Wednesday, December 13, 2017

Nature Communications -13 December 2017

 
Nature Communications

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Nature Spotlight on Nano Carbon Technology in Japan 

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Japan's historical leadership in the field of nanocarbon research is being challenged. 

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13 December 2017 
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Nature Outlook: Climate Change

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Poster on: The expanding CRISPR toolbox 

The CRISPR-Cas9 system can do a lot more than gene editing. This Poster, from Nature Methods, explores the newest possibilities of CRISPR. 

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Nature Index 2017 Science Inc. 

This supplement investigates the changing role of corporate institutions in the world of science and the costs and benefits to high-quality research of these evolving arrangements.

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Atmospheric pressure mass spectrometric imaging of live hippocampal tissue slices with subcellular spatial resolution OPEN
Jae Young Kim, Eun Seok Seo, Hyunmin Kim, Ji-Won Park, Dong-Kwon Lim & Dae Won Moon

Ambient mass spectrometry-based approaches have found application in biology and medicine. Here the authors report a mass spectrometric imaging method (ambient nanoPALDI) for live hippocampal tissues, based on gold nanorodassisted femtosecond laser desorption and subsequent non-thermal plasma induced ionization.

13 December 2017 | doi: 10.1038/s41467-017-02216-6
Mass spectrometry  Molecular neuroscience 

PI3Kδ activates E2F1 synthesis in response to mRNA translation stress OPEN
Sivakumar Vadivel Gnanasundram, Slovénie Pyndiah, Chrysoula Daskalogianni, Kate Armfield, Karin Nylander, Joanna B. Wilson & Robin Fåhraeus

The oncogenic activity of EBNA1 protein is unknown; it contains a glycine and alanine repeat sequence (GAr) which regulates its own translation in cis. Here the authors show that GAr stimulates PI3Kδ-mediated induction of E2F1 translation, leading to c-Myc induction and stimulation of proliferation.

13 December 2017 | doi: 10.1038/s41467-017-02282-w
Cancer  Cell biology  Molecular biology 

In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering OPEN
Qianxin Wu, Quentin R. V. Ferry, Toni A. Baeumler, Yale S. Michaels, Dimitrios M. Vitsios, Omer Habib, Roland Arnold, Xiaowei Jiang, Stefano Maio, Bruno R. Steinkraus, Marta Tapia, Paolo Piazza, Ni Xu, Georg A. Holländer, Thomas A. Milne, Jin-Soo Kim, Anton J. Enright, Andrew R. Bassett & Tudor A. Fulga

RNA regulatory elements (RREs) are important post-transcriptional control features but studying them requires disrupting their activity without disturbing cellular homeostasis. Here the authors present GenERA, a CRISPR-Cas9 screening platform of in situ analysis of native RREs.

13 December 2017 | doi: 10.1038/s41467-017-00686-2
CRISPR-Cas9 genome editing  Genetic engineering  miRNAs 

SYK kinase mediates brown fat differentiation and activation OPEN
Marko Knoll, Sally Winther, Anirudh Natarajan, Huan Yang, Mengxi Jiang, Prathapan Thiru, Aliakbar Shahsafaei, Tony E. Chavarria, Dudley W. Lamming, Lei Sun, Jacob B. Hansen & Harvey F. Lodish

Spleen protein tyrosine kinase (Syk) has so far been mainly studied in haematopoietic and immune cells. Here, the authors show that Syk also has a role in brown adipose tissue, where it regulates the formation of brown adipocytes and their thermogenic activation in response to β-adrenergic stimulation.

13 December 2017 | doi: 10.1038/s41467-017-02162-3
Cell signalling  Differentiation  Metabolism  Transcription 

Vocal learning promotes patterned inhibitory connectivity OPEN
Mark N. Miller, Chung Yan J. Cheung & Michael S. Brainard

Complex motor behaviors such as birdsong are learned through practice and are thought to depend on specific excitatory connectivity in premotor circuits. Here the authors show that song learning in Bengalese Finches is associated with enrichment of inhibitory network connectivity that can affect specific song features.

13 December 2017 | doi: 10.1038/s41467-017-01914-5
Learning and memory  Motor control  Neural circuits 

A pH-gated conformational switch regulates the phosphatase activity of bifunctional HisKA-family histidine kinases OPEN
Yixiang Liu, Joshua Rose, Shaojia Huang, Yangbo Hu, Qiong Wu, Dan Wang, Conggang Li, Maili Liu, Pei Zhou & Ling Jiang

Bacteria adapt to changing environmental conditions through signal transduction mediated by the two-component system (TCS). Here, the authors combine X-ray crystallography and NMR studies to characterize a pH-gated conformational switch that regulates the phosphatase activity of TCS bifunctional histidine kinases.

13 December 2017 | doi: 10.1038/s41467-017-02310-9
Biochemistry  Microbiology  NMR spectroscopy  X-ray crystallography 

Ultrathin graphene oxide-based hollow fiber membranes with brush-like CO2-philic agent for highly efficient CO2 capture OPEN
Fanglei Zhou, Huynh Ngoc Tien, Weiwei L. Xu, Jung-Tsai Chen, Qiuli Liu, Ethan Hicks, Mahdi Fathizadeh, Shiguang Li & Miao Yu

Membrane separation technologies show promise for CO2 capture, but typically suffer from a trade-off between permeance and selectivity. Here, the authors produce hollow fiber membranes coated with graphene oxide and a CO2-philic agent that can efficiently separate CO2 from flue gas under wet conditions.

13 December 2017 | doi: 10.1038/s41467-017-02318-1
Graphene  Mechanical and structural properties and devices  Porous materials  Surface chemistry 

Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase OPEN
Sina Reckel, Charlotte Gehin, Delphine Tardivon, Sandrine Georgeon, Tim Kükenshöner, Frank Löhr, Akiko Koide, Lena Buchner, Alejandro Panjkovich, Aline Reynaud, Sara Pinho, Barbara Gerig, Dmitri Svergun, Florence Pojer, Peter Güntert, Volker Dötsch, Shohei Koide, Anne-Claude Gavin & Oliver Hantschel

The Bcr-Abl tyrosine kinases p210 and p190 are linked to different leukemias and differ by the Dbl homology (DH) and Pleckstrin-homology (PH) domains. Here the authors characterize structures of the Bcr-Abl p210 DH and PH domains and find that the PH domain is important for the cellular localization and signaling network of p210.

13 December 2017 | doi: 10.1038/s41467-017-02313-6
Kinases  SAXS  Solution-state NMR  X-ray crystallography 

Molecular basis of differential 3′ splice site sensitivity to anti-tumor drugs targeting U2 snRNP OPEN
Luisa Vigevani, André Gohr, Thomas Webb, Manuel Irimia & Juan Valcárcel

Several families of natural compounds target core components of the pre-mRNA splicing machinery and display anti-tumor activity. Here the authors show that particular sequence features can be linked to drug response, and that drugs with very similar chemical structures display substantially different effects on splicing regulation.

13 December 2017 | doi: 10.1038/s41467-017-02007-z
Drug development  Mechanism of action  RNA splicing  Small molecules 

CTCF driven TERRA transcription facilitates completion of telomere DNA replication OPEN
Kate Beishline, Olga Vladimirova, Stephen Tutton, Zhuo Wang, Zhong Deng & Paul M. Lieberman

TERRA RNA is involved in maintaining stability during telomere repeat replication. Here the authors, by using CRISPR/Cas9, mutate CTCF-binding sites at start site of TERRA transcripts and find that subtelomeric CTCF facilitates telomeric DNA replication by promoting TERRA transcription.

13 December 2017 | doi: 10.1038/s41467-017-02212-w
Fragile sites  Telomeres 

Atomic-resolution three-dimensional hydration structures on a heterogeneously charged surface OPEN
Kenichi Umeda, Lidija Zivanovic, Kei Kobayashi, Juha Ritala, Hiroaki Kominami, Peter Spijker, Adam S. Foster & Hirofumi Yamada

Local hydration structures at solid-liquid interfaces are important in catalytic, electrochemical, and biological processes. Here, the authors demonstrate atomic-scale 3D hydration structures around the boundary on a heterogeneous mineral surface using atomic force microscopy experiments and molecular dynamics simulations.

13 December 2017 | doi: 10.1038/s41467-017-01896-4
Atomic force microscopy  Characterization and analytical techniques  Molecular dynamics  Scanning probe microscopy 

Metasurface-assisted phase-matching-free second harmonic generation in lithium niobate waveguides OPEN
Cheng Wang, Zhaoyi Li, Myoung-Hwan Kim, Xiao Xiong, Xi-Feng Ren, Guang-Can Guo, Nanfang Yu & Marko Lončar

Phase matching is a crucial condition for nonlinear optical processes. Here, Wang et al. demonstrate that a gradient metasurface composed of phased array antennas allows phase-matching-free frequency conversion over a pump wavelength range of almost 100 nm.

13 December 2017 | doi: 10.1038/s41467-017-02189-6
Metamaterials  Nonlinear optics 

Sexual recombination and increased mutation rate expedite evolution of Escherichia coli in varied fitness landscapes OPEN
George L. Peabody V, Hao Li & Katy C. Kao

Sexual recombination and mutation rate may play different roles in adaptive evolution depending on the fitness landscape. Here, Peabody et al. examine how the two factors affect the rate of adaptation of an E. coli strain capable of sexual recombination, under different conditions during experimental evolution.

13 December 2017 | doi: 10.1038/s41467-017-02323-4
Antimicrobial resistance  Bacterial evolution  Experimental evolution 

Targeted inhibition of STAT/TET1 axis as a therapeutic strategy for acute myeloid leukemia OPEN
Xi Jiang, Chao Hu, Kyle Ferchen, Ji Nie, Xiaolong Cui, Chih-Hong Chen, Liting Cheng, Zhixiang Zuo, William Seibel, Chunjiang He, Yixuan Tang, Jennifer R. Skibbe, Mark Wunderlich, William C. Reinhold, Lei Dong, Chao Shen, Stephen Arnovitz, Bryan Ulrich, Jiuwei Lu, Hengyou Weng et al.

Ten-eleven translocation 1 (TET1) is a critical oncoprotein in AML. Here, the authors identify 2 compounds that target the binding of STAT3/5 specifically to the TET1 promoter, inhibiting its expression and AML cell viability.

13 December 2017 | doi: 10.1038/s41467-017-02290-w
Acute myeloid leukaemia  Drug development  Target validation 

Structural insight into catalytic mechanism of PET hydrolase OPEN
Xu Han, Weidong Liu, Jian-Wen Huang, Jiantao Ma, Yingying Zheng, Tzu-Ping Ko, Limin Xu, Ya-Shan Cheng, Chun-Chi Chen & Rey-Ting Guo

Poly-ethylene terephthalate (PET) is a widely used plastic which accumulates in the environment with detrimental consequences. Here the authors report crystal structures of a PET-hydrolyzing enzyme from the microbe Ideonella sakaiensis bound to substrate and product analogs, and suggest a catalytic mechanism for its PET-degrading activity.

13 December 2017 | doi: 10.1038/s41467-017-02255-z
Enzyme mechanisms  Hydrolases  X-ray crystallography 

Breast cancer metastasis suppressor OTUD1 deubiquitinates SMAD7 OPEN

The activation of TGF-β signaling has been implicated in cancer metastasis. Here, the authors show that OTUD1 suppresses metastasis by antagonizing the TGF-β pathway via the deubiquitination of SMAD7, and its loss correlates with poor prognosis in breast cancer.

13 December 2017 | doi: 10.1038/s41467-017-02029-7
Metastasis  Ubiquitylation 

Oxytocin enhances observational fear in mice OPEN
Marc T. Pisansky, Leah R. Hanson, Irving I. Gottesman & Jonathan C. Gewirtz

Oxytocin modulates social behaviours in mammals. Here the authors demonstrate that observational fear, a measure of empathy-like behaviour in rodents, is modulated by oxytocin.

13 December 2017 | doi: 10.1038/s41467-017-02279-5
Emotion  Social behaviour 

Infection via mosquito bite alters Zika virus tissue tropism and replication kinetics in rhesus macaques OPEN
Dawn M. Dudley, Christina M. Newman, Joseph Lalli, Laurel M. Stewart, Michelle R. Koenig, Andrea M. Weiler, Matthew R. Semler, Gabrielle L. Barry, Katie R. Zarbock, Mariel S. Mohns, Meghan E. Breitbach, Nancy Schultz-Darken, Eric Peterson, Wendy Newton, Emma L. Mohr, Saverio Capuano III, Jorge E. Osorio, Shelby L. O’Connor, David H. O’Connor, Thomas C. Friedrich et al.

Vector saliva can affect infectivity and pathogenesis of vector-borne viruses, but this hasn’t been studied for Zika virus infection. Here, Dudley et al. show that mosquito-mediated Zika infection of macaques results in altered replication kinetics and greater sequence heterogeneity.

13 December 2017 | doi: 10.1038/s41467-017-02222-8
Viral evolution  Viral pathogenesis  Virus–host interactions 

Nucleotide– and Mal3-dependent changes in fission yeast microtubules suggest a structural plasticity view of dynamics OPEN
Ottilie von Loeffelholz, Neil A. Venables, Douglas Robert Drummond, Miho Katsuki, Robert Cross & Carolyn A. Moores

Microtubules are vital and highly conserved components of the cytoskeleton. Here the authors carry out a structural analysis of fission yeast microtubules in the presence and absence of the microtubule end-binding protein Mal3 that demonstrates structural plasticity amongst microtubule polymers.

13 December 2017 | doi: 10.1038/s41467-017-02241-5
Cryoelectron tomography  Cytoskeletal proteins  Microtubules 

A large multi-ethnic genome-wide association study identifies novel genetic loci for intraocular pressure OPEN
Hélène Choquet, Khanh K. Thai, Jie Yin, Thomas J. Hoffmann, Mark N. Kvale, Yambazi Banda, Catherine Schaefer, Neil Risch, K. Saidas Nair, Ronald Melles & Eric Jorgenson

Intraocular pressure (IOP) is a major risk factor for glaucoma. Here, Choquet and co-authors perform a multi-ethnic genome-wide association study of repeat IOP measurements in 69,756 individuals and identify 40 novel loci, 36 of which show directionally consistent effects in glaucoma.

13 December 2017 | doi: 10.1038/s41467-017-01913-6
Genetics research  Genome-wide association studies  Risk factors 

Engineering cell signaling using tunable CRISPR–Cpf1-based transcription factors OPEN
Yuchen Liu, Jinghong Han, Zhicong Chen, Hanwei Wu, Hongsong Dong & Guohui Nie

Cpf1 has been repurposed as a transcriptional repressor in bacteria and plants. Here, the authors construct activators and repressors in human cells using Cpf1 coupled to riboswitches and GPCRs.

13 December 2017 | doi: 10.1038/s41467-017-02265-x
CRISPR-Cas9 genome editing  Synthetic biology 

Dielectric anomalies and interactions in the three-dimensional quadratic band touching Luttinger semimetal Pr2Ir2O7  OPEN
Bing Cheng, T. Ohtsuki, Dipanjan Chaudhuri, S. Nakatsuji, Mikk Lippmaa & N. P. Armitage

The electronic structure of Pr2Ir2O7 contains a quadratic band touching, which is expected to lead to unusual interaction-driven behavior. Here, the authors use spectroscopic measurements to observe signatures of strong interactions but also that Fermi liquid behavior is retained at low temperatures.

13 December 2017 | doi: 10.1038/s41467-017-02121-y
Electronic properties and materials  Surfaces, interfaces and thin films  Topological insulators 

Mating system manipulation and the evolution of sex-biased gene expression in Drosophila  OPEN
Paris Veltsos, Yongxiang Fang, Andrew R. Cossins, Rhonda R. Snook & Michael G. Ritchie

Sexual selection on males is thought to favour male-biased gene expression. Here, Veltsos et al. experimentally evolve Drosophila pseudoobscura under different mating systems and, contrary to expectation, most often find masculinization of the transcriptome under monogamy rather than under elevated polyandry.

12 December 2017 | doi: 10.1038/s41467-017-02232-6
Evolutionary genetics  Gene expression  Sexual selection 

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria OPEN
Aude Bernheim, Alicia Calvo-Villamañán, Clovis Basier, Lun Cui, Eduardo P. C. Rocha, Marie Touchon & David Bikard

The double-strand breaks generated by CRISPR-Cas systems are the target of multiple DNA repair pathways. Here the authors find incompatibility between NHEJ and type II-A CRISPR-Cas systems due to Csn2 mediated inhibition of end-joining.

12 December 2017 | doi: 10.1038/s41467-017-02350-1
CRISPR-Cas systems  Molecular evolution  Non-homologous-end joining 

Lipoteichoic acid deficiency permits normal growth but impairs virulence of Streptococcus pneumoniae  OPEN
Nathalie Heß, Franziska Waldow, Thomas P. Kohler, Manfred Rohde, Bernd Kreikemeyer, Alejandro Gómez-Mejia, Torsten Hain, Dominik Schwudke, Waldemar Vollmer, Sven Hammerschmidt & Nicolas Gisch

Teichoic acid is bound to peptidoglycan (wall teichoic acid, WTA) or to membrane glycolipids (lipoteichoic acid, LTA) in most Gram-positive bacteria. Here, the authors identify a putative ligase required for the assembly of LTA, but not WTA, and important for Streptococcus pneumoniae virulence in mouse models.

12 December 2017 | doi: 10.1038/s41467-017-01720-z
Bacterial pathogenesis  Bacteriology  Glycobiology  Pathogens 

Reproducible flaws unveil electrostatic aspects of semiconductor electrochemistry OPEN
Yan B. Vogel, Long Zhang, Nadim Darwish, Vinicius R. Gonçales, Anton Le Brun, J. Justin Gooding, Angela Molina, Gordon G. Wallace, Michelle L. Coote, Joaquin Gonzalez & Simone Ciampi

Most electrical devices must pass charges across semiconductor interfaces, yet redox-active molecular behavior obscures comprehension of these processes. Here, the authors develop a model to describe redox processes on semiconductor surfaces and gauge these interactions electrochemically.

12 December 2017 | doi: 10.1038/s41467-017-02091-1
Electrochemistry  Electronic devices  Electronic properties and materials 

Structure of outer membrane protein G in lipid bilayers OPEN
Joren S. Retel, Andrew J. Nieuwkoop, Matthias Hiller, Victoria A. Higman, Emeline Barbet-Massin, Jan Stanek, Loren B. Andreas, W. Trent Franks, Barth-Jan van Rossum, Kutti R. Vinothkumar, Lieselotte Handel, Gregorio Giuseppe de Palma, Benjamin Bardiaux, Guido Pintacuda, Lyndon Emsley, Werner Kühlbrandt & Hartmut Oschkinat

Porins, like OmpG, are embedded in the outer membrane of bacteria and facilitate uptake and secretion of nutrients and ions. Here the authors present a protocol for solid state NMR structure determination of proteins larger than 25 kDa and use it to structurally characterize membrane embedded OmpG.

12 December 2017 | doi: 10.1038/s41467-017-02228-2
Protein folding  Solid-state NMR 

The mitochondrial negative regulator MCJ is a therapeutic target for acetaminophen-induced liver injury OPEN
Lucía Barbier-Torres, Paula Iruzubieta, David Fernández-Ramos, Teresa C. Delgado, Daniel Taibo, Virginia Guitiérrez-de-Juan, Marta Varela-Rey, Mikel Azkargorta, Nicolas Navasa, Pablo Fernández-Tussy, Imanol Zubiete-Franco, Jorge Simon, Fernando Lopitz-Otsoa, Sofia Lachiondo-Ortega, Javier Crespo, Steven Masson, Misti Vanette McCain, Erica Villa, Helen Reeves, Felix Elortza et al.

Acetaminophen-induced liver injury is one of the most common causes of liver failure and has to be treated within hours of the overdose. Here Barbier-Torres et al. show that targeting MCJ, a mitochondrial negative regulator, even 24 h after the overdose protects liver from acetaminophen-induced damage.

12 December 2017 | doi: 10.1038/s41467-017-01970-x
Hepatotoxicity  Mitochondria 

Fluctuations in instantaneous frequency predict alpha amplitude during visual perception OPEN
Stephanie Nelli, Sirawaj Itthipuripat, Ramesh Srinivasan & John T. Serences

Though the amplitude and frequency of neural oscillations in the alpha band are related to dissociable visual processes, they are not independent mathematically. Here, the authors show that fluctuations in instantaneous frequency predict alpha amplitude during visual discrimination tasks.

12 December 2017 | doi: 10.1038/s41467-017-02176-x
Dynamical systems  Perception 

IRF8-dependent molecular complexes control the Th9 transcriptional program OPEN
Etienne Humblin, Marion Thibaudin, Fanny Chalmin, Valentin Derangère, Emeric Limagne, Corentin Richard, Richard A. Flavell, Sandy Chevrier, Sylvain Ladoire, Hélène Berger, Romain Boidot, Lionel Apetoh, Frédérique Végran & François Ghiringhelli

Interferon regulatory factors IRF regulate lymphoid development, but the specific function of IRF8 in helper T-cell polarization is unclear. Here the authors show that IRF8 forms a complex with IRF4, PU.1 and BATF to modulate the Th9 transcription program and expression of IL-4 and IL-9.

12 December 2017 | doi: 10.1038/s41467-017-01070-w
CD4-positive T cells  Tumour immunology 

High efficiency and long-term intracellular activity of an enzymatic nanofactory based on metal-organic frameworks OPEN
Xizhen Lian, Alfredo Erazo-Oliveras, Jean-Philippe Pellois & Hong-Cai Zhou

Cellular delivery of proteins is currently limited by inefficient release from their carrier or by altering the protein structure after chemical modification. Here the authors use metal-organic frameworks which act as nanofactories and show a supported enzymatic activity for an extended period of time.

12 December 2017 | doi: 10.1038/s41467-017-02103-0
Biomedical materials  Metal–organic frameworks  Nanoparticles 

Bri2 BRICHOS client specificity and chaperone activity are governed by assembly state OPEN
Gefei Chen, Axel Abelein, Harriet E. Nilsson, Axel Leppert, Yuniesky Andrade-Talavera, Simone Tambaro, Lovisa Hemmingsson, Firoz Roshan, Michael Landreh, Henrik Biverstål, Philip J. B. Koeck, Jenny Presto, Hans Hebert, André Fisahn & Jan Johansson

The BRICHOS domain is a chaperone that can act against amyloid-β peptide fibril formation and non-fibrillar protein aggregation. Here the authors use a multidisciplinary approach and show that the Bri2 BRICHOS domain has qualitatively different chaperone activities depending on its quaternary structure.

12 December 2017 | doi: 10.1038/s41467-017-02056-4
Biophysical methods  Chaperones  Diseases of the nervous system  Electron microscopy  Electrophysiology 

Identification and characterization of two functional variants in the human longevity gene FOXO3  OPEN
Friederike Flachsbart, Janina Dose, Liljana Gentschew, Claudia Geismann, Amke Caliebe, Carolin Knecht, Marianne Nygaard, Nandini Badarinarayan, Abdou ElSharawy, Sandra May, Anne Luzius, Guillermo G. Torres, Marlene Jentzsch, Michael Forster, Robert Häesler, Kathrin Pallauf, Wolfgang Lieb, Céline Derbois, Pilar Galan, Dmitriy Drichel et al.

FOXO3 is one of the few established longevity genes. Here, the authors fine-map the FOXO3-longevity association to two intronic SNPs and, using luciferase assays and EMSAs, show that these SNPs affect binding of transcription factors CTCF and SRF and associate with FOXO3 expression.

12 December 2017 | doi: 10.1038/s41467-017-02183-y
Functional genomics  Genetic association study  Genetics 

A Paleocene penguin from New Zealand substantiates multiple origins of gigantism in fossil Sphenisciformes OPEN
Gerald Mayr, R. Paul Scofield, Vanesa L. De Pietri & Alan J. D. Tennyson

The oldest known penguin fossils date to approximately 62 million years ago. Here, Mayr et al. describe Kumimanu biceae, an extinct penguin from approximately 55–60 million years ago, which represents an independent origin of giant size soon after the evolutionary transition from flight to diving.

12 December 2017 | doi: 10.1038/s41467-017-01959-6
Palaeontology  Taxonomy 

Pulsed electroconversion for highly selective enantiomer synthesis OPEN
Chularat Wattanakit, Thittaya Yutthalekha, Sunpet Asssavapanumat, Veronique Lapeyre & Alexander Kuhn

Synthesis of chiral molecules mostly relies on asymmetric catalysis. Here, the authors developed a pulsed electrochemical method to convert a prochiral ketone into the corresponding chiral alcohols with very high enantioselectivity on chiral-imprinted mesoporous platinum.

12 December 2017 | doi: 10.1038/s41467-017-02190-z
Asymmetric synthesis  Electrochemistry  Physical chemistry 

Insights into the structure and assembly of a bacterial cellulose secretion system OPEN
Petya Violinova Krasteva, Joaquin Bernal-Bayard, Laetitia Travier, Fernando Ariel Martin, Pierre-Alexandre Kaminski, Gouzel Karimova, Rémi Fronzes & Jean-Marc Ghigo

Many Gram-negative bacteria secrete exopolysaccharides via functionally homologous synthase-dependent systems. Here the authors use electron microscopy to reveal that biofilm-promoting cellulose in E. coli is secreted by a conserved multi-component secretion system with a megadalton-sized asymmetric architecture.

12 December 2017 | doi: 10.1038/s41467-017-01523-2
Bacterial secretion  Bacterial structural biology  Biofilms  Electron microscopy 

Highly enantioselective catalytic synthesis of chiral pyridines OPEN
Ravindra P. Jumde, Francesco Lanza, Tilde Pellegrini & Syuzanna R. Harutyunyan

Chiral pyridines are valuable building blocks in medicinal chemistry applications. Here, the authors report the copper-catalysed Lewis acid-assisted asymmetric alkylation of β-substituted alkenyl pyridines with Grignard reagents affording chiral pyridines with excellent enantioselectivity.

12 December 2017 | doi: 10.1038/s41467-017-01966-7
Homogeneous catalysis  Medicinal chemistry  Chemical synthesis 

Polymorphic design of DNA origami structures through mechanical control of modular components OPEN
Chanseok Lee, Jae Young Lee & Do-Nyun Kim

The use of staple strands paired with scaffold strands allows the creation of a diverse array of DNA origami nanostructures. Here the authors rationally design a set of staples with variable hinges allowing controllable geometry and flexibility of the final structure.

12 December 2017 | doi: 10.1038/s41467-017-02127-6
DNA nanostructures  Nanostructures  Structural properties 

Multiplexed 3D super-resolution imaging of whole cells using spinning disk confocal microscopy and DNA-PAINT OPEN
Florian Schueder, Juanita Lara-Gutiérrez, Brian J. Beliveau, Sinem K. Saka, Hiroshi M. Sasaki, Johannes B. Woehrstein, Maximilian T. Strauss, Heinrich Grabmayr, Peng Yin & Ralf Jungmann

Existing methods for nanoscale visualization of biological targets in thick samples require complex hardware. Here, the authors combine the standard spinning disk confocal (SDC) microscopy with DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) to image proteins, DNA and RNA deep in cells.

12 December 2017 | doi: 10.1038/s41467-017-02028-8
Confocal microscopy  Single-molecule biophysics  Super-resolution microscopy 

H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1 OPEN
Renata Z. Jurkowska, Su Qin, Goran Kungulovski, Wolfram Tempel, Yanli Liu, Pavel Bashtrykov, Judith Stiefelmaier, Tomasz P. Jurkowski, Srikanth Kudithipudi, Sara Weirich, Raluca Tamas, Hong Wu, Ludmila Dombrovski, Peter Loppnau, Richard Reinhardt, Jinrong Min & Albert Jeltsch

SETDB1 is a histone methyltransferase that generates H3K9me3 marks in euchromatic regions. Here the authors show that the triple Tudor domain (3TD) of SETDB1 binds histone H3 tails containing K14 acetylation combined with K9 methylation, and that the K9me–K14ac modification defines a novel chromatin state enriched at SETDB1 binding sites.

12 December 2017 | doi: 10.1038/s41467-017-02259-9
Epigenetics  Histone analysis  Histone post-translational modifications  Transferases 

An oomycete plant pathogen reprograms host pre-mRNA splicing to subvert immunity OPEN
Jie Huang, Lianfeng Gu, Ying Zhang, Tingxiu Yan, Guanghui Kong, Liang Kong, Baodian Guo, Min Qiu, Yang Wang, Maofeng Jing, Weiman Xing, Wenwu Ye, Zhe Wu, Zhengguang Zhang, Xiaobo Zheng, Mark Gijzen, Yuanchao Wang & Suomeng Dong

Various effectors of plant pathogens modulate host cell biology. Here, Huang et al. show PsAvr3c, an avirulence effector from oomycete plant pathogen Phytophthora sojae, can reprogram host pre-mRNA splicing for immune modulation.

12 December 2017 | doi: 10.1038/s41467-017-02233-5
Effectors in plant pathology  Plant molecular biology 

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors OPEN
Pau Martin-Malpartida, Marta Batet, Zuzanna Kaczmarska, Regina Freier, Tiago Gomes, Eric Aragón, Yilong Zou, Qiong Wang, Qiaoran Xi, Lidia Ruiz, Angela Vea, José A. Márquez, Joan Massagué & Maria J. Macias

Smad transcription factors are part of the TGF-β signal transduction pathways and are recruited to the genome by cell lineage-defining factors. Here, the authors identify specific Smad binding GC-rich motifs and provide structural information showing Smad3 and Smad4 bound to these motifs.

12 December 2017 | doi: 10.1038/s41467-017-02054-6
Molecular biology  Structural biology  Transcription 

Peritoneal tissue-resident macrophages are metabolically poised to engage microbes using tissue-niche fuels OPEN
Luke C. Davies, Christopher M. Rice, Erika M. Palmieri, Philip R. Taylor, Douglas B. Kuhns & Daniel W. McVicar

Tissue-resident marcophages have both generic and tissue-specific functions, but how the latter functions are imbued is still unclear. Here the authors show that peritoneal macrophages express a specialised genetic programme to utilise the locally enriched glutamate for a metabolic setting that facilitates protective in situ immunity.

12 December 2017 | doi: 10.1038/s41467-017-02092-0
Innate immunity  Metabolic pathways  Metabolomics  Peritoneal macrophages 

A miR-327–FGF10–FGFR2-mediated autocrine signaling mechanism controls white fat browning OPEN
Carina Fischer, Takahiro Seki, Sharon Lim, Masaki Nakamura, Patrik Andersson, Yunlong Yang, Jennifer Honek, Yangang Wang, Yanyan Gao, Fang Chen, Nilesh J. Samani, Jun Zhang, Masato Miyake, Seiichi Oyadomari, Akihiro Yasue, Xuri Li, Yun Zhang, Yizhi Liu & Yihai Cao

White adipocytes can be stimulated to express thermogenic genes in a process known as beiging. Here, the authors show that miR-327 is downregulated during beiging, which releases FGF10 from inhibition and supports beige adipocyte formation via signaling through FGFR2.

12 December 2017 | doi: 10.1038/s41467-017-02158-z
miRNAs  Obesity  Type 2 diabetes 

Dynamical trade-offs arise from antagonistic coevolution and decrease intraspecific diversity OPEN
Weini Huang, Arne Traulsen, Benjamin Werner, Teppo Hiltunen & Lutz Becks

How a trait evolves depends on the shape of its fitness trade-off. Here, Huang et al. demonstrate evolution of trade-off shape in an experimental predator-prey system and develop a mathematical model of trait evolution when the underlying trade-off can also evolve.

12 December 2017 | doi: 10.1038/s41467-017-01957-8
Coevolution  Evolutionary theory 

Balancing mcr-1 expression and bacterial survival is a delicate equilibrium between essential cellular defence mechanisms OPEN
Qiue Yang, Mei Li, Owen B. Spiller, Diego O. Andrey, Philip Hinchliffe, Hui Li, Craig MacLean, Pannika Niumsup, Lydia Powell, Manon Pritchard, Andrei Papkou, Yingbo Shen, Edward Portal, Kirsty Sands, James Spencer, Uttapoln Tansawai, David Thomas, Shaolin Wang, Yang Wang, Jianzhong Shen et al.

The plasmid-encoded MCR-1 enzyme modifies bacterial lipid A, thus conferring resistance to the antibiotic colistin. Here, Yang et al. show that MCR-1 expression can decrease in vitro growth rate, fitness and immune stimulation, and can reduce virulence in a Galleria mellonella infection model.

12 December 2017 | doi: 10.1038/s41467-017-02149-0
Antimicrobial resistance  Cellular microbiology 

A modular synthesis of tetracyclic meroterpenoid antibiotics OPEN
Raphael Wildermuth, Klaus Speck, Franz-Lucas Haut, Peter Mayer, Bianka Karge, Mark Brönstrup & Thomas Magauer

Polycyclic meroterpenoids show a wide range of biological activities. Here, the authors report a modular approach to synthesize a number of natural and non-natural tetracyclic meroterpenoids, which display antibiotic activity against methicillin-resistant Staphylococcus aureus.

12 December 2017 | doi: 10.1038/s41467-017-02061-7
Asymmetric synthesis  Chemical libraries  Natural product synthesis 

Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity OPEN
Ian P. Winters, Shin-Heng Chiou, Nicole K. Paulk, Christopher D. McFarland, Pranav V. Lalgudi, Rosanna K. Ma, Leszek Lisowski, Andrew J. Connolly, Dmitri A. Petrov, Mark A. Kay & Monte M. Winslow

Genome editing technologies enable the rapid interrogation of genetic alterations. Here, the authors present a CRISPR/Cas9-based platform to simultaneously investigate multiple activating point mutations in de novo cancers in mice; and generate panels of Kras-variants in different tissues to induce cancer.

12 December 2017 | doi: 10.1038/s41467-017-01519-y
Cancer genetics  Cancer models  Functional genomics  Genetic engineering  Oncogenes 

The representation of colored objects in macaque color patches OPEN
Le Chang, Pinglei Bao & Doris Y. Tsao

Neurons in the inferotemporal cortex (IT) encode object identity; however, how object color is represented here is not well understood. Here the authors report that neurons from three color patches in macaque IT encode significant information regarding the hue and shape of objects in a hierarchical manner.

12 December 2017 | doi: 10.1038/s41467-017-01912-7
Colour vision  Sensory processing 

Forming quasicrystals by monodisperse soft core particles OPEN
Mengjie Zu, Peng Tan & Ning Xu

Quasicrystals with structural symmetries forbidden in crystals have been found in alloys or mono-component systems composed of anisotropic units. Zu et al. show a formation of two-dimensional quasicrystals in an isotropic soft solid with a spring-like potential, which challenges the existing theory.

12 December 2017 | doi: 10.1038/s41467-017-02316-3
Colloids  Structure of solids and liquids 

Controlling supercurrents and their spatial distribution in ferromagnets OPEN
Kaveh Lahabi, Morten Amundsen, Jabir Ali Ouassou, Ewout Beukers, Menno Pleijster, Jacob Linder, Paul Alkemade & Jan Aarts

Controlling supercurrent pathways in a Josephson junction can lead to new functionalities. Here, Lahabi et al. demonstrate the tailoring of two distinct supercurrent channels in a ferromagnetic disk containing a magnetic vortex.

12 December 2017 | doi: 10.1038/s41467-017-02236-2
Spintronics  Superconducting properties and materials 

Uncovering active precursors in colloidal quantum dot synthesis OPEN
Leah C. Frenette & Todd D. Krauss

Little is understood about the chemical evolution of precursors to quantum dots. Here, the authors find that under the high temperature conditions typical of CdSe quantum dot synthesis, precursors decompose into highly reactive species in a critical first step before forming monomers and finally nanocrystals.

12 December 2017 | doi: 10.1038/s41467-017-01936-z
Materials chemistry  Nanoparticle synthesis  Quantum dots 

Complement C3a signaling facilitates skeletal muscle regeneration by regulating monocyte function and trafficking OPEN
Congcong Zhang, Chunxiao Wang, Yulin Li, Takashi Miwa, Chang Liu, Wei Cui, Wen-Chao Song & Jie Du

Regeneration of skeletal muscle is accompanied by a transitory inflammatory phase. Here the authors show that the complement C3 component is activated following muscle injury, and signals through the alternative complement pathway to regulate immune cell infiltration and muscle regeneration.

12 December 2017 | doi: 10.1038/s41467-017-01526-z
Complement cascade  Muscle stem cells  Skeletal muscle 

Loss of the molecular clock in myeloid cells exacerbates T cell-mediated CNS autoimmune disease OPEN
Caroline E. Sutton, Conor M. Finlay, Mathilde Raverdeau, James O. Early, Joseph DeCourcey, Zbigniew Zaslona, Luke A. J. O’Neill, Kingston H. G. Mills & Annie M. Curtis

Circadian controls of immune responses by the molecular clock have been reported, but the underlying mechanisms are unclear. Here the authors show that the master circadian gene, Bmal1, is essential for modulating the homeostasis of myeloid cells to control pro-inflammatory IL-17+/IFN-γ+ T cells in autoimmunity.

12 December 2017 | doi: 10.1038/s41467-017-02111-0
Autoimmunity  CD4-positive T cells  Circadian regulation  Monocytes and macrophages 

Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity OPEN
Pengxiang Fan, Abigail M. Miller, Xiaoxiao Liu, A. Daniel Jones & Robert L. Last

Plants produce large numbers of structurally diverse metabolites through multistep pathways that often use the same precursors. Here the authors utilize the pathway leading to the production of acylated sucroses in the tomato plant to illustrate how metabolite diversity can arise through biochemical pathway evolution.

12 December 2017 | doi: 10.1038/s41467-017-02045-7
Metabolomics  Molecular evolution  Secondary metabolism 

Voltage-gated sodium channels assemble and gate as dimers OPEN
Jérôme Clatot, Malcolm Hoshi, Xiaoping Wan, Haiyan Liu, Ankur Jain, Krekwit Shinlapawittayatorn, Céline Marionneau, Eckhard Ficker, Taekjip Ha & Isabelle Deschênes

Voltage-gated sodium channels are expressed in excitable tissues and mutations have been linked to cardiac arrhythmias and channelopathies. Here the authors show that the sodium channel α-subunits interact to form a dimer and gate as dimer and that this functional dimerisation is conserved.

12 December 2017 | doi: 10.1038/s41467-017-02262-0
Cardiovascular genetics  Ion transport 

Multinational patterns of seasonal asymmetry in human movement influence infectious disease dynamics OPEN
Amy Wesolowski, Elisabeth zu Erbach-Schoenberg, Andrew J. Tatem, Christopher Lourenço, Cecile Viboud, Vivek Charu, Nathan Eagle, Kenth Engø-Monsen, Taimur Qureshi, Caroline O. Buckee & C. J. E. Metcalf

Fine scale mobile phone data is improving capacity to understand seasonal patterns in human movement. Here, the authors use multi-year movement data across three nations, as well as a model of pathogen spread, to understand the consequences of seasonal travel for disease dynamics.

12 December 2017 | doi: 10.1038/s41467-017-02064-4
Developing world  Ecological epidemiology  Ecological modelling  Environmental social sciences 

Endocytosis regulates TDP-43 toxicity and turnover OPEN
Guangbo Liu, Alyssa N. Coyne, Fen Pei, Spencer Vaughan, Matthew Chaung, Daniela C. Zarnescu & J. Ross Buchan

Impaired turnover of TDP-43 by impaired autophagy or proteasomal function have been suggested to be the cause of TDP-43 accumulation, a hallmark of ALS. Here the authors demonstrate that endocytosis is also important for regulating TDP-43 turnover and toxicity.

12 December 2017 | doi: 10.1038/s41467-017-02017-x
Amyotrophic lateral sclerosis  Endocytosis 

PEPD is a pivotal regulator of p53 tumor suppressor OPEN
Lu Yang, Yun Li, Arup Bhattacharya & Yuesheng Zhang

p53 is a pivotal tumour suppressor that is activated by various cellular stress inducers. Here, the authors show that peptidase D (PEPD) promotes the growth of cancer cells by suppressing p53 and that the complex PEPD-p53 is critical for robust p53 activation in response to stress signals.

12 December 2017 | doi: 10.1038/s41467-017-02097-9
Stress signalling  Tumour-suppressor proteins 

Comprehensive phase diagram of two-dimensional space charge doped Bi2Sr2CaCu2O8+x  OPEN
Edoardo Sterpetti, Johan Biscaras, Andreas Erb & Abhay Shukla

The determination of the phase diagram of cuprate superconductors involves chemical doping which introduces disorder and could mask intrinsic effects. Sterpetti et al. establish this phase diagram with transport measurements in ultra-thin samples by modulating the carrier density with an alternative electrostatic method.

12 December 2017 | doi: 10.1038/s41467-017-02104-z
Superconducting properties and materials  Surfaces, interfaces and thin films 

Round complexity in the local transformations of quantum and classical states OPEN
Eric Chitambar & Min-Hsiu Hsieh

Operational paradigms for distributed quantum and classical information processing involve multiple rounds of public communication. Here the authors consider the minimum number of communication rounds needed to perform the locality-constrained task of entanglement transformation.

12 December 2017 | doi: 10.1038/s41467-017-01887-5
Information theory and computation  Quantum information 

Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans OPEN
Ananyo Choudhury, Michèle Ramsay, Scott Hazelhurst, Shaun Aron, Soraya Bardien, Gerrit Botha, Emile R. Chimusa, Alan Christoffels, Junaid Gamieldien, Mahjoubeh J. Sefid-Dashti, Fourie Joubert, Ayton Meintjes, Nicola Mulder, Raj Ramesar, Jasper Rees, Kathrine Scholtz, Dhriti Sengupta, Himla Soodyall, Philip Venter, Louise Warnich et al.

African populations show a high level of genetic diversity and extensive regional admixture. Here, the authors sequence the whole genomes of 24 South African individuals of different ethnolinguistic origin and find substantive genomic divergence between two southeastern Bantu-speaking groups.

12 December 2017 | doi: 10.1038/s41467-017-00663-9
Evolutionary biology  Genetic variation  Population genetics 

Harmonic phase in polar liquids and spin ice OPEN
Steven T. Bramwell

Spin ice materials can be described using idealised models of frustrated magnetism and have motivated a revisiting of the theory of interacting dipolar systems. Bramwell shows that Onsager’s theory of polar liquids describes the Coulomb phase and predicts a distinct ‘harmonic phase’ at finite temperature.

12 December 2017 | doi: 10.1038/s41467-017-02102-1
Magnetic properties and materials  Statistical physics 

Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase OPEN
Jeannette Abplanalp, Mario Leutert, Emilie Frugier, Kathrin Nowak, Roxane Feurer, Jiro Kato, Hans V. A. Kistemaker, Dmitri V. Filippov, Joel Moss, Amedeo Caflisch & Michael O. Hottiger

Protein ADP-ribosylation has emerged as a key post translational modification that regulates several stress responses. Here the authors characterize ARH3 as a major serine-specific mono–ADP-­ribosylhydrolase and use a proteomics approach to identify the cellular targets of ARH3.

12 December 2017 | doi: 10.1038/s41467-017-02253-1
Histone post-translational modifications  Hydrolases  PolyADP-ribosylation  Proteomics 

p16Ink4a and p21Cip1/Waf1 promote tumour growth by enhancing myeloid-derived suppressor cells chemotaxis OPEN
Atsushi Okuma, Aki Hanyu, Sugiko Watanabe & Eiji Hara

Both p16Ink4a and p21Cip1/Waf1 are known oncosuppressors and have a role in senescence. Here, the authors show a pro-tumorigenic role for these two proteins: high expression in myeloid-derived suppressor cells stimulates their chemotactic function, favouring tumour progression.

12 December 2017 | doi: 10.1038/s41467-017-02281-x
Cell migration  Tumour immunology 

Protein quantitative trait locus study in obesity during weight-loss identifies a leptin regulator OPEN
Jérôme Carayol, Christian Chabert, Alessandro Di Cara, Claudia Armenise, Gregory Lefebvre, Dominique Langin, Nathalie Viguerie, Sylviane Metairon, Wim H. M. Saris, Arne Astrup, Patrick Descombes, Armand Valsesia & Jörg Hager

Although many genetic variants are known for obesity, their function remains largely unknown. Here, in a weight-loss intervention cohort, the authors identify protein quantitative trait loci associated with BMI at baseline and after weight loss and find FAM46A to be a regulator of leptin in adipocytes.

12 December 2017 | doi: 10.1038/s41467-017-02182-z
Gene regulation  Obesity  Proteome  Quantitative trait 

parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages OPEN
Enrique Peñalver, Antonio Arillo, Xavier Delclòs, David Peris, David A. Grimaldi, Scott R. Anderson, Paul C. Nascimbene & Ricardo Pérez-de la Fuente

Fossils of ticks are rare, and little is known about their ancient hosts. Here, Peñalver and colleagues describe ticks in Cretaceous amber, including representatives of the new family Deinocrotonidae, which are associated with a dinosaur feather and nest biota.

12 December 2017 | doi: 10.1038/s41467-017-01550-z
Palaeoecology  Palaeontology 

Laboratory layered latte OPEN
Nan Xue, Sepideh Khodaparast, Lailai Zhu, Janine K. Nunes, Hyoungsoo Kim & Howard A. Stone

The ability to form density layering in a fluid in a simple and repeatable way is of relevance to a number of industrial and environmental processes. Here Xue et al. show formation of layers by simple injection of a hot liquid into a warm one at a predetermined critical pouring velocity.

12 December 2017 | doi: 10.1038/s41467-017-01852-2
Fluid dynamics  Gels and hydrogels 

Coupling between oxygen redox and cation migration explains unusual electrochemistry in lithium-rich layered oxides OPEN
William E. Gent, Kipil Lim, Yufeng Liang, Qinghao Li, Taylor Barnes, Sung-Jin Ahn, Kevin H. Stone, Mitchell McIntire, Jihyun Hong, Jay Hyok Song, Yiyang Li, Apurva Mehta, Stefano Ermon, Tolek Tyliszczak, David Kilcoyne, David Vine, Jin-Hwan Park, Seok-Kwang Doo, Michael F. Toney, Wanli Yang et al.

Lithium ion battery electrodes employing anion redox exhibit high energy densities but suffer from poor cyclability. Here the authors reveal that the voltage of anion redox is strongly affected by structural changes that occur during battery cycling, explaining its unique electrochemical properties.

12 December 2017 | doi: 10.1038/s41467-017-02041-x
Batteries  Solid-state chemistry 

Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate OPEN
Matthieu D. Lavigne, Dimitris Konstantopoulos, Katerina Z. Ntakou-Zamplara, Anastasios Liakos & Maria Fousteri

Precise orchestration of gene expression regulation upon DNA damage is essential for genome integrity. Here the authors identify a novel widespread stress-triggered defence mechanism that promotes rapid transcription-driven genomic surveillance thus limiting mutagenesis and shaping cancer genomes.

12 December 2017 | doi: 10.1038/s41467-017-02145-4
Cancer genomics  Melanoma  Nucleotide excision repair  Transcription 

Prodigious submarine landslides during the inception and early growth of volcanic islands OPEN
James E. Hunt & Ian Jarvis

As volcanic islands grow via subaerial shield-building and edifice growth, large submarine landslides occur. Here, the authors reconstruct the emergence of the Canary Islands via turbidites created by submarine landslides as the islands grew, showing that slides are multi-stage.

12 December 2017 | doi: 10.1038/s41467-017-02100-3
Natural hazards  Sedimentology  Volcanology 

Gli1 identifies osteogenic progenitors for bone formation and fracture repair OPEN
Yu Shi, Guangxu He, Wen-Chih Lee, Jennifer A. McKenzie, Matthew J. Silva & Fanxin Long

Skeletal progenitors in postnatal mice are highly heterogeneous. Using lineage tracing and RNA-seq the authors show that Gli1+ cells give rise to all osteoblasts in mice, including those required for healing of bone fractures.

11 December 2017 | doi: 10.1038/s41467-017-02171-2
Bone  Bone development  Regeneration 

Functional reduction in pollination through herbivore-induced pollinator limitation and its potential in mutualist communities OPEN
Paul Glaum & André Kessler

Herbivory-induced volatile organic compounds reduce pollinator visits to plants. Here, Glaum and Kessler show that despite reducing individual fitness, herbivore-induced changes can indirectly benefit overall community resilience, explaining species persistence in antagonized mutualistic communities.

11 December 2017 | doi: 10.1038/s41467-017-02072-4
Community ecology  Herbivory  Plant signalling  Theoretical ecology 

Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration OPEN
Pontus Nordenfelt, Travis I. Moore, Shalin B. Mehta, Joseph Mathew Kalappurakkal, Vinay Swaminathan, Nobuyasu Koga, Talley J. Lambert, David Baker, Jennifer C. Waters, Rudolf Oldenbourg, Tomomi Tani, Satyajit Mayor, Clare M. Waterman & Timothy A. Springer

Integrin αβ heterodimer cell surface receptors mediate adhesive interactions that provide traction for cell migration. Here the authors show that actin flow can orient cell surface integrins during leukocyte migration, suggesting integrin activation by cytoskeletal force.

11 December 2017 | doi: 10.1038/s41467-017-01848-y
Actin  Integrin signalling  Integrins  Molecular imaging  Polarization microscopy 

Identification of regulatory targets for the bacterial Nus factor complex OPEN
Gabriele Baniulyte, Navjot Singh, Courtney Benoit, Richard Johnson, Robert Ferguson, Mauricio Paramo, Anne M. Stringer, Ashley Scott, Pascal Lapierre & Joseph T. Wade

The Nus factor complex regulates rRNA folding and prevents Rho-dependent transcription termination in bacteria. Here, Baniulyte et al. show that it also inhibits translation of one of the Nus factor-encoding genes, suhB, and probably regulates the expression of other genes in diverse bacterial species.

11 December 2017 | doi: 10.1038/s41467-017-02124-9
Bacterial genetics  Bacterial transcription  Gene regulation 

Migratory dendritic cells acquire and present lymphatic endothelial cell-archived antigens during lymph node contraction OPEN
Ross M. Kedl, Robin S. Lindsay, Jeffrey M. Finlon, Erin D. Lucas, Rachel S. Friedman & Beth A. Jirón Tamburini

Viral infection and vaccination both induce lasting persistence of antigens for protective responses. Here the authors show that migratory dendritic cells, independent of the transcription factor BatF3 for their development, contribute to “archived antigen” exchange with lymphatic endothelial cells.

11 December 2017 | doi: 10.1038/s41467-017-02247-z
Antigen-presenting cells  Lymph node  Lymphatic vessels  Conventional dendritic cells 

Pseudogap phase of cuprate superconductors confined by Fermi surface topology OPEN
N. Doiron-Leyraud, O. Cyr-Choinière, S. Badoux, A. Ataei, C. Collignon, A. Gourgout, S. Dufour-Beauséjour, F. F. Tafti, F. Laliberté, M.-E. Boulanger, M. Matusiak, D. Graf, M. Kim, J.-S. Zhou, N. Momono, T. Kurosawa, H. Takagi & Louis Taillefer

High-temperature superconductors exhibit pseudogap behaviour that remains of unknown origin, despite many years of intensive study. Here the authors study the onset of the pseudogap under pressure, providing evidence that it requires a hole-like Fermi surface and constraining future theoretical developments.

11 December 2017 | doi: 10.1038/s41467-017-02122-x
Electronic properties and materials  Superconducting properties and materials 

Loss of PBRM1 rescues VHL dependent replication stress to promote renal carcinogenesis OPEN
Judit Espana-Agusti, Anne Warren, Su Kit Chew, David J. Adams & Athena Matakidou

Mutations in VHL have been linked to clear cell renal cancer, but the molecular mechanisms involved remain unclear. Here the authors generate a mouse model closely mimicking the human disease and show that VHL loss induces DNA replication stress that is rescued by the concomitant loss of PBRM1 permitting transformation.

11 December 2017 | doi: 10.1038/s41467-017-02245-1
Cancer models  Chromatin remodelling  Mechanisms of disease  Renal cell carcinoma  Stalled forks 

Cell cycle-dependent phosphorylation regulates RECQL4 pathway choice and ubiquitination in DNA double-strand break repair OPEN
Huiming Lu, Raghavendra A. Shamanna, Jessica K. de Freitas, Mustafa Okur, Prabhat Khadka, Tomasz Kulikowicz, Priscella P. Holland, Jane Tian, Deborah L. Croteau, Anthony J. Davis & Vilhelm A. Bohr

DNA double-strand break (DSB) repair is a tightly regulated process that can occur via non-homologous end joining (NHEJ) or homologous recombination (HR). Here, the authors investigate how RECQL4 modulates DSB repair pathway choice by differentially regulating NHEJ and HR in a cell cycle-dependent manner.

11 December 2017 | doi: 10.1038/s41467-017-02146-3
DNA  Mechanisms of disease 

Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments OPEN
Yuval Malka, Avital Steiman-Shimony, Eran Rosenthal, Liron Argaman, Leonor Cohen-Daniel, Eliran Arbib, Hanah Margalit, Tommy Kaplan & Michael Berger

Most mammalian genes contain alternative polyadenylation sites. Here, the authors provide evidence that mRNA can be cleaved post-transcriptionally to generate mRNAs with shorter 3-´UTRs and stable autonomous uncapped 3´-UTR sequences.

11 December 2017 | doi: 10.1038/s41467-017-02099-7
Data processing  RNA  RNA metabolism  Transcriptomics 

Electrical synapses convey orientation selectivity in the mouse retina OPEN
Amurta Nath & Gregory W. Schwartz

Visual input received by photoreceptors is relayed to retinal ganglion cells (RGCs), which have selectivity for inputs of certain orientations. Here, the authors show that gap junction-mediated input onto one type of RGC contributes to its orientation selectivity.

11 December 2017 | doi: 10.1038/s41467-017-01980-9
Gap junctions  Neural circuits  Retina  Sensory processing 

Phenotypic plasticity promotes recombination and gene clustering in periodic environments OPEN
Davorka Gulisija & Joshua B. Plotkin

Selection for recombination requires genetic diversity and negative linkage disequilibrium, which can be produced by coevolutionary arms races. Here the authors propose a qualitatively different scenario that can favour recombination in seasonal environments through the ‘genomic storage effect’.

11 December 2017 | doi: 10.1038/s41467-017-01952-z
Evolutionary theory  Population genetics 

The LPS-inducible lncRNA Mirt2 is a negative regulator of inflammation OPEN
Meng Du, Lin Yuan, Xin Tan, Dandan Huang, Xiaojing Wang, Zhe Zheng, Xiaoxiang Mao, Xiangrao Li, Liu Yang, Kun Huang, Fengxiao Zhang, Yan Wang, Xi Luo, Dan Huang & Kai Huang

Excessive inflammation can be tissue destructive and contributes to auotinflammatory diseases and sepsis pathology. Here the authors show that the lncRNA Mirt2 is an endogenous negative feedback regulator of LPS-induced inflammation by limiting ubiquitination of TRAF6 and NF-κB activation.

11 December 2017 | doi: 10.1038/s41467-017-02229-1
Acute inflammation  Long non-coding RNAs 

Sporadic low-velocity volumes spatially correlate with shallow very low frequency earthquake clusters OPEN
Takashi Tonegawa, Eiichiro Araki, Toshinori Kimura, Takeshi Nakamura, Masaru Nakano & Kensuke Suzuki

In the Nankai subduction zone a low-velocity zone (LVZ) has been detected. Here, the authors present shear wave velocity profiles to show that low frequency earthquakes correlate with the distribution of the LVZ in the Nankai subduction zone.

11 December 2017 | doi: 10.1038/s41467-017-02276-8
Geophysics  Seismology  Tectonics 

Mineral surface chemistry control for origin of prebiotic peptides OPEN
Valentina Erastova, Matteo T. Degiacomi, Donald G. Fraser & H. Chris Greenwell

Clay is thought to have played a part in the origin of life. Here, the authors show that layered double hydroxides, a type of clay little studied despite its presumed prevalence on the early Earth, can facilitate the formation of small proteins.

11 December 2017 | doi: 10.1038/s41467-017-02248-y
Computational chemistry  Molecular dynamics  Chemical origin of life 

Solution-phase synthesis of Al13 using a dendrimer template OPEN
Tetsuya Kambe, Naoki Haruta, Takane Imaoka & Kimihisa Yamamoto

Superatoms—clusters that exhibit some of the properties of elemental atoms—could serve as building blocks for functional materials, but their synthesis outside of the gas phase is highly challenging. Here, the authors use a dendrimer template to successfully produce Al13 in solution.

11 December 2017 | doi: 10.1038/s41467-017-02250-4
Inorganic chemistry  Nanoparticles  Synthesis and processing 

Mapping the ecological networks of microbial communities OPEN
Yandong Xiao, Marco Tulio Angulo, Jonathan Friedman, Matthew K. Waldor, Scott T. Weiss & Yang-Yu Liu

Understanding ecological interactions in microbial communities is limited by lack of informative longitudinal abundance data necessary for reliable inference. Here, Xiao et al. develop a method to infer the interactions between microbes based on their abundances in steady-state samples.

11 December 2017 | doi: 10.1038/s41467-017-02090-2
Microbial communities  Community ecology  Ecological networks  Population dynamics 

Efficient dissolved organic carbon production and export in the oligotrophic ocean OPEN
Saeed Roshan & Timothy DeVries

The degree of regional variability in marine dissolved organic carbon (DOC) export production is poorly constrained on a global scale. Here, the authors combine an artificial neural network and a data-constrained ocean circulation model to show that the efficiency of DOC export varies 3-fold across regions.

11 December 2017 | doi: 10.1038/s41467-017-02227-3
Carbon cycle  Marine chemistry 

Magnetostriction-polarization coupling in multiferroic Mn2MnWO6  OPEN
Man-Rong Li, Emma E. McCabe, Peter W. Stephens, Mark Croft, Liam Collins, Sergei V. Kalinin, Zheng Deng, Maria Retuerto, Arnab Sen Gupta, Haricharan Padmanabhan, Venkatraman Gopalan, Christoph P. Grams, Joachim Hemberger, Fabio Orlandi, Pascal Manuel, Wen-Min Li, Chang-Qing Jin, David Walker & Martha Greenblatt

Double corundum-related polar magnets are promising for multiferroic and magnetoelectric applications in spintronics, but are limited by the challenging design and synthesis. Here the authors report the synthesis of Mn2MnWO6 as well as its appealing multiferroic and magnetoelectric properties.

11 December 2017 | doi: 10.1038/s41467-017-02003-3
Ferroelectrics and multiferroics  Solid-state chemistry 

Calcination does not remove all carbon from colloidal nanocrystal assemblies OPEN
Pratyasha Mohapatra, Santosh Shaw, Deyny Mendivelso-Perez, Jonathan M. Bobbitt, Tiago F. Silva, Fabian Naab, Bin Yuan, Xinchun Tian, Emily A. Smith & Ludovico Cademartiri

Synthesis of all-inorganic nanomaterials often relies on organic templates, which are assumed to then be fully removed by calcination. Here, the authors use elastic backscattering spectroscopy to challenge this assumption, finding that calcination leaves behind considerable carbon content that can severely affect material function.

11 December 2017 | doi: 10.1038/s41467-017-02267-9
Design, synthesis and processing  Nanoscale materials 

A mechanistic theory for aquatic food chain length OPEN
Colette L. Ward & Kevin S. McCann

Multiple environmental drivers of food chain length (FCL) have been proposed, but empirical support has been contradictory. Here the authors argue that the magnitude of vertical energy flux in ecological communities underlies two commonly evaluated drivers of FCL and show that the effects of these two drivers are context-dependent.

11 December 2017 | doi: 10.1038/s41467-017-02157-0
Food webs  Theoretical ecology 

EGFR feedback-inhibition by Ran-binding protein 6 is disrupted in cancer OPEN
Barbara Oldrini, Wan-Ying Hsieh, Hediye Erdjument-Bromage, Paolo Codega, Maria Stella Carro, Alvaro Curiel-García, Carl Campos, Maryam Pourmaleki, Christian Grommes, Igor Vivanco, Daniel Rohle, Craig M. Bielski, Barry S. Taylor, Travis J. Hollmann, Marc Rosenblum, Paul Tempst, John Blenis, Massimo Squatrito & Ingo K. Mellinghoff

The epidermal growth factor receptor (EGFR) signalling is regulated at multiple levels. Here the authors show that the importin RanBP6 acts as a tumor suppressor in Glioblastoma and  regulates EGFR signalling through promoting translocation of STAT3 to the nuclei and repressing EGFR transcription.

11 December 2017 | doi: 10.1038/s41467-017-02185-w
CNS cancer  Growth factor signalling 

Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis OPEN
Emmanouil I. Athanasiadis, Jan G. Botthof, Helena Andres, Lauren Ferreira, Pietro Lio & Ana Cvejic

Traditionally marker-based approaches are used to define haematopoietic cell type or state. Here, the authors use single-cell RNA-seq to establish a cellular hierarchy of lineage development in zebrafish haematopoiesis, and propose a refined model of developmental progression of haematopoietic cells.

11 December 2017 | doi: 10.1038/s41467-017-02305-6
Cell biology  Haematopoietic stem cells  Transcriptomics 

Estimation of immune cell content in tumour tissue using single-cell RNA-seq data OPEN
Max Schelker, Sonia Feau, Jinyan Du, Nav Ranu, Edda Klipp, Gavin MacBeath, Birgit Schoeberl & Andreas Raue

Mathematical approaches can be used to assess immune cell composition from the tumour's bulk expression data. Here the authors optimise the CYBERSORT-based deconvolution algorithm by including cell type-specific reference gene expression profiles generated from tumour-derived single-cell RNA sequencing data.

11 December 2017 | doi: 10.1038/s41467-017-02289-3
Cancer microenvironment  Statistical methods  Tumour immunology 

Live bearing promotes the evolution of sociality in reptiles OPEN
Ben Halliwell, Tobias Uller, Barbara R. Holland & Geoffrey M. While

Live birth may be a precursor for parent-offspring associations and subsequent sociality, but the ubiquity of live birth in mammals and parental care in birds precludes testing the relationship in those clades. Here the authors show that live birth, but not egg attendance, is associated with the evolution of social grouping in squamate reptiles.

11 December 2017 | doi: 10.1038/s41467-017-02220-w
Evolutionary ecology  Social evolution 

Two-dimensional topological superconductivity in Pb/Co/Si(111) OPEN
Gerbold C. Ménard, Sébastien Guissart, Christophe Brun, Raphaël T. Leriche, Mircea Trif, François Debontridder, Dominique Demaille, Dimitri Roditchev, Pascal Simon & Tristan Cren

One-dimensional topological superconductors are predicted to host zero-energy Majorana fermions at their extremities. Here, the authors observe dispersive edge states in a monolayer of Pb/Si(111) coupled to a ferromagnetic domain.

11 December 2017 | doi: 10.1038/s41467-017-02192-x
Superconducting properties and materials  Surfaces, interfaces and thin films  Two-dimensional materials 

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing OPEN
Karsten Bach, Sara Pensa, Marta Grzelak, James Hadfield, David J. Adams, John C. Marioni & Walid T. Khaled

There is a need to understand how mammary epithelial cells respond to changes at various developmental stages. Here, the authors use single-cell RNA sequencing of mammary epithelial cells at different adult developmental stages, identifying different cell types and charting their developmental trajectory.

11 December 2017 | doi: 10.1038/s41467-017-02001-5
Computational biology and bioinformatics  Developmental biology 

CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing OPEN
Miguel A. Moreno-Mateos, Juan P. Fernandez, Romain Rouet, Charles E. Vejnar, Maura A. Lane, Emily Mis, Mustafa K. Khokha, Jennifer A. Doudna & Antonio J. Giraldez

Cpf1 is a promising addition to the CRISPR toolkit but displays wide variability of activity in different eurkaryotes. Here the authors identify temperature as a modulator of activity and use this to efficiently edit ectothermic vertebrate species.

08 December 2017 | doi: 10.1038/s41467-017-01836-2
CRISPR-Cas9 genome editing  Genetic engineering 

Spectroscopic identification of active sites for the oxygen evolution reaction on iron-cobalt oxides OPEN
Rodney D. L. Smith, Chiara Pasquini, Stefan Loos, Petko Chernev, Katharina Klingan, Paul Kubella, Mohammad Reza Mohammadi, Diego Gonzalez-Flores & Holger Dau

Optimization of electrocatalysts requires an understanding of all active reaction sites. Here, the authors combine X-ray absorption spectroscopy and electrochemistry to identify cobalt atoms with different coordination geometries and probe their contribution to electrocatalytic water oxidation.

08 December 2017 | doi: 10.1038/s41467-017-01949-8
Characterization and analytical techniques  Electrocatalysis  Electrochemistry 

Alloy-assisted deposition of three-dimensional arrays of atomic gold catalyst for crystal growth studies OPEN
Yin Fang, Yuanwen Jiang, Mathew J. Cherukara, Fengyuan Shi, Kelliann Koehler, George Freyermuth, Dieter Isheim, Badri Narayanan, Alan W. Nicholls, David N. Seidman, Subramanian K. R. S. Sankaranarayanan & Bozhi Tian

Parallel patterning of atoms over a large surface would represent a major advance over current serial methods of single atom manipulation. Here, the authors explore a periodic instability from liquid alloy droplets for high-throughput atom printing.

08 December 2017 | doi: 10.1038/s41467-017-02025-x
Nanowires  Self-assembly  Solid-state chemistry  Synthesis and processing 

Redox-switchable breathing behavior in tetrathiafulvalene-based metal–organic frameworks OPEN
Jian Su, Shuai Yuan, Hai-Ying Wang, Lan Huang, Jing-Yuan Ge, Elizabeth Joseph, Junsheng Qin, Tahir Cagin, Jing-Lin Zuo & Hong-Cai Zhou

Modulating the adsorption behaviours of metal-organic frameworks using external stimuli is desirable, but challenging to achieve. Here, Zhou and colleagues design an indium-based MOF in which tetrathiafulvalene ligands undergo reversible redox reactions that alter the framework breathing behaviour.

08 December 2017 | doi: 10.1038/s41467-017-02256-y
Inorganic chemistry  Metal–organic frameworks  Porous materials 

Exceptional increase in the creep life of magnesium rare-earth alloys due to localized bond stiffening OPEN
Deep Choudhuri, Srivilliputhur G. Srinivasan, Mark A. Gibson, Yufeng Zheng, David L. Jaeger, Hamish L. Fraser & Rajarshi Banerjee

Adding very small amounts of zinc to magnesium alloys containing rare earth elements dramatically improves their creep life. Here, the authors use first principles calculations and atomic-scale characterization to show that this is due to stiff covalent bonding of zinc and rare earth elements such as neodymium.

08 December 2017 | doi: 10.1038/s41467-017-02112-z
Electronic structure  Mechanical properties  Metals and alloys 

Viscosity jump in the lower mantle inferred from melting curves of ferropericlase OPEN
Jie Deng & Kanani K. M. Lee

Viscosity increase in the mantle may cause slab stagnation and plume deflection, but the cause has been unclear. Here, the authors perform experiments showing that the viscosity of ferropericlase increases by 10–100 times from 750 to 1250 km depth indicating a single mechanism for these observations.

08 December 2017 | doi: 10.1038/s41467-017-02263-z
Geodynamics  Geophysics  Mineralogy 

Tuning the interactions between chiral plasmonic films and living cells OPEN
Xueli Zhao, Liguang Xu, Maozhong Sun, Wei Ma, Xiaoling Wu, Chuanlai Xu & Hua Kuang

Chiral surfaces are emerging as important biomaterial components, as they can modulate cell behavior. Here, the authors modify plasmonic nanoparticle films with amino acid isomers, and find that the chirality of the film remarkably affects cell proliferation, adhesion, and directional differentiation.

08 December 2017 | doi: 10.1038/s41467-017-02268-8
Biomedical materials  Nanobiotechnology  Nanoscale materials 

Spatial competition constrains resistance to targeted cancer therapy OPEN
Katarina Bacevic, Robert Noble, Ahmed Soffar, Orchid Wael Ammar, Benjamin Boszonyik, Susana Prieto, Charles Vincent, Michael E. Hochberg, Liliana Krasinska & Daniel Fisher

Adaptive therapy aims to control tumours by exploiting competition between therapy-sensitive and resistant cells. Here, the authors show that tumour spatial structure is a critical parameter for adaptive therapy as competition for space increases fitness differentials, allowing suppression of resistance with low-dose treatments.

08 December 2017 | doi: 10.1038/s41467-017-01516-1
Cancer therapeutic resistance  Cell division 

Immune stealth-driven O2 serotype prevalence and potential for therapeutic antibodies against multidrug resistant Klebsiella pneumoniae  OPEN

Therapeutics to combat multidrug-resistant bacteria such as Klebsiella pneumoniae are needed. Here the authors show immune evasion drives lipopolysaccharide O2 serotype expansion in multidrug-resistant isolates, and anti-O-antigen human monoclonal antibodies synergize with antibiotics to protect mice from infection.

08 December 2017 | doi: 10.1038/s41467-017-02223-7
Bacteriology  Clinical microbiology  Pathogens 

Serendipity and strategy in rapid innovation OPEN
T. M. A. Fink, M. Reeves, R. Palma & R. S. Farr

Organizations can take different approaches to innovation: they can either follow a strategic process or a serendipitous perspective. Here Fink et al. develop a statistical model to analyse how components combine to obtain a product and thus explain the mechanism behind the two approaches.

08 December 2017 | doi: 10.1038/s41467-017-02042-w
Statistical physics  Technology 

RAN translation at C9orf72-associated repeat expansions is selectively enhanced by the integrated stress response OPEN
Katelyn M. Green, M. Rebecca Glineburg, Michael G. Kearse, Brittany N. Flores, Alexander E. Linsalata, Stephen J. Fedak, Aaron C. Goldstrohm, Sami J. Barmada & Peter K. Todd

A nucleotide repeat expansion in C9orf72 is a common genetic cause of neurodegenerative disorders. Here, the authors provide insight into the molecular mechanism by which this repeat undergoes Repeat-Associated Non-AUG (RAN) translation, implicating the integrated stress response and eIF2α phosphorylation.

08 December 2017 | doi: 10.1038/s41467-017-02200-0
Amyotrophic lateral sclerosis  Genetics of the nervous system  RNA metabolism  Translation 

Bioinspired graphene membrane with temperature tunable channels for water gating and molecular separation OPEN
Jingchong Liu, Nü Wang, Li-Juan Yu, Amir Karton, Wen Li, Weixia Zhang, Fengyun Guo, Lanlan Hou, Qunfeng Cheng, Lei Jiang, David A. Weitz & Yong Zhao

The smart regulation of substance permeability is highly desirable for membrane separation technologies. Here, the authors design a poly(N-isopropylacrylamide)-grafted graphene oxide membrane with temperature tunable lamellar spaces, allowing for water gating and size-variable molecular separations.

08 December 2017 | doi: 10.1038/s41467-017-02198-5
Graphene  Organic–inorganic nanostructures  Soft materials 

Input-dependent regulation of excitability controls dendritic maturation in somatosensory thalamocortical neurons OPEN
Laura Frangeul, Vassilis Kehayas, Jose V. Sanchez-Mut, Sabine Fièvre, K. Krishna-K, Gabrielle Pouchelon, Ludovic Telley, Camilla Bellone, Anthony Holtmaat, Johannes Gräff, Jeffrey D. Macklis & Denis Jabaudon

Sensory input and neuronal activity are crucial for proper morphological development of neurons. Here, Frangeul and colleagues show that membrane excitability is a critical component of dendritic development in mouse somatosensory thalamocortical neurons.

08 December 2017 | doi: 10.1038/s41467-017-02172-1
Development of the nervous system  Somatosensory system  Synaptic plasticity 

Brain insulin resistance impairs hippocampal synaptic plasticity and memory by increasing GluA1 palmitoylation through FoxO3a OPEN
Matteo Spinelli, Salvatore Fusco, Marco Mainardi, Federico Scala, Francesca Natale, Rosita Lapenta, Andrea Mattera, Marco Rinaudo, Domenica Donatella Li Puma, Cristian Ripoli, Alfonso Grassi, Marcello D’Ascenzo & Claudio Grassi

Metabolic diseases have been associated with cognitive impairment. Here, the authors show that brain insulin resistance induced by high-fat diet leads to increased palmitoylation of AMPA receptors and thus changes in hippocampal plasticity, learning and memory.

08 December 2017 | doi: 10.1038/s41467-017-02221-9
Metabolism  Molecular neuroscience  Synaptic plasticity 

Ballistic geometric resistance resonances in a single surface of a topological insulator OPEN
Hubert Maier, Johannes Ziegler, Ralf Fischer, Dmitriy Kozlov, Ze Don Kvon, Nikolay Mikhailov, Sergey A. Dvoretsky & Dieter Weiss

Ballistic motion on nanometer scale of topological surface states has rarely been studied. Here, Maier et al. report pronounced geometric resistance resonances of high-mobility Dirac electrons in strained HgTe, suggesting a ballistic effect in three-dimensional topological insulators.

08 December 2017 | doi: 10.1038/s41467-017-01684-0
Electronic devices  Electronic properties and materials  Topological insulators 

Demonstration of ultra-high recyclable energy densities in domain-engineered ferroelectric films OPEN
Hongbo Cheng, Jun Ouyang, Yun-Xiang Zhang, David Ascienzo, Yao Li, Yu-Yao Zhao & Yuhang Ren

Dielectric capacitors offer high-power delivery materials for energy-storage, yet suffer from low energy densities. Here, the authors prepared ferroelectric Ba(Zr0.2,Ti0.8)O3 that utilizes polydomain nanostructures to delay electric polarization saturation and boost energy densities.

08 December 2017 | doi: 10.1038/s41467-017-02040-y
Electronic devices  Electronic properties and materials  Ferroelectrics and multiferroics 

Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution OPEN
Ann-Marie Baker, Weini Huang, Xiao-Ming Mindy Wang, Marnix Jansen, Xiao-Jun Ma, Jeffrey Kim, Courtney M. Anderson, Xingyong Wu, Liuliu Pan, Nan Su, Yuling Luo, Enric Domingo, Timon Heide, Andrea Sottoriva, Annabelle Lewis, Andrew D. Beggs, Nicholas A. Wright, Manuel Rodriguez-Justo, Emily Park, Ian Tomlinson et al.

Methods that analyze intra-tumor genetic heterogeneity often do not preserve the spatial context of tumor subclones. Here, the authors present BaseScope, a mutation-specific RNA in situ hybridization assay and spatially map colorectal cancer and adenoma KRAS, BRAF and PIK3CA driver gene mutant subclones.

08 December 2017 | doi: 10.1038/s41467-017-02295-5
Colorectal cancer  Genetic techniques  Tumour heterogeneity 

The dynamic dimer structure of the chaperone Trigger Factor OPEN
Leonor Morgado, Björn M. Burmann, Timothy Sharpe, Adam Mazur & Sebastian Hiller

The bacterial chaperone Trigger Factor (TF) is a dynamic protein and its dimer structure is unknown. Here the authors present a protocol combining NMR, computational and biophysical methods for the structural characterization of large dynamic protein complexes and show that TF forms a symmetric head-to-tail dimer.

08 December 2017 | doi: 10.1038/s41467-017-02196-7
Chaperones  Solution-state NMR 

Induced unconventional superconductivity on the surface states of Bi2Te3 topological insulator OPEN
Sophie Charpentier, Luca Galletti, Gunta Kunakova, Riccardo Arpaia, Yuxin Song, Reza Baghdadi, Shu Min Wang, Alexei Kalaboukhov, Eva Olsson, Francesco Tafuri, Dmitry Golubev, Jacob Linder, Thilo Bauch & Floriana Lombardi

Proximity effect may induce unconventional superconductivity in the topologically protected surface states of a topological insulator, however experimental evidence remains rare. Here, Charpentier et al. report proximity effect induced superconductivity in nanoscale Josephson junctions and suggest an unconventional p-wave order parameter.

08 December 2017 | doi: 10.1038/s41467-017-02069-z
Superconducting devices  Superconducting properties and materials  Topological insulators 

Crystal structure of an RNA-cleaving DNAzyme OPEN
Hehua Liu, Xiang Yu, Yiqing Chen, Jing Zhang, Baixing Wu, Lina Zheng, Phensinee Haruehanroengra, Rui Wang, Suhua Li, Jinzhong Lin, Jixi Li, Jia Sheng, Zhen Huang, Jinbiao Ma & Jianhua Gan

RNA-cleaving DNA enzymes are catalytic DNA that can cleave RNA in a sequence-specific manner. Here, the authors report three crystal structures of the 8–17 DNAzyme that include the pre-catalytic state of the RNA cleavage reaction, providing insight into the catalytic mechanism and may guide the rational design of DNAzymes.

08 December 2017 | doi: 10.1038/s41467-017-02203-x
DNA  Enzyme mechanisms  Ribozymes  X-ray crystallography 

Atlantic deep water provenance decoupled from atmospheric CO2 concentration during the lukewarm interglacials OPEN
Jacob N. W. Howe & Alexander M. Piotrowski

How deep ocean circulation is linked to changes in atmospheric CO2 concentration remains uncertain. Here, the authors show that deep equatorial Atlantic Ocean water mass provenance was similar throughout all interglacials of the past 800 kyr, despite variable interglacial atmospheric CO2 concentrations.

08 December 2017 | doi: 10.1038/s41467-017-01939-w
Palaeoceanography  Palaeoclimate 

Andean mountain building and magmatic arc migration driven by subduction-induced whole mantle flow OPEN
W. P. Schellart

The Andean orogeny commenced in the Cretaceous, but was preceded by backarc extension starting in the Jurassic. Here, the author presents a 4D geodynamic subduction model reproducing the evolution of overriding plate deformation along with a progressive decrease in slab dip, explaining Jurassic-present arc migration.

08 December 2017 | doi: 10.1038/s41467-017-01847-z
Geodynamics  Geophysics  Tectonics  Volcanology 

Hippocampal oxytocin receptors are necessary for discrimination of social stimuli OPEN
Tara Raam, Kathleen M. McAvoy, Antoine Besnard, Alexa Veenema & Amar Sahay

While oxytocin is known to be critical for social recognition, the functions of oxytocin receptors (Oxtrs) in the hippocampus are not known. This study shows that Oxtrs in anterior dentate gyrus and CA2/CA3 pyramidal cells recruit population-based coding to mediate discrimination of social stimuli.

08 December 2017 | doi: 10.1038/s41467-017-02173-0
Social behaviour  Social neuroscience 

Different carotenoid conformations have distinct functions in light-harvesting regulation in plants OPEN
Nicoletta Liguori, Pengqi Xu, Ivo H.M. van Stokkum, Bart van Oort, Yinghong Lu, Daniel Karcher, Ralph Bock & Roberta Croce

Carotenoids can dissipate excess energy captured by photosynthetic light-harvesting complexes to prevent photodamage. Here, via spectroscopic and in silico approaches, Liguori et al. resolve different carotenoid dark states and propose conformational changes that permit them to act as either energy donors or quenchers.

08 December 2017 | doi: 10.1038/s41467-017-02239-z
Antenna complex  Bioenergetics  Light responses  Light stress 

An assessment of the global impact of 21st century land use change on soil erosion OPEN
Pasquale Borrelli, David A. Robinson, Larissa R. Fleischer, Emanuele Lugato, Cristiano Ballabio, Christine Alewell, Katrin Meusburger, Sirio Modugno, Brigitta Schütt, Vito Ferro, Vincenzo Bagarello, Kristof Van Oost, Luca Montanarella & Panos Panagos

Human activity and related land use change are the primary cause of soil erosion. Here, the authors show the impacts of 21st century global land use change on soil erosion based on an unprecedentedly high resolution global model that provides insights into the mitigating effects of conservation agriculture.

08 December 2017 | doi: 10.1038/s41467-017-02142-7
Carbon cycle  Environmental impact  Geomorphology  Sustainability 

Tree co-occurrence and transcriptomic response to drought OPEN
Nathan G. Swenson, Yoshiko Iida, Robert Howe, Amy Wolf, María Natalia Umaña, Krittika Petprakob, Benjamin L. Turner & Keping Ma

Drought has a major influence on plant distribution. Here, Swenson et al. show that a similar gene expression response to experimental drought outperforms traditional functional traits and phylogenetic relatedness as a predictor of co-occurrence of tree species in a natural stand.

08 December 2017 | doi: 10.1038/s41467-017-02034-w
Community ecology  Forest ecology 

Semiconductor SERS enhancement enabled by oxygen incorporation OPEN
Zuhui Zheng, Shan Cong, Wenbin Gong, Jinnan Xuan, Guohui Li, Weibang Lu, Fengxia Geng & Zhigang Zhao

The application of non-metal-oxide semiconductor materials as surface-enhanced Raman spectroscopy (SERS) substrates is impeded by their low SERS enhancement and detection sensitivity. Here, the authors develop a general oxygen incorporation strategy to magnify these parameters.

08 December 2017 | doi: 10.1038/s41467-017-02166-z
Materials for optics  Optical materials and structures  Sensors 

HEB is required for the specification of fetal IL-17-producing γδ T cells OPEN
Tracy S. H. In, Ashton Trotman-Grant, Shawn Fahl, Edward L. Y. Chen, Payam Zarin, Amanda J. Moore, David L. Wiest, Juan Carlos Zúñiga-Pflücker & Michele K. Anderson

The γδ T cell pool includes abundant IL-17-producing cells that protect mucosal surfaces, but the signals that control γδ T cell specification are unclear. Here the authors identify a role for the transcription factor HEB, and antagonistic activity of Id3, in the development of these cells.

08 December 2017 | doi: 10.1038/s41467-017-02225-5
Gammadelta T cells  Gene regulation in immune cells  Lymphopoiesis 

Scaling of Yu-Shiba-Rusinov energies in the weak-coupling Kondo regime OPEN
Nino Hatter, Benjamin W. Heinrich, Daniela Rolf & Katharina J. Franke

The description of a paramagnetic impurity on a superconductor remains elusive in the weak-coupling Kondo regime. Here, Hatter et al. correlate the energy of the Yu-Shiba-Rusinov bound states with the intensity of the Kondo resonances in such a regime, revealing a behavior well described by classical spin models.

08 December 2017 | doi: 10.1038/s41467-017-02277-7
Magnetic properties and materials  Superconducting properties and materials 

Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice OPEN
Raquel Chamorro-Garcia, Carlos Diaz-Castillo, Bassem M. Shoucri, Heidi Käch, Ron Leavitt, Toshi Shioda & Bruce Blumberg

Early life exposure to endocrine disrupting chemicals has been linked to increased adiposity during adulthood. Here Chamorro-García et al. show that ancestral exposure to the obesogen tributyltin causes obesity in untreated F4 generation male descendants by inducing heritable changes in genome architecture that promote a thrifty phenotype.

08 December 2017 | doi: 10.1038/s41467-017-01944-z
DNA methylation  Obesity 

Multivalent cross-linking of actin filaments and microtubules through the microtubule-associated protein Tau OPEN
Yunior Cabrales Fontela, Harindranath Kadavath, Jacek Biernat, Dietmar Riedel, Eckhard Mandelkow & Markus Zweckstetter

The microtubule associated protein Tau also interacts with filamentous actin. Here the authors combine biophysical experiments and NMR studies to characterize the structural changes that occur in Tau upon binding to filamentous actin and show that phosphorylation of serine 262 attenuates actin binding of Tau.

07 December 2017 | doi: 10.1038/s41467-017-02230-8
Neural ageing  Solution-state NMR 

Tailoring crystallization phases in metallic glass nanorods via nucleus starvation OPEN
Sungwoo Sohn, Yujun Xie, Yeonwoong Jung, Jan Schroers & Judy J. Cha

Crystallising a bulk metallic glass usually results in separate phases. Here, the authors use metallic glass nanorods to show that as the sample size approaches the nucleation scale lengths, the crystallization behavior is dictated by the lack of nuclei and nanorods crystallise into a single phase.

07 December 2017 | doi: 10.1038/s41467-017-02153-4
Glasses  Nanowires  Phase transitions and critical phenomena  Transmission electron microscopy 

Evidence for a topological excitonic insulator in InAs/GaSb bilayers OPEN
Lingjie Du, Xinwei Li, Wenkai Lou, Gerard Sullivan, Kai Chang, Junichiro Kono & Rui-Rui Du

Weakly bound electron–hole pairs may condensate in two-dimensional systems, but experimental evidence has been lacking. Here, Du et al. report optical spectroscopic and electronic transport evidences for the formation of an excitonic insulator gap in topological InAs/GaSb quantum wells.

07 December 2017 | doi: 10.1038/s41467-017-01988-1
Electronic properties and materials  Topological insulators 

NLRP11 attenuates Toll-like receptor signalling by targeting TRAF6 for degradation via the ubiquitin ligase RNF19A OPEN
Chenglei Wu, Zexiong Su, Meng Lin, Jiayu Ou, Wei Zhao, Jun Cui & Rong-Fu Wang

NLRP11 is a primate-specific NOD-like receptor with unclear function. Here the authors show NLRP11 is an inhibitory protein that targets TRAF6 for K48 ubiquitination-mediated proteasomal degradation to limit inflammatory responses.

07 December 2017 | doi: 10.1038/s41467-017-02073-3
Innate immunity  Signal transduction  Ubiquitylation 

On the impact of capillarity for strength at the nanoscale OPEN
Nadiia Mameka, Jürgen Markmann & Jörg Weissmüller

Nanoscale crystals can experience lattice instability and a tension-compression asymmetry of their strength. Here, Mameka and colleagues scrutinize the proposition that these phenomena arise from surface-induced stress, finding that the surface tension contributes significantly, while the surface stress does not measurably impact the nanomechanical behaviour.

07 December 2017 | doi: 10.1038/s41467-017-01434-2
Nanowires  Structural properties 

low neurotrophin receptor CD271 regulates phenotype switching in melanoma OPEN
Gaetana Restivo, Johanna Diener, Phil F. Cheng, Gregor Kiowski, Mario Bonalli, Thomas Biedermann, Ernst Reichmann, Mitchell P. Levesque, Reinhard Dummer & Lukas Sommer

The aggressive nature of melanoma cells relies on their ability to switch from a high-proliferative/low-invasive to a low-proliferative/high-invasive state; however, the mechanisms governing this switch are unclear. Here, using in vivo models of human melanoma, the authors show that CD271 is a key regulator of phenotype switching and metastasis formation.

07 December 2017 | doi: 10.1038/s41467-017-01573-6
Melanoma  Metastasis 

Roles of two types of heparan sulfate clusters in Wnt distribution and signaling in Xenopus  OPEN
Yusuke Mii, Takayoshi Yamamoto, Ritsuko Takada, Shuji Mizumoto, Makoto Matsuyama, Shuhei Yamada, Shinji Takada & Masanori Taira

Wnt proteins mediate embryonic development but how protein localization and patterning is regulated is unclear. Here, the authors show that distinct structures with different heparan sulfate modifications (‘N-sulfo-rich’ and ‘N-acetyl-rich’) regulate cellular localization and signal transduction of Wnt8 in Xenopus.

07 December 2017 | doi: 10.1038/s41467-017-02076-0
Embryonic induction  Glycobiology  Morphogen signalling 

The end-joining factor Ku acts in the end-resection of double strand break-free arrested replication forks OPEN
Ana Teixeira-Silva, Anissia Ait Saada, Julien Hardy, Ismail Iraqui, Marina Charlotte Nocente, Karine Fréon & Sarah A. E. Lambert

Terminally arrested replication forks are restarted through homologous recombination after processing single-stranded DNA gaps. Here the authors show that resection is regulated by the NHEJ factor Ku, helping to fine-tune recombination at forks.

07 December 2017 | doi: 10.1038/s41467-017-02144-5
DNA recombination  Stalled forks 

Malaria parasite DNA-harbouring vesicles activate cytosolic immune sensors OPEN
Xavier Sisquella, Yifat Ofir-Birin, Matthew A. Pimentel, Lesley Cheng, Paula Abou Karam, Natália G. Sampaio, Jocelyn Sietsma Penington, Dympna Connolly, Tal Giladi, Benjamin J. Scicluna, Robyn A. Sharples, Andreea Waltmann, Dror Avni, Eli Schwartz, Louis Schofield, Ziv Porat, Diana S. Hansen, Anthony T. Papenfuss, Emily M. Eriksson, Motti Gerlic et al.

STING is an intracellular DNA sensor that can alter response to infection, but in the case of malaria it is unclear how parasite DNA in red blood cells (RBCs) reaches DNA sensors in immune cells. Here the authors show that STING in human monocytes can sense P. falciparum nucleic acids transported from infected RBCs via parasite extracellular vesicles.

07 December 2017 | doi: 10.1038/s41467-017-02083-1
Parasite host response  Pattern recognition receptors 

Differentially evolved glucosyltransferases determine natural variation of rice flavone accumulation and UV-tolerance OPEN
Meng Peng, Raheel Shahzad, Ambreen Gul, Hizar Subthain, Shuangqian Shen, Long Lei, Zhigang Zheng, Junjie Zhou, Dandan Lu, Shouchuang Wang, Elsayed Nishawy, Xianqing Liu, Takayuki Tohge, Alisdair R. Fernie & Jie Luo

In contrast to flavonols, the functions of plant flavones are largely unknown. Here, the authors report the two differentially evolved glucosyltranferases (flavone 7-O-glucosyltransferase and flavone 5-O-glucosyltransferase) determine natural variation of rice flavone accumulation and UV-tolerance.

07 December 2017 | doi: 10.1038/s41467-017-02168-x
Agricultural genetics  Genome-wide association studies  Natural variation in plants  Plant genetics 

Controlled spin switching in a metallocene molecular junction OPEN
M. Ormaza, P. Abufager, B. Verlhac, N. Bachellier, M.-L. Bocquet, N. Lorente & L. Limot

Manipulating spin states of molecules in a controllable manner is essential to develop the molecule-based spintronics technologies. Here, Ormaza et al. show how to use the interaction between a single metallocene molecule and a metallic surface to reversibly switch spin from 1 to ½ in a junction.

07 December 2017 | doi: 10.1038/s41467-017-02151-6
Characterization and analytical techniques  Electronic structure  Magnetic properties and materials  Surfaces, interfaces and thin films 

Auditory closed-loop stimulation of EEG slow oscillations strengthens sleep and signs of its immune-supportive function OPEN
Luciana Besedovsky, Hong-Viet V. Ngo, Stoyan Dimitrov, Christoph Gassenmaier, Rainer Lehmann & Jan Born

Circulating hormones undergo fluctuations during sleep. Here, the authors increase electroencephalographic slow oscillations (SO) during sleep in men using an auditory closed-loop stimulation, and show that the circulating level of cortisol, aldosterone and immune cell count can be altered.

07 December 2017 | doi: 10.1038/s41467-017-02170-3
Endocrinology  Neuroimmunology  Slow-wave sleep 

REST regulates the cell cycle for cardiac development and regeneration OPEN
Donghong Zhang, Yidong Wang, Pengfei Lu, Ping Wang, Xinchun Yuan, Jiangyun Yan, Chenleng Cai, Ching-Pin Chang, Deyou Zheng, Bingruo Wu & Bin Zhou

The mechanisms regulating cardiomyocyte proliferation during development and cardiac regeneration are incompletely understood. The authors show that the transcription factor REST regulates cardiomyocyte proliferation by binding and repressing the cell cycle inhibitor p21.

07 December 2017 | doi: 10.1038/s41467-017-02210-y
Cardiac regeneration  Cell growth  Cell proliferation  Heart development 

Stateful characterization of resistive switching TiO2 with electron beam induced currents OPEN
Brian D. Hoskins, Gina C. Adam, Evgheni Strelcov, Nikolai Zhitenev, Andrei Kolmakov, Dmitri B. Strukov & Jabez J. McClelland

Oxide-based memristors hold promise for artificial neuromorphic computing, yet the detail of the switching mechanism—filament formation—remains largely unknown. Hoskins et al. provide nanoscale imaging of this process using electron beam induced current microscopy and relate it to resistive states.

07 December 2017 | doi: 10.1038/s41467-017-02116-9
Electrical and electronic engineering  Electronic devices 

Characterization of a membrane-bound C-glucosyltransferase responsible for carminic acid biosynthesis in Dactylopius coccus Costa OPEN
Rubini Kannangara, Lina Siukstaite, Jonas Borch-Jensen, Bjørn Madsen, Kenneth T. Kongstad, Dan Staerk, Mads Bennedsen, Finn T. Okkels, Silas A. Rasmussen, Thomas O. Larsen, Rasmus J. N. Frandsen & Birger Lindberg Møller

Carminic acid is a widely applied red colorant that is still harvested from insects because its biosynthesis is not fully understood. Here, the authors identify and characterize a membrane-bound C-glucosyltransferase catalyzing the final step during carminic acid biosynthesis.

07 December 2017 | doi: 10.1038/s41467-017-02031-z
Glycosylation  Natural product synthesis  Transferases 

Rhythmic potassium transport regulates the circadian clock in human red blood cells OPEN
Erin A. Henslee, Priya Crosby, Stephen J. Kitcatt, Jack S. W. Parry, Andrea Bernardini, Rula G. Abdallat, Gabriella Braun, Henry O. Fatoyinbo, Esther J. Harrison, Rachel S. Edgar, Kai F. Hoettges, Akhilesh B. Reddy, Rita I. Jabr, Malcolm von Schantz, John S. O’Neill & Fatima H. Labeed

Circadian rhythms usually rely on cyclic variations in gene expression. Red blood cells, however, display circadian rhythms while being devoid of nuclear DNA. Here, Henslee and colleagues show that circadian rhythms in isolated human red blood cells are dependent on rhythmic transport of K+ ions.

07 December 2017 | doi: 10.1038/s41467-017-02161-4
Blood flow  Circadian rhythms  Electrophysiology 

Allosteric pyruvate kinase-based “logic gate” synergistically senses energy and sugar levels in Mycobacterium tuberculosis  OPEN
Wenhe Zhong, Liang Cui, Boon Chong Goh, Qixu Cai, Peiying Ho, Yok Hian Chionh, Meng Yuan, Abbas El Sahili, Linda A. Fothergill-Gilmore, Malcolm D. Walkinshaw, Julien Lescar & Peter C. Dedon

Pyruvate kinase (PYK) controls glycolytic flux. Here, the authors combine biochemical, structural and computational modelling studies to characterize the allosteric mechanisms regulating Mycobacterium tuberculosis PYK activity and show that AMP and glucose-6-phosphate are synergistic allosteric activators of the enzyme.

07 December 2017 | doi: 10.1038/s41467-017-02086-y
Enzyme mechanisms  Infectious diseases  Metabolomics  Pathogens  X-ray crystallography 
 
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