafiq, Kerry Fenwick, Amanda Swain, Sebastian Guettler, Jung-Min Lee, Elizabeth M. Swisher, Stoyno Stoynov et al.

The mechanisms of PARP inhibitor (PARPi) resistance are poorly understood. Here the authors employ a CRISPR mutagenesis approach to identify PARP1 mutants causing PARPi resistance and find that PARP1 mutations are tolerated in BRCA1 mutated cells, suggesting alternative resistance mechanisms.

10 May 2018 | doi: 10.1038/s41467-018-03917-2
Cancer genomics  CRISPR-Cas9 genome editing  DNA damage response 

Chiral Landau levels in Weyl semimetal NbAs with multiple topological carriers OPEN
Xiang Yuan , Zhongbo Yan, Chaoyu Song, Mengyao Zhang, Zhilin Li, Cheng Zhang, Yanwen Liu, Weiyi Wang, Minhao Zhao, Zehao Lin, Tian Xie, Jonathan Ludwig, Yuxuan Jiang, Xiaoxing Zhang, Cui Shang, Zefang Ye, Jiaxiang Wang, Feng Chen, Zhengcai Xia, Dmitry Smirnov et al.

How the carriers behave in a Weyl semimetal if they occupy the lowest Landau level remains elusive. Here, the authors report evidences of electrons occupying zeroth chiral Landau levels with distinct linear dispersion behaviors for two inequivalent Weyl nodes in a Weyl semimetal NbAs.

10 May 2018 | doi: 10.1038/s41467-018-04080-4
Topological matter 

Structural basis for cofilin binding and actin filament disassembly OPEN
Kotaro Tanaka, Shuichi Takeda, Kaoru Mitsuoka, Toshiro Oda, Chieko Kimura-Sakiyama, Yuichiro Maéda & Akihiro Narita

Cofilin is a small actin-binding protein that accelerates actin turnover by disassembling actin filaments. Here the authors present the 3.8 Å cryo-EM structure of a cofilin-decorated actin filament and discuss mechanistic implications.

10 May 2018 | doi: 10.1038/s41467-018-04290-w
Biophysics  Cryoelectron microscopy  Cytoskeletal proteins  Molecular biology 

TGF-β induces miR-100 and miR-125b but blocks let-7a through LIN28B controlling PDAC progression OPEN
Silvia Ottaviani, Justin Stebbing, Adam E. Frampton, Sladjana Zagorac, Jonathan Krell, Alexander de Giorgio, Sara M. Trabulo, Van T. M. Nguyen, Luca Magnani, Hugang Feng, Elisa Giovannetti, Niccola Funel, Thomas M. Gress, Long R. Jiao, Ylenia Lombardo, Nicholas R. Lemoine, Christopher Heeschen & Leandro Castellano

In pancreatic ductal adenocarcinoma, TGF-β/Activin induce epithelial-to-mesenchymal transition (EMT) and stemness. Here, the authors show that TGF-β induces pro-tumourigenic miR-100 and miR-125b, but blocks anti-tumourigenic let-7a maturation via LIN28B, regulating pathways to promote stemness, EMT and tumourigenesis.

10 May 2018 | doi: 10.1038/s41467-018-03962-x
Cancer stem cells  Cell biology 

The effects of mutational processes and selection on driver mutations across cancer types OPEN
Daniel Temko, Ian P. M. Tomlinson, Simone Severini, Benjamin Schuster-Böckler & Trevor A. Graham

A central question in cancer research is how specific driver mutations are acquired and maintained during cancer development. Here Temko et al. use public sequencing data to infer the effect of mutation and selection on a set of driver mutations and suggest that selection frequently dominates.

10 May 2018 | doi: 10.1038/s41467-018-04208-6
Cancer genomics  Genome informatics 

The thioredoxin-1 system is essential for fueling DNA synthesis during T-cell metabolic reprogramming and proliferation OPEN
Jonathan Muri, Sebastian Heer, Mai Matsushita, Lea Pohlmeier, Luigi Tortola, Tobias Fuhrer, Marcus Conrad, Nicola Zamboni, Jan Kisielow & Manfred Kopf

Thioredoxin (Trx), Trx reductase, Txnip and NADPH together comprise the Trx system. Here the authors make a T cell-specific thioredoxin reductase-1 knockout mouse to show how this system reprograms cellular metabolism to enable T cell development, proliferation and responses.

10 May 2018 | doi: 10.1038/s41467-018-04274-w
Cell death and immune response  Lymphocyte activation 

CRISPR-LbCpf1 prevents choroidal neovascularization in a mouse model of age-related macular degeneration OPEN
Taeyoung Koo, Sung Wook Park, Dong Hyun Jo, Daesik Kim, Jin Hyoung Kim, Hee-Yeon Cho, Jeungeun Kim, Jeong Hun Kim & Jin-Soo Kim

The CRISPR endonuclease LbCpf1 is reported to have greater efficiency and specificity than Cas9. Here, the authors use LbCpf1 to target the angiogenesis-related genes VEGF and HIF1a, and show that delivery of the nuclease using AAV9 is effective in mouse models of macular degeneration.

10 May 2018 | doi: 10.1038/s41467-018-04175-y
Gene therapy  Macular degeneration 

Light-driven transformable optical agent with adaptive functions for boosting cancer surgery outcomes OPEN
Ji Qi, Chao Chen, Xiaoyan Zhang, Xianglong Hu, Shenglu Ji, Ryan T. K. Kwok, Jacky W. Y. Lam, Dan Ding & Ben Zhong Tang

The combination of imaging techniques in cancer treatment often involves a trade-off in properties due to the opposite working mechanisms. Here, the authors report on a material that avoids the trade-off by switching from photoacoustic imaging to fluorescence imaging upon an external light trigger

10 May 2018 | doi: 10.1038/s41467-018-04222-8
Cancer imaging  Cancer therapy  Chemistry  Imaging  Materials chemistry 

Determination of hot carrier energy distributions from inversion of ultrafast pump-probe reflectivity measurements OPEN
Tal Heilpern, Manoj Manjare, Alexander O. Govorov, Gary P. Wiederrecht, Stephen K. Gray & Hayk Harutyunyan

The determination of thermal and non-thermal carrier populations in plasmonic systems generally requires assumptions on the types of distributions present. Here, Heilpern et al. directly determine such populations in thin film pump-probe measurements using a double inversion procedure.

10 May 2018 | doi: 10.1038/s41467-018-04289-3
Electronic properties and materials  Nanophotonics and plasmonics  Optical spectroscopy  Ultrafast photonics 

Single molecule fate of HIV-1 envelope reveals late-stage viral lattice incorporation OPEN
Carmen A. Buttler, Nairi Pezeshkian, Melissa V. Fernandez, Jesse Aaron, Sofya Norman, Eric O. Freed & Schuyler B. van Engelenburg

HIV particles contain a relatively low amount of viral envelope (Env), but underlying packaging mechanisms are poorly understood. Here, the authors use superresolution microscopy and show that Env distribution is biased toward the necks of cell-associated particles during assembly.

10 May 2018 | doi: 10.1038/s41467-018-04220-w
HIV infections  Single-molecule biophysics  Super-resolution microscopy 

Reversible glycosidic switch for secure delivery of molecular nanocargos OPEN
Pierre-Alain Burnouf, Yu-Lin Leu, Yu-Cheng Su, Kenneth Wu, Wei-Chi Lin & Steve R. Roffler

Retention of drugs loaded into liposomes is a major challenge to effective targeted drug delivery. Here, the authors report on the modification of drugs with a glycosidic pH sensitive switch to improve encapsulation and retention of drugs and demonstrate application in an in vivo cancer model.

10 May 2018 | doi: 10.1038/s41467-018-04225-5
Biomedical materials  Chemical modification  Drug delivery  Nanotechnology in cancer 
 
  Latest Addendum    
 
Addendum: Fermiology and electron dynamics of trilayer nickelate La4Ni3O10 OPEN
Haoxiang Li, Xiaoqing Zhou, Thomas Nummy, Junjie Zhang, Victor Pardo, Warren E. Pickett, J. F. Mitchell & D. S. Dessau
16 May 2018 | doi: 10.1038/s41467-018-04106-x
Electronic properties and materials  Superconducting properties and materials 
 
  Latest Author Corrections    
 
Author Correction: Fermiology and electron dynamics of trilayer nickelate La4Ni3O10 OPEN
Haoxiang Li, Xiaoqing Zhou, Thomas Nummy, Junjie Zhang, Victor Pardo, Warren E. Pickett, J. F. Mitchell & D. S. Dessau
11 May 2018 | doi: 10.1038/s41467-018-04105-y
Electronic properties and materials  Superconducting properties and materials 

Author Correction: Towards an arthritis flare-responsive drug delivery system OPEN
Nitin Joshi, Jing Yan, Seth Levy, Sachin Bhagchandani, Kai V. Slaughter, Nicholas E. Sherman, Julian Amirault, Yufeng Wang, Logan Riegel, Xueyin He, Tan Shi Rui, Michael Valic, Praveen K. Vemula, Oscar R. Miranda, Oren Levy, Ellen M. Gravallese, Antonios O. Aliprantis, Joerg Ermann & Jeffrey M. Karp
11 May 2018 | doi: 10.1038/s41467-018-04346-x
Biomedical engineering  Drug delivery  Rheumatoid arthritis 
 
  Latest Publisher Corrections    
 
Publisher Correction: High power surface emitting terahertz laser with hybrid second- and fourth-order Bragg gratings OPEN
Yuan Jin, Liang Gao, Ji Chen, Chongzhao Wu, John L. Reno & Sushil Kumar
14 May 2018 | doi: 10.1038/s41467-018-04400-8
Quantum cascade lasers  Semiconductor lasers 

Publisher Correction: Laser-accelerated particle beams for stress testing of materials OPEN
M. Barberio, M. Scisciò, S. Vallières, F. Cardelli, S. N. Chen, G. Famulari, T. Gangolf, G. Revet, A. Schiavi, M. Senzacqua & P. Antici
14 May 2018 | doi: 10.1038/s41467-018-04345-y
Characterization and analytical techniques  Mechanical properties  Plasma-based accelerators 
 

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