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woensdag 10 januari 2018

Nature Communications -10 January 2018

 
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Ancient environmental DNA reveals shifts in dominant mutualisms during the late Quaternary OPEN
Martin Zobel, John Davison, Mary E. Edwards, Christian Brochmann, Eric Coissac, Pierre Taberlet, Eske Willerslev & Mari Moora

Recently, an eDNA metabarcoding data set was used to describe northern high-latitude vegetation during the past 50,000 years. Here, Zobel et al. use the data set to examine how the abundance of key plant mutualistic traits changed during this period and discuss possible environmental drivers.

10 January 2018 | doi: 10.1038/s41467-017-02421-3
Biodiversity  Biogeography  Climate-change ecology  Community ecology  Palaeoclimate 

Membrane shape-mediated wave propagation of cortical protein dynamics OPEN
Zhanghan Wu, Maohan Su, Cheesan Tong, Min Wu & Jian Liu

Traveling waves in the cell cortex can propagate much faster than actin waves, and the mechanism is unknown. Here the authors propose a mechanochemical feedback model for traveling waves that incorporates membrane shape changes and recruitment of F-BAR proteins that enables fast wave propagation.

10 January 2018 | doi: 10.1038/s41467-017-02469-1
Actin  Computational biophysics  Membrane biophysics 

Large-scale ocean connectivity and planktonic body size OPEN
Ernesto Villarino, James R. Watson, Bror Jönsson, Josep M. Gasol, Guillem Salazar, Silvia G. Acinas, Marta Estrada, Ramón Massana, Ramiro Logares, Caterina R. Giner, Massimo C. Pernice, M. Pilar Olivar, Leire Citores, Jon Corell, Naiara Rodríguez-Ezpeleta, José Luis Acuña, Axayacatl Molina-Ramírez, J. Ignacio González-Gordillo, Andrés Cózar, Elisa Martí et al.

Body size is hypothesised to be a major determinant of β-diversity in passively-dispersing marine organisms. Here, Villarino et al. show that plankton body size determines rates of dispersal along marine currents, with shorter dispersal and higher species spatial turnover in larger organisms.

10 January 2018 | doi: 10.1038/s41467-017-02535-8
Biodiversity  Macroecology  Microbial ecology 

Maturation of the gut microbiome and risk of asthma in childhood OPEN
Jakob Stokholm, Martin J. Blaser, Jonathan Thorsen, Morten A. Rasmussen, Johannes Waage, Rebecca K. Vinding, Ann-Marie M. Schoos, Asja Kunøe, Nadia R. Fink, Bo L. Chawes, Klaus Bønnelykke, Asker D. Brejnrod, Martin S. Mortensen, Waleed Abu Al-Soud, Søren J. Sørensen & Hans Bisgaard

Colonization of commensal bacteria is thought to impact immune development, especially in the earliest years of life. Here, the authors show, by analyzing the development of the gut microbiome of 690 children, that microbial composition at the age of 1 year is associated with asthma diagnosed in the first 5 years of life.

10 January 2018 | doi: 10.1038/s41467-017-02573-2
Inflammatory diseases  Microbiome  Paediatric research 

The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading OPEN
Brooke M. Gardner, Dominic T. Castanzo, Saikat Chowdhury, Goran Stjepanovic, Matthew S. Stefely, James H. Hurley, Gabriel C. Lander & Andreas Martin

Pex1 and Pex6 form a heterohexameric Type-2 AAA-ATPase motor whose function in peroxisomal matrix-protein import is still debated. Here, the authors combine structural, biochemical, and cell-biological approaches to show that Pex1/Pex6 is a protein unfoldase, which supports a role in mechanical unfolding of peroxin proteins.

10 January 2018 | doi: 10.1038/s41467-017-02474-4
Electron microscopy  Enzyme mechanisms  Mechanisms of disease  Peroxisomes  X-ray crystallography 

Multilayer networks reveal the spatial structure of seed-dispersal interactions across the Great Rift landscapes OPEN
Sérgio Timóteo, Marta Correia, Susana Rodríguez-Echeverría, Helena Freitas & Ruben Heleno

Species interaction networks have been usually delimited by perceived habitat borders. Here, seed-dispersal is analyzed as a regional multilayer network of interconnected habitats, highlighting the key role of versatile dispersers for the functional cohesion of the whole Gorongosa landscape.

10 January 2018 | doi: 10.1038/s41467-017-02658-y
Community ecology  Ecological networks  Tropical ecology 

Green synthesis of graphene oxide by seconds timescale water electrolytic oxidation OPEN
Songfeng Pei, Qinwei Wei, Kun Huang, Hui-Ming Cheng & Wencai Ren

Graphene oxide is a graphene derivative showing wide applications, but it suffers from harsh synthetic conditions and long reaction time. Pei et al. show a green electrochemical method to fully oxidize the graphite lattice in a few seconds, which is over 100 times faster than existing methods.

10 January 2018 | doi: 10.1038/s41467-017-02479-z
Synthesis of graphene 

Desumoylase SENP6 maintains osteochondroprogenitor homeostasis by suppressing the p53 pathway OPEN
Jianshuang Li, Di Lu, Hong Dou, Huadie Liu, Kevin Weaver, Wenjun Wang, Jiada Li, Edward T.H. Yeh, Bart O. Williams, Tao Yang & Ling Zheng

Osteochondroprogenitors are essential cells for skeletal development and homeostasis. Here the authors show that the desumoylase SENP6 suppresses p53 activity by desumoylating and stabilising TRIM28, and that SENP6 ablation leads to skeletal abnormalities, senescence in osteochondroprogenitors and chondrocytes, and premature ageing.

10 January 2018 | doi: 10.1038/s41467-017-02413-3
Bone development  Cartilage development  Mesenchymal stem cells  Senescence 

Integrative genomic and transcriptomic analysis of leiomyosarcoma OPEN
Priya Chudasama, Sadaf S. Mughal, Mathijs A. Sanders, Daniel Hübschmann, Inn Chung, Katharina I. Deeg, Siao-Han Wong, Sophie Rabe, Mario Hlevnjak, Marc Zapatka, Aurélie Ernst, Kortine Kleinheinz, Matthias Schlesner, Lina Sieverling, Barbara Klink, Evelin Schröck, Remco M. Hoogenboezem, Bernd Kasper, Christoph E. Heilig, Gerlinde Egerer et al.

The molecular genetic landscape of leiomyosarcoma (LMS) is largely unknown. Here, the authors identify frequent DNA copy number alterations, whole-genome duplication, TP53 and RB1 inactivation, alternative telomere lengthening, and genomic imprints of defective DNA repair via homologous recombination as a potential therapeutic target in LMS patients.

10 January 2018 | doi: 10.1038/s41467-017-02602-0
Cancer genomics  Sarcoma 

Biotransformation of polyunsaturated fatty acids to bioactive hepoxilins and trioxilins by microbial enzymes OPEN
Jung-Ung An, Yong-Seok Song, Kyoung-Rok Kim, Yoon-Joo Ko, Do-Young Yoon & Deok-Kun Oh

Hepoxilins (HXs) and trioxilins (TrXs) are lipid metabolites with roles in inflammation and insulin secretion. Here, the authors discover a prokaryotic source of HXs and TrXs, identify the biosynthetic enzymes and heterologously express HXs and TrXs in E. coli.

09 January 2018 | doi: 10.1038/s41467-017-02543-8
Biocatalysis  Metabolic engineering  Multienzyme complexes 

The evolution of substrate discrimination in macrolide antibiotic resistance enzymes OPEN
Andrew C. Pawlowski, Peter J. Stogios, Kalinka Koteva, Tatiana Skarina, Elena Evdokimova, Alexei Savchenko & Gerard D. Wright

New antibiotics with reduced potential for resistance are urgently needed. Here, the authors use a multidisciplinary approach to characterize substrate discrimination in macrolide resistance kinases and present a strategy for the prediction of mutations that expand the substrate range of antibiotic-inactivating enzymes.

09 January 2018 | doi: 10.1038/s41467-017-02680-0
Antimicrobial resistance  Kinases  Molecular evolution  X-ray crystallography 

SIRT6-dependent cysteine monoubiquitination in the PRE-SET domain of Suv39h1 regulates the NF-κB pathway OPEN
Irene Santos-Barriopedro, Laia Bosch-Presegué, Anna Marazuela-Duque, Carolina de la Torre, Carlota Colomer, Berta N. Vazquez, Thomas Fuhrmann, Bárbara Martínez-Pastor, Wenfu Lu, Thomas Braun, Eva Bober, Thomas Jenuwein, Lourdes Serrano, Manel Esteller, Zhenbang Chen, Silvia Barceló-Batllori, Raúl Mostoslavsky, Lluis Espinosa & Alejandro Vaquero

Sirtuins are involved in the regulation of responses to diverse types of cellular stress. Here the authors describe the SirT6-dependent cysteine monoubiquitination of the histone methyltransferase Suv39h1 as part of a regulatory circuit for the NF-κB pathway.

09 January 2018 | doi: 10.1038/s41467-017-02586-x
Chromatin  Gene silencing  Histone post-translational modifications 

Zika virus infection induces host inflammatory responses by facilitating NLRP3 inflammasome assembly and interleukin-1β secretion OPEN
Wenbiao Wang, Geng Li, De Wu, Zhen Luo, Pan Pan, Mingfu Tian, Yingchong Wang, Feng Xiao, Aixin Li, Kailang Wu, Xiaohong Liu, Lang Rao, Fang Liu, Yingle Liu & Jianguo Wu

The NLRP3 inflammasome plays an important role in antiviral host responses. Here, the authors reveal that the polymerase of Zika virus binds NLRP3 to facilitate inflammasome complex assembly and induce production of IL-1β in human macrophages, human PBMCs and mice, resulting in pathogenesis in mice.

09 January 2018 | doi: 10.1038/s41467-017-02645-3
Inflammasome  Virus–host interactions 

Development of an oral once-weekly drug delivery system for HIV antiretroviral therapy OPEN
Ameya R. Kirtane, Omar Abouzid, Daniel Minahan, Taylor Bensel, Alison L. Hill, Christian Selinger, Anna Bershteyn, Morgan Craig, Shirley S. Mo, Hormoz Mazdiyasni, Cody Cleveland, Jaimie Rogner, Young-Ah Lucy Lee, Lucas Booth, Farhad Javid, Sarah J. Wu, Tyler Grant, Andrew M. Bellinger, Boris Nikolic, Alison Hayward et al.

Poor adherence to daily antiretrovirals can significantly affect treatment efficacy, but oral long-acting antiretrovirals are currently lacking. Here, the authors develop a once-weekly oral dosage form for anti-HIV drugs, assess its pharmacokinetics in pigs, and model its impact on viral resistance and disease epidemics.

09 January 2018 | doi: 10.1038/s41467-017-02294-6
Biomedical engineering  Biomedical materials  Chemical engineering  HIV infections 

Tectonically-triggered sediment and carbon export to the Hadal zone OPEN
Rui Bao, Michael Strasser, Ann P. McNichol, Negar Haghipour, Cameron McIntyre, Gerold Wefer & Timothy I. Eglinton

Within sediments in deep ocean trenches an earthquake record may be observed. Here, the authors present 14C data on bulk organic carbon (OC) and thermal decomposition from a sediment core in the Japan Trench and match OC values with known earthquake events.

09 January 2018 | doi: 10.1038/s41467-017-02504-1
Carbon cycle  Sedimentology 

Engineering human pluripotent stem cells into a functional skeletal muscle tissue OPEN
Lingjun Rao, Ying Qian, Alastair Khodabukus, Thomas Ribar & Nenad Bursac

The generation of functional skeletal muscle tissue from human pluripotent stem cells has not been reported. Here, the authors describe engineering of contractile skeletal muscle bundles in culture, which become vascularized and maintain functionality when transplanted into mice.

09 January 2018 | doi: 10.1038/s41467-017-02636-4
Skeletal muscle  Stem-cell differentiation  Tissue engineering 

Dynamic metal-ligand coordination for multicolour and water-jet rewritable paper OPEN
Yun Ma, Pengfei She, Kenneth Yin Zhang, Huiran Yang, Yanyan Qin, Zihan Xu, Shujuan Liu, Qiang Zhao & Wei Huang

Rewritable paper is environmentally favourable, but its practical realization is stifled by limited ink colour versatility and poor image retention times. Here, the authors exploit the relatively stable but reversible nature of metal–organic coordination bonds to produce long-lasting and multicoloured inks for rewritable paper.

09 January 2018 | doi: 10.1038/s41467-017-02452-w
Coordination chemistry  Information storage  Inorganic chemistry  Optical materials 

Pushing nuclear magnetic resonance sensitivity limits with microfluidics and photo-chemically induced dynamic nuclear polarization OPEN
Miguel Mompeán, Rosa M. Sánchez-Donoso, Antonio de la Hoz, Vittorio Saggiomo, Aldrik H. Velders & M. Victoria Gomez

Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique with an inherently low sensitivity. Here, the authors present a combination of microcoils with photo-chemically induced dynamic nuclear polarization to boost NMR sensitivity down to sub-picomole detection limits.

09 January 2018 | doi: 10.1038/s41467-017-02575-0
Chemical physics  Physical chemistry 

Human cytomegalovirus-encoded US9 targets MAVS and STING signaling to evade type I interferon immune responses OPEN
Hyun jin Choi, Areum Park, Sujin Kang, Eunhye Lee, Taeyun A. Lee, Eun A. Ra, Jiseon Lee, Sungwook Lee & Boyoun Park

MAVS and STING signaling are central to interferon-inducing antiviral immunity. Here, the authors show how the human cytomegalovirus protein US9 can evade this immunity by antagonizing these pathways.

09 January 2018 | doi: 10.1038/s41467-017-02624-8
Immune evasion  Viral immune evasion 

3D single-molecule super-resolution microscopy with a tilted light sheet OPEN
Anna-Karin Gustavsson, Petar N. Petrov, Maurice Y. Lee, Yoav Shechtman & W. E. Moerner

Light-sheet single-molecule 3D super-resolution microscopes can’t image close to a coverslip or may require complex apparatus. Here the authors overcome such limitations using a tilted light sheet strategy with long axial range point spread functions on a standard inverted microscope.

09 January 2018 | doi: 10.1038/s41467-017-02563-4
Light-sheet microscopy  Super-resolution microscopy 

GLP-1 release and vagal afferent activation mediate the beneficial metabolic and chronotherapeutic effects of D-allulose OPEN
Yusaku Iwasaki, Mio Sendo, Katsuya Dezaki, Tohru Hira, Takehiro Sato, Masanori Nakata, Chayon Goswami, Ryohei Aoki, Takeshi Arai, Parmila Kumari, Masaki Hayakawa, Chiaki Masuda, Takashi Okada, Hiroshi Hara, Daniel J. Drucker, Yuichiro Yamada, Masaaki Tokuda & Toshihiko Yada

The sweetener D-allulose has beneficial metabolic effects in animal models, but its mechanism of action was unclear. Here the authors report that D-allulose triggers GLP-1 release in the gut and GLP-1R signaling on vagal afferents, counteracting arrhythmic overeating, obesity and diabetes.

09 January 2018 | doi: 10.1038/s41467-017-02488-y
Obesity  Type 2 diabetes 

Mapping the microscale origins of magnetic resonance image contrast with subcellular diamond magnetometry OPEN
Hunter C. Davis, Pradeep Ramesh, Aadyot Bhatnagar, Audrey Lee-Gosselin, John F. Barry, David R. Glenn, Ronald L. Walsworth & Mikhail G. Shapiro

Magnetic resonance imaging derives its contrast from local magnetic fields, however the connection between these fields and macroscale contrast has not been established through direct experiments. Here, Davis et al. use diamond magnetometry to map local magnetic fields within mammalian cells with sub-micron resolution and predict macroscale contrast.

09 January 2018 | doi: 10.1038/s41467-017-02471-7
Applied optics  Imaging techniques  Magnetic resonance imaging 

TDRD5 binds piRNA precursors and selectively enhances pachytene piRNA processing in mice OPEN
Deqiang Ding, Jiali Liu, Uros Midic, Yingjie Wu, Kunzhe Dong, Ashley Melnick, Keith E. Latham & Chen Chen

Pachytene piRNAs are abundant piRNAs in mammalian adult testes but their biogenesis pathway is not fully understood. Here, the authors identify TDRD5 as a piRNA biogenesis factor in mice, showing that it binds piRNA precursors and promotes pachytene piRNA production from specific transcript regions.

09 January 2018 | doi: 10.1038/s41467-017-02622-w
Piwi RNAs  RNA-binding proteins  Spermatogenesis 

Integrated omics dissection of proteome dynamics during cardiac remodeling OPEN
Edward Lau, Quan Cao, Maggie P. Y. Lam, Jie Wang, Dominic C. M. Ng, Brian J. Bleakley, Jessica M. Lee, David A. Liem, Ding Wang, Henning Hermjakob & Peipei Ping

Transcriptome data provide only a partial picture of disease states. Here, via integration of transcript-, protein abundance and protein turnover data for a mouse model of cardiac hypertrophy, the authors uncover additional disease gene signatures, and show that turnover data sheds unique light on posttranslational regulation.

09 January 2018 | doi: 10.1038/s41467-017-02467-3
Cardiac hypertrophy  Proteomics  Systems biology 

Differential Pd-nanocrystal facets demonstrate distinct antibacterial activity against Gram-positive and Gram-negative bacteria OPEN
Ge Fang, Weifeng Li, Xiaomei Shen, Jose Manuel Perez-Aguilar, Yu Chong, Xingfa Gao, Zhifang Chai, Chunying Chen, Cuicui Ge & Ruhong Zhou

Noble metal nanoparticles are potential antibacterial agents, perhaps owing to their enzyme-like activities. Here, the authors find that the exposed facets of palladium nanocrystals demonstrate their specific antibacterial behavior against both Gram-positive and Gram-negative bacteria.

09 January 2018 | doi: 10.1038/s41467-017-02502-3
Antibiotics  Nanoparticles 

Freshwater lake to salt-water sea causing widespread hydrate dissociation in the Black Sea OPEN
Vincent Riboulot, Stephan Ker, Nabil Sultan, Yannick Thomas, Bruno Marsset, Carla Scalabrin, Livio Ruffine, Cédric Boulart & Gabriel Ion

Gas hydrates are maintained via a balance of temperature and pressure, if this changes then destabilization may occur. Here, the authors show instead that due to recent changes in the salinity of the sea water of the Black Sea, gas hydrates may become destabilized with widespread methane seepage.

09 January 2018 | doi: 10.1038/s41467-017-02271-z
Geophysics  Natural hazards  Sedimentology 

Multiple entry pathways within the efflux transporter AcrB contribute to multidrug recognition OPEN
Martijn Zwama, Seiji Yamasaki, Ryosuke Nakashima, Keisuke Sakurai, Kunihiko Nishino & Akihito Yamaguchi

Multidrug transporters possess several drug binding sites. Here the authors describe a transport path specific for planar aromatic cations in the E. coli multi-drug transporter AcrB.

09 January 2018 | doi: 10.1038/s41467-017-02493-1
Membrane proteins  Pathogens  Permeation and transport 

Guiding of relativistic electron beams in dense matter by laser-driven magnetostatic fields OPEN
M. Bailly-Grandvaux, J. J. Santos, C. Bellei, P. Forestier-Colleoni, S. Fujioka, L. Giuffrida, J. J. Honrubia, D. Batani, R. Bouillaud, M. Chevrot, J. E. Cross, R. Crowston, S. Dorard, J.-L. Dubois, M. Ehret, G. Gregori, S. Hulin, S. Kojima, E. Loyez, J.-R. Marquès et al.

Efficient energy transport by laser-driven relativistic electron beams is crucial in many applications including inertial confinement fusion, and particle acceleration. Here the authors demonstrate relativistic electron beam guiding in dense plasma with an externally imposed high magnetic field.

09 January 2018 | doi: 10.1038/s41467-017-02641-7
Laser-produced plasmas  Plasma-based accelerators 

Click beetle luciferase mutant and near infrared naphthyl-luciferins for improved bioluminescence imaging OPEN
Mary P. Hall, Carolyn C. Woodroofe, Monika G. Wood, Ivo Que, Moniek van’t Root, Yanto Ridwan, Ce Shi, Thomas A. Kirkland, Lance P. Encell, Keith V. Wood, Clemens Löwik & Laura Mezzanotte

Red-shifted bioluminescence emission is needed to improve deep tissue imaging resolution. Here, the authors develop a click beetle red luciferase mutant and two naphthyl-luciferin substrates, and show the ability of the new luciferin/luciferase pairing for deep tissue multispectral tomography in mice.

09 January 2018 | doi: 10.1038/s41467-017-02542-9
3-D reconstruction  Bioluminescence imaging  Sensors and probes 

Structural absorption by barbule microstructures of super black bird of paradise feathers OPEN
Dakota E. McCoy, Teresa Feo, Todd Alan Harvey & Richard O. Prum

Physical structure is known to contribute to the appearance of bird plumage through structural color and specular reflection. Here, McCoy, Feo, and colleagues demonstrate how a third mechanism, structural absorption, leads to low reflectance and super black color in birds of paradise feathers.

09 January 2018 | doi: 10.1038/s41467-017-02088-w
Biomechanics  Optical materials and structures  Sexual selection 

Peptidomimetic blockade of MYB in acute myeloid leukemia OPEN
Kavitha Ramaswamy, Lauren Forbes, Gerard Minuesa, Tatyana Gindin, Fiona Brown, Michael G. Kharas, Andrei V. Krivtsov, Scott A. Armstrong, Eric Still, Elisa de Stanchina, Birgit Knoechel, Richard Koche & Alex Kentsis

MYB activity is a key factor for the maintenance of acute myeloid leukemias but it is also a difficult target. Here, the authors develop a peptidomimetic (MYBMIM) that prevents the interaction of the trans-activation domain of MYB with the KIX domain of CBP/P300 and inhibits leukaemia growth.

09 January 2018 | doi: 10.1038/s41467-017-02618-6
Acute myeloid leukaemia  Cancer models 

Deep level transient spectroscopic investigation of phosphorus-doped silicon by self-assembled molecular monolayers OPEN
Xuejiao Gao, Bin Guan, Abdelmadjid Mesli, Kaixiang Chen & Yaping Dan

Molecular monolayer doping has been used as an enabling method for the fabrication of shallow junctions in CMOS devices. Here, Gao et al. show that an undesirable reduced ionization rate during this process can be induced by carbon defects, which electronically deactivate phosphorus dopants in silicon.

09 January 2018 | doi: 10.1038/s41467-017-02564-3
Electronic properties and materials  Molecular self-assembly 

Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases OPEN
Rachel Fellows, Jérémy Denizot, Claudia Stellato, Alessandro Cuomo, Payal Jain, Elena Stoyanova, Szabina Balázsi, Zoltán Hajnády, Anke Liebert, Juri Kazakevych, Hector Blackburn, Renan Oliveira Corrêa, José Luís Fachi, Fabio Takeo Sato, Willian R. Ribeiro, Caroline Marcantonio Ferreira, Hélène Perée, Mariangela Spagnuolo, Raphaël Mattiuz, Csaba Matolcsi et al.

Histone post-translational modifications are known key regulators of gene expression. Here, the authors characterize histone crotonylation at histone H3 lysine 18 in intestinal epithelia and find that it is a highly dynamic cell cycle regulated mark under the regulation of the HDAC deacetylases.

09 January 2018 | doi: 10.1038/s41467-017-02651-5
Gene expression  Histone post-translational modifications  Metabolomics  Nucleosomes 

Picosecond pulse shaping of single photons using quantum dots OPEN
B. C. Pursley, S. G. Carter, M. K. Yakes, A. S. Bracker & D. Gammon

Tailoring single photons’ pulse shapes could have applications such as time-bin encoding or interfacing different photon emitters. Here, the authors achieve pulse shaping of Raman single photons from InGaAs quantum dots on a picosecond timescale, much shorter than the radiative lifetime.

09 January 2018 | doi: 10.1038/s41467-017-02552-7
Quantum dots  Quantum optics  Single photons and quantum effects 

Fast intensity adaptation enhances the encoding of sound in Drosophila OPEN
Jan Clemens, Nofar Ozeri-Engelhard & Mala Murthy

Complex auditory stimuli such as courtship song are sensed by mechanosensory neurons (JONs) in Drosophila antennae. Here the authors report two forms of adaptation in JONs that correct for antennal position (mean) as well as background sound intensity (variance) to maintain sensitivity to natural sensory stimuli.

09 January 2018 | doi: 10.1038/s41467-017-02453-9
Auditory system  Cellular neuroscience  Computational neuroscience 

Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs OPEN
Andrea MacFadden, Zoe O’Donoghue, Patricia A. G. C. Silva, Erich G. Chapman, René C. Olsthoorn, Mark G. Sterken, Gorben P. Pijlman, Peter J. Bredenbeek & Jeffrey S. Kieft

Subgenomic flavivirus RNAs are generated by a host exoribonuclease and play an important role in virus replication and pathogenesis. Here, the authors show the mechanism by which subgenomic flavivirus RNAs are generated and identify two structurally distinct sfRNA classes in flaviviruses.

09 January 2018 | doi: 10.1038/s41467-017-02604-y
RNA  Structural biology  Virus–host interactions 

Experimental noise cutoff boosts inferability of transcriptional networks in large-scale gene-deletion studies OPEN
C. F. Blum, N. Heramvand, A. S. Khonsari & M. Kollmann

Reliable inference of gene interactions from perturbation experiments remains a challenge. Here, the authors quantify the upper limits of transcriptional network inference from knockout screens, identify the key determinants of accuracy, and introduce an unbiased and scalable inference algorithm.

09 January 2018 | doi: 10.1038/s41467-017-02489-x
Biochemical networks  Gene regulatory networks  Network topology 

Unidirectional spin-Hall and Rashba−Edelstein magnetoresistance in topological insulator-ferromagnet layer heterostructures OPEN
Yang Lv, James Kally, Delin Zhang, Joon Sue Lee, Mahdi Jamali, Nitin Samarth & Jian-Ping Wang

Unidirectional spin Hall magnetoresistance enables the new spintronic devices but is limited by the low amplitude or working temperature. Here, the authors report the large unidirectional spin Hall magnetoresistance in a topological insulator and ferromagnetic metal bilayer system at relatively higher temperature.

09 January 2018 | doi: 10.1038/s41467-017-02491-3
Electrical and electronic engineering  Electronic and spintronic devices  Magnetic properties and materials 

Unidirectional spin density wave state in metallic (Sr1−xLa x )2IrO4 OPEN
Xiang Chen, Julian L. Schmehr, Zahirul Islam, Zach Porter, Eli Zoghlin, Kenneth Finkelstein, Jacob P. C. Ruff & Stephen D. Wilson

Electron-doped Sr2IrO4 is an intriguing material for searching for an unconventional superconducting state. Here the authors demonstrate that a spin density wave state exists in the metallic phase of electron-doped Sr2IrO4 which provides a link between the electronic phase diagrams of the hole-doped cuprates and the electron-doped iridates.

09 January 2018 | doi: 10.1038/s41467-017-02647-1
Magnetic properties and materials  Superconducting properties and materials 

Phf8 histone demethylase deficiency causes cognitive impairments through the mTOR pathway OPEN
Xuemei Chen, Shuai Wang, Ying Zhou, Yanfei Han, Shengtian Li, Qing Xu, Longyong Xu, Ziqi Zhu, Youming Deng, Lu Yu, Lulu Song, Adele Pin Chen, Juan Song, Eiki Takahashi, Guang He, Lin He, Weidong Li & Charlie Degui Chen

Mutations in PHF8 gene are genetically associated with X-linked mental retardation. Here, Chen et al. show that Phf8 KO mouse have cognitive and synaptic plasticity impairment, and pharmacological inhibition of mTOR signaling can partially alleviate such defects.

09 January 2018 | doi: 10.1038/s41467-017-02531-y
Epigenetics  Neurological disorders 

Weakly perturbative imaging of interfacial water with submolecular resolution by atomic force microscopy OPEN
Jinbo Peng, Jing Guo, Prokop Hapala, Duanyun Cao, Runze Ma, Bowei Cheng, Limei Xu, Martin Ondráček, Pavel Jelínek, Enge Wang & Ying Jiang

Scanning probe microscopy has been extensively applied to probe interfacial water but the probes tend to disturb the structure of water easily. Here, the authors report submolecular-resolution imaging of water clusters within the nearly non-invasive region by qPlus noncontact atomic force microscopy.

09 January 2018 | doi: 10.1038/s41467-017-02635-5
Atomic force microscopy  Chemical physics  Scanning probe microscopy 

Structure function and engineering of multifunctional non-heme iron dependent oxygenases in fungal meroterpenoid biosynthesis OPEN
Yu Nakashima, Takahiro Mori, Hitomi Nakamura, Takayoshi Awakawa, Shotaro Hoshino, Miki Senda, Toshiya Senda & Ikuro Abe

Non-heme iron and α-ketoglutarate (αKG) oxygenases play a major role in fungal meroterpenoid biosynthesis, but their mechanism remains elusive. Here the authors present crystal structures of two oxygenases, AusE and PrhA, which provide insights into the multifunctional nature of these enzymes.

09 January 2018 | doi: 10.1038/s41467-017-02371-w
Enzyme mechanisms  X-ray crystallography 

Nanoparticle elasticity directs tumor uptake OPEN
Peng Guo, Daxing Liu, Kriti Subramanyam, Biran Wang, Jiang Yang, Jing Huang, Debra T. Auguste & Marsha A. Moses

Nanoparticle elasticity is thought to play an important role in drug delivery, but is little studied. Here, the authors use nanolipogels with tunable moduli to study the effect of particle elasticity on in vitro cellular uptake and in vivo tumor uptake, finding that stiffer particles are not as easily internalized.

09 January 2018 | doi: 10.1038/s41467-017-02588-9
Cell–particle interactions  Drug delivery  Nanoscale biophysics 

Punctuated evolution of canonical genomic aberrations in uveal melanoma OPEN
Matthew G. Field, Michael A. Durante, Hima Anbunathan, Louis Z. Cai, Christina L. Decatur, Anne M. Bowcock, Stefan Kurtenbach & J. William Harbour

Uveal melanoma (UM), the most common primary eye cancer, is strongly linked to mutations in the tumor suppressor BAP1. Here, the authors analyze 151 primary UM samples to find that BAP1 and other canonical genomic aberrations arise in an early punctuated burst followed by neutral tumor evolution.

09 January 2018 | doi: 10.1038/s41467-017-02428-w
Cancer genomics  Eye cancer 

From stable Sb- and Bi-centered radicals to a compound with a Ga=Sb double bond OPEN
Chelladurai Ganesamoorthy, Christoph Helling, Christoph Wölper, Walter Frank, Eckhard Bill, George E. Cutsail III & Stephan Schulz

Radicals of heavy main-group elements represent important intermediates in chemical synthesis, yet few have been isolated. Here the authors stabilize neutral stibinyl and bismuthinyl radicals using gallium-based ligands, and reduce the former to afford a Ga=Sb double bond-containing complex.

08 January 2018 | doi: 10.1038/s41467-017-02581-2
Chemical bonding  Reactive precursors 

Gas hydrate dissociation off Svalbard induced by isostatic rebound rather than global warming OPEN
Klaus Wallmann, M. Riedel, W. L. Hong, H. Patton, A. Hubbard, T. Pape, C. W. Hsu, C. Schmidt, J. E. Johnson, M. E. Torres, K. Andreassen, C. Berndt & G. Bohrmann

Methane seepage from continental slopes has been attributed to gas hydrate dissociation induced by anthropogenic bottom water warming. Here, the authors show that hydrates dissociated before the Anthropocene when the isostatic rebound induced by deglaciation of the Arctic ice sheet outpaced eustatic sea-level rise.

08 January 2018 | doi: 10.1038/s41467-017-02550-9
Carbon cycle  Geochemistry  Projection and prediction 

Heisenberg-scaling measurement of the single-photon Kerr non-linearity using mixed states OPEN
Geng Chen, Nati Aharon, Yong-Nan Sun, Zi-Huai Zhang, Wen-Hao Zhang, De-Yong He, Jian-Shun Tang, Xiao-Ye Xu, Yaron Kedem, Chuan-Feng Li & Guang-Can Guo

Quantum metrology usually relies on entanglement or squeezing for pursuing Heisenberg-limited precision. In this work, instead, the authors demonstrate Heisenberg-scaling measurement of a single photon Kerr’s nonlinearity using less-demanding mixed states.

08 January 2018 | doi: 10.1038/s41467-017-02487-z
Quantum metrology  Quantum optics 

Synaptotagmin-11 is a critical mediator of parkin-linked neurotoxicity and Parkinson’s disease-like pathology OPEN
Changhe Wang, Xinjiang Kang, Li Zhou, Zuying Chai, Qihui Wu, Rong Huang, Huadong Xu, Meiqin Hu, Xiaoxuan Sun, Suhua Sun, Jie Li, Ruiying Jiao, Panli Zuo, Lianghong Zheng, Zhenyu Yue & Zhuan Zhou

Mutations in the parkin, an ubiquitin ligase, are linked to Parkinson’s disease. Here the authors show that synaptotagmin-11 is a parkin substrate and that its upregulation affects dopamine release, triggers degeneration, and causes motor impairment.

08 January 2018 | doi: 10.1038/s41467-017-02593-y
Neurodegeneration  Parkinson's disease 

Cryo EM structure of intact rotary H+-ATPase/synthase from Thermus thermophilus OPEN
Atsuko Nakanishi, Jun-ichi Kishikawa, Masatada Tamakoshi, Kaoru Mitsuoka & Ken Yokoyama

H+-ATPases employ a rotary catalytic mechanism to couple ATP synthesis/hydrolysis with proton translocation through the membrane. Here, the authors use high-resolution cryoEM to characterize three rotational states of a bacterial H+-ATPase, providing a more detailed model of its catalytic mechanism.

08 January 2018 | doi: 10.1038/s41467-017-02553-6
Bioenergetics  Cryoelectron microscopy  Enzyme mechanisms 

Dynamic changes in carbonate chemistry in the microenvironment around single marine phytoplankton cells OPEN
Abdul Chrachri, Brian M. Hopkinson, Kevin Flynn, Colin Brownlee & Glen L. Wheeler

The supply of CO2 to large marine phytoplankton cells is potentially limited by their diffusive boundary layer. Here, using direct microelectrode measurements, the authors show that extracellular carbonic anhydrase acts to maintain the concentration of CO2 at the cell surface to overcome this problem.

08 January 2018 | doi: 10.1038/s41467-017-02426-y
Carbon cycle  Marine biology  Marine chemistry  Photosynthesis 

Linked cycles of oxidative decarboxylation of glyoxylate as protometabolic analogs of the citric acid cycle OPEN
Greg Springsteen, Jayasudhan Reddy Yerabolu, Julia Nelson, Chandler Joel Rhea & Ramanarayanan Krishnamurthy

The citric acid cycle (TCA) is a fundamental metabolic pathway to release stored energy in living organisms. Here, the authors report two linked cycles of reactions that each oxidize glyoxylate into CO2 and generate intermediates shared with the modern TCA cycle, shedding light into a plausible TCA protometabolism.

08 January 2018 | doi: 10.1038/s41467-017-02591-0
Metabolic pathways  Organic chemistry  Chemical origin of life  Reaction mechanisms 

Yolk sac macrophage progenitors traffic to the embryo during defined stages of development OPEN
C. Stremmel, R. Schuchert, F. Wagner, R. Thaler, T. Weinberger, R. Pick, E. Mass, H. C. Ishikawa-Ankerhold, A. Margraf, S. Hutter, R. Vagnozzi, S. Klapproth, J. Frampton, S. Yona, C. Scheiermann, J. D. Molkentin, U. Jeschke, M. Moser, M. Sperandio, S. Massberg et al.

Tissue-resident macrophages are derived from yolk sac progenitors but how and when these progenitors enter is unclear. Here the authors use fate mapping and intravital microscopy to track the movement of resident macrophage precursors from the yolk sac to fetal tissues during development.

08 January 2018 | doi: 10.1038/s41467-017-02492-2
Haematopoietic stem cells  Imaging the immune system  Innate immunity  Leukopoiesis 

Multi-day rhythms modulate seizure risk in epilepsy OPEN
Maxime O. Baud, Jonathan K. Kleen, Emily A. Mirro, Jason C. Andrechak, David King-Stephens, Edward F. Chang & Vikram R. Rao

The ability to identify periods of heightened seizure risk could enable new treatments for patients with epilepsy. Here, the authors describe long term EEG recordings from 37 patients which allow them to identify multi-day fluctuations in interictal activity.

08 January 2018 | doi: 10.1038/s41467-017-02577-y
Electroencephalography – EEG  Epilepsy 

Auditory opportunity and visual constraint enabled the evolution of echolocation in bats OPEN
Jeneni Thiagavel, Clément Cechetto, Sharlene E. Santana, Lasse Jakobsen, Eric J. Warrant & John M. Ratcliffe

Substantial evidence now supports the idea that the ancestral bat was a small, night flying predator capable of laryngeal echolocation. Here, the authors confirm this hypothesis using phylogenetic comparative analyses and further suggest an underlying tradeoff between echolocation and vision in both ancient and modern species and an association between sensory specialization and diet.

08 January 2018 | doi: 10.1038/s41467-017-02532-x
Animal behaviour  Evolutionary ecology  Phylogenetics 

Silencing of the lncRNA Zeb2-NAT facilitates reprogramming of aged fibroblasts and safeguards stem cell pluripotency OPEN
Bruno Bernardes de Jesus, Sérgio Pires Marinho, Sara Barros, António Sousa-Franco, Catarina Alves-Vale, Tânia Carvalho & Maria Carmo-Fonseca

The efficiency of somatic cell reprogramming is lowered by ageing. Here the authors show that the transcription factor Zeb2 and its long non-coding RNA Zeb2-NAT are expressed at high levels in older fibroblasts and their inhibition increases reprogramming efficiency.

08 January 2018 | doi: 10.1038/s41467-017-01921-6
Ageing  Embryonic stem cells  Long non-coding RNAs  Reprogramming 

High temperature limit of photosynthetic excitons OPEN
Margus Rätsep, Renata Muru & Arvi Freiberg

Excitons in light-harvesting complexes are known to significantly improve solar energy harnessing. Here, the authors investigate and explain extreme robustness against temperature of excitons in purple photosynthetic bacteria.

08 January 2018 | doi: 10.1038/s41467-017-02544-7
Molecular self-assembly  Nanoscale biophysics  Structural properties 

Strain control of oxygen kinetics in the Ruddlesden-Popper oxide La1.85Sr0.15CuO4 OPEN
Tricia L. Meyer, Ryan Jacobs, Dongkyu Lee, Lu Jiang, John W. Freeland, Changhee Sohn, Takeshi Egami, Dane Morgan & Ho Nyung Lee

The desirable functional properties of complex oxide materials are often influenced by the presence of oxygen defects and epitaxial strain. Meyer et al. demonstrate the role of oxygen defect kinetics in the strain control of the superconducting transition temperature of LSCO.

08 January 2018 | doi: 10.1038/s41467-017-02568-z
Electronic properties and materials  Superconducting properties and materials  Surfaces, interfaces and thin films 

Controllable deuteration of halogenated compounds by photocatalytic D2O splitting OPEN
Cuibo Liu, Zhongxin Chen, Chenliang Su, Xiaoxu Zhao, Qiang Gao, Guo-Hong Ning, Hai Zhu, Wei Tang, Kai Leng, Wei Fu, Bingbing Tian, Xinwen Peng, Jing Li, Qing-Hua Xu, Wu Zhou & Kian Ping Loh

Developing convenient deuterium labeling procedures is important in organic synthesis and the pharmaceutical industry. Here, the authors report a mild photocatalytic strategy for controllable deuteration of halides using D2O as the reagent and porous CdSe nanosheets as the catalyst.

08 January 2018 | doi: 10.1038/s41467-017-02551-8
Heterogeneous catalysis  Photocatalysis  Two-dimensional materials 

Versatile and on-demand biologics co-production in yeast OPEN
Jicong Cao, Pablo Perez-Pinera, Ky Lowenhaupt, Ming-Ru Wu, Oliver Purcell, Cesar de la Fuente-Nunez & Timothy K. Lu

The ability to combine the production of multiple biologics into a single ‘on demand’ system could help in situations where resources are limited. Here the authors demonstrate a proof-of-concept approach for the co-production of three biologics, allowing singular, mixed and combination drug products.

08 January 2018 | doi: 10.1038/s41467-017-02587-w
Biologics  Expression systems  Recombinant protein therapy  Synthetic biology 

Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components OPEN
Michal Razew, Zbigniew Warkocki, Michal Taube, Adam Kolondra, Mariusz Czarnocki-Cieciura, Elzbieta Nowak, Karolina Labedzka-Dmoch, Aleksandra Kawinska, Jakub Piatkowski, Pawel Golik, Maciej Kozak, Andrzej Dziembowski & Marcin Nowotny

The mitochondrial RNA degradosome (mtEXO) plays an essential role in the regulation of mitochondrial gene expression and is composed of the 3′-to-5′ exoribonuclease Dss1 and the helicase Suv3. Here the authors present the RNA bound mtEXO crystal structure and give insights into its mechanism.

08 January 2018 | doi: 10.1038/s41467-017-02570-5
Enzyme mechanisms  Multienzyme complexes  RNA decay  SAXS  X-ray crystallography 

HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis OPEN
TingDong Yan, Wen Fong Ooi, Aditi Qamra, Alice Cheung, DongLiang Ma, Gopinath Meenakshi Sundaram, Chang Xu, Manjie Xing, LaiFong Poon, Jing Wang, Yan Ping Loh, Jess Hui Jie Ho, Joscelyn Jun Quan Ng, Muhammad Khairul Ramlee, Luay Aswad, Steve G. Rozen, Sujoy Ghosh, Frederic A. Bard, Prabha Sampath, Vinay Tergaonkar et al.

The expression of telomerase catalytic subunit hTERT is frequently upregulated in many cancers. Here, the authors show HoxC5 and miR-615-3p can negatively regulate hTERT to impede tumorigenesis by targeting the newly evolved cis-regulatory genomic elements of hTERT.

08 January 2018 | doi: 10.1038/s41467-017-02601-1
Cancer genomics  Transcriptional regulatory elements 

Experimental evidence for bipolaron condensation as a mechanism for the metal-insulator transition in rare-earth nickelates OPEN
Jacob Shamblin, Maximilian Heres, Haidong Zhou, Joshua Sangoro, Maik Lang, Joerg Neuefeind, J. A. Alonso & Steven Johnston

Rare-earth nickelates undergo a metal-to-insulator transition accompanied by the formation of ordered lattice distortions, but the role of the lattice in the metallic phase remains unclear. Here the authors provide evidence that the metal is a polaronic liquid that freezes into the insulating state.

08 January 2018 | doi: 10.1038/s41467-017-02561-6
Electronic properties and materials  Phase transitions and critical phenomena 

Injured adult motor and sensory axons regenerate into appropriate organotypic domains of neural progenitor grafts OPEN
Jennifer N. Dulin, Andrew F. Adler, Hiromi Kumamaru, Gunnar H. D. Poplawski, Corinne Lee-Kubli, Hans Strobl, Daniel Gibbs, Ken Kadoya, James W. Fawcett, Paul Lu & Mark H. Tuszynski

Understanding how transplanted cells interact with the host nervous system will be important for cell based neural regeneration approaches. Here, the authors study the sensory fate of neural progenitor cell grafts transplanted to the injured spinal cord, and show that host axons retain the ability to distinguish appropriate and inappropriate graft targets.

08 January 2018 | doi: 10.1038/s41467-017-02613-x
Lamination  Neural stem cells  Spinal cord injury 

One-step fermentative production of aromatic polyesters from glucose by metabolically engineered Escherichia coli strains OPEN
Jung Eun Yang, Si Jae Park, Won Jun Kim, Hyeong Jun Kim, Bumjoon J. Kim, Hyuk Lee, Jihoon Shin & Sang Yup Lee

Fermentative production of aromatic polyesters from glucose has been unsuccessful. Here, the authors achieve the objective by one-step fermentation of metabolically engineered E. coli expressing a isocaprenoyl-CoA:2-hydroxyisocaproate CoA-transferase and an evolved polyhydroxyalkanoate synthase.

08 January 2018 | doi: 10.1038/s41467-017-02498-w
Biopolymers  Metabolic engineering 

A non-dispersion strategy for large-scale production of ultra-high concentration graphene slurries in water OPEN
Lei Dong, Zhongxin Chen, Xiaoxu Zhao, Jianhua Ma, Shan Lin, Mengxiong Li, Yang Bao, Leiqiang Chu, Kai Leng, Hongbin Lu & Kian Ping Loh

Large-scale graphene production remains challenging because of the tendency of graphene to stack with itself, which requires its dispersion in large amounts of solvent. Here the authors achieve the environmentally favourable production of highly concentrated graphene in water through a non-dispersion, flocculation strategy.

08 January 2018 | doi: 10.1038/s41467-017-02580-3
Synthesis and processing  Synthesis of graphene  Two-dimensional materials 

Carotenoid metabolism strengthens the link between feather coloration and individual quality OPEN
Ryan J. Weaver, Eduardo S. A. Santos, Anna M. Tucker, Alan E. Wilson & Geoffrey E. Hill

Studies of honest signaling have found an inconsistent relationship between carotenoid coloration and individual quality. Here, Weaver et al. compare dietary and biochemically converted carotenoid coloration using meta-analyses and show that converted carotenoids drive relationships with quality measures.

08 January 2018 | doi: 10.1038/s41467-017-02649-z
Behavioural ecology  Sexual selection 

Mechanistic insights into the role of prenyl-binding protein PrBP/δ in membrane dissociation of phosphodiesterase 6 OPEN
Bilal M. Qureshi, Andrea Schmidt, Elmar Behrmann, Jörg Bürger, Thorsten Mielke, Christian M. T. Spahn, Martin Heck & Patrick Scheerer

The prenyl-binding protein PrBP/δ is a solubilization factor involved in trafficking of prenylated proteins. Here the authors present the ligand-free apo-PrBP/δ structure and propose a "solubilization by depletion" mechanism, where PrBP/δ sequesters only soluble rod photoreceptor phosphodiesterase (PDE6), leading to a dissociation of membrane-bound PDE6.

08 January 2018 | doi: 10.1038/s41467-017-02569-y
Electron microscopy  X-ray crystallography 

Ceramic nanowelding OPEN
Liqiang Zhang, Yushu Tang, Qiuming Peng, Tingting Yang, Qiunan Liu, Yuecun Wang, Yongfeng Li, Congcong Du, Yong Sun, Lishan Cui, Fan Yang, Tongde Shen, Zhiwei Shan & Jianyu Huang

Fabricating complex nanodevices requires joining techniques such as welding, common for metals but still out of reach for ceramics. Here the authors use MgO as a solder in a transmission electron microscope with a CO2 atmosphere to weld ceramic nanowires, and show their novel technique can also weld bulk ceramics.

08 January 2018 | doi: 10.1038/s41467-017-02590-1
Ceramics  NEMS  Transmission electron microscopy 

A proline deletion in IFNAR1 impairs IFN-signaling and underlies increased resistance to tuberculosis in humans OPEN
Guoliang Zhang, Nicole A. deWeerd, Sebastian A. Stifter, Lei Liu, Boping Zhou, Wenfei Wang, Yiping Zhou, Binwu Ying, Xuejiao Hu, Antony Y. Matthews, Magda Ellis, James A. Triccas, Paul J. Hertzog, Warwick J. Britton, Xinchun Chen & Carl G. Feng

The role of type I interferons in bacterial infection is less clear than it is in viral infection. Here, the authors show that genetic variation of the human IFNAR1 gene is associated with decreased susceptibility to tuberculosis and identify a role for the IFNAR1 inter-domain region in the cytokine response.

08 January 2018 | doi: 10.1038/s41467-017-02611-z
Disease genetics  Interferons  Tuberculosis 

Oxidation of Atg3 and Atg7 mediates inhibition of autophagy OPEN
Karen Frudd, Thomas Burgoyne & Joseph Robert Burgoyne

A dysfunction of autophagy can be detected in aged tissues, but how this is regulated is unclear. Here, the authors show in vitro and in aged mice aorta, that inhibition of LC3 lipidation under conditions of oxidative stress causes oxidation of Atg3 and Atg7, preventing autophagosome maturation.

08 January 2018 | doi: 10.1038/s41467-017-02352-z
Macroautophagy  Post-translational modifications 

Achieving the Heisenberg limit in quantum metrology using quantum error correction OPEN
Sisi Zhou, Mengzhen Zhang, John Preskill & Liang Jiang

The possibility to reach Heisenberg-limited quantum measurements in the presence of noise is a long-standing problem. Here, the authors derive a necessary and sufficient condition on the noise acting on any finite-dimensional probe to establish whether the Heisenberg limit is reachable using quantum error correction.

08 January 2018 | doi: 10.1038/s41467-017-02510-3
Quantum information  Quantum mechanics  Quantum metrology 

Interneuron-specific signaling evokes distinctive somatostatin-mediated responses in adult cortical astrocytes OPEN
Letizia Mariotti, Gabriele Losi, Annamaria Lia, Marcello Melone, Angela Chiavegato, Marta Gómez-Gonzalo, Michele Sessolo, Serena Bovetti, Angelo Forli, Micaela Zonta, Linda Maria Requie, Iacopo Marcon, Arianna Pugliese, Cécile Viollet, Bernhard Bettler, Tommaso Fellin, Fiorenzo Conti & Giorgio Carmignoto

Interneurons in the neocortex have functional and morphological subtypes. Here, Mariotti and colleagues show that activation of parvalbumin-expressing interneurons evokes depressing calcium responses in astrocytes while somatostatin-expressing interneurons evoke potentiating astrocytic responses.

08 January 2018 | doi: 10.1038/s41467-017-02642-6
Astrocyte  Cellular neuroscience  Inhibition 

Acetylacetone photodynamics at a seeded free-electron laser OPEN
R. J. Squibb, M. Sapunar, A. Ponzi, R. Richter, A. Kivimäki, O. Plekan, P. Finetti, N. Sisourat, V. Zhaunerchyk, T. Marchenko, L. Journel, R. Guillemin, R. Cucini, M. Coreno, C. Grazioli, M. Di Fraia, C. Callegari, K. C. Prince, P. Decleva, M. Simon et al.

The first steps in photochemical processes involve changes in electronic and geometric structure on extremely short timescales. Here, the authors report femtosecond dynamics in prototypical acetylacetone, by pump-probe photoexcitation-photoemission experiments and static and dynamics calculations.

04 January 2018 | doi: 10.1038/s41467-017-02478-0
Atomic and molecular interactions with photons  Electronic structure of atoms and molecules 

Acculturation orientations affect the evolution of a multicultural society OPEN
E. Yagmur Erten, Pieter van den Berg & Franz J. Weissing

Cross-cultural interactions can cause cultural change, a process known as acculturation. Here, Erten et al. develop a model of cultural change under immigration, considering individuals’ orientations towards acculturation, and find that willingness to interact cross-culturally and resident cultural conservatism favour cultural coexistence.

04 January 2018 | doi: 10.1038/s41467-017-02513-0
Cultural evolution  Culture  Evolutionary theory  Human behaviour 

Light-tuned selective photosynthesis of azo- and azoxy-aromatics using graphitic C3N4  OPEN
Yitao Dai, Chao Li, Yanbin Shen, Tingbin Lim, Jian Xu, Yongwang Li, Hans Niemantsverdriet, Flemming Besenbacher, Nina Lock & Ren Su

The synthesis of azo- and azoxy-aromatic dyes via photoreduction of nitroaromatics is hindered by high costs and low catalytic efficiencies and selectivities. Here the authors demonstrate the facile synthesis of these important dyes from their corresponding nitroaromatic precursors by using an inexpensive graphitic C3N4 photocatalyst.

04 January 2018 | doi: 10.1038/s41467-017-02527-8
Photocatalysis  Solar energy  Sustainability 

KSHV episomes reveal dynamic chromatin loop formation with domain-specific gene regulation OPEN
Mel Campbell, Tadashi Watanabe, Kazushi Nakano, Ryan R. Davis, Yuanzhi Lyu, Clifford G. Tepper, Blythe Durbin-Johnson, Masahiro Fujimuro & Yoshihiro Izumiya

Genomic loops and their temporal dynamics play an important role in gene expression of DNA viruses, but are incompletely understood. Here, the authors use capture Hi-C analyses and identify genomic architectural dynamics of KSHV that are regulated by the viral transactivator K-Rta.

04 January 2018 | doi: 10.1038/s41467-017-02089-9
Chromatin structure  Gene regulation  Herpes virus  Transcription factors 

A neural basis for antagonistic control of feeding and compulsive behaviors OPEN
Leandra R. Mangieri, Yungang Lu, Yuanzhong Xu, Ryan M. Cassidy, Yong Xu, Benjamin R. Arenkiel & Qingchun Tong

Feeding disorders are often comorbid with compulsive behaviours but the underlying neural circuits are not known. Here the authors demonstrate that glutamatergic and GABAergic projections from the LH to the PVH exert antagonistic effects on grooming and feeding via modulation of PVH neuron activity.

04 January 2018 | doi: 10.1038/s41467-017-02534-9
Hypothalamus  Neural circuits 

Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors OPEN
Jay H. Kalin, Muzhou Wu, Andrea V. Gomez, Yun Song, Jayanta Das, Dawn Hayward, Nkosi Adejola, Mingxuan Wu, Izabela Panova, Hye Jin Chung, Edward Kim, Holly J. Roberts, Justin M. Roberts, Polina Prusevich, Jeliazko R. Jeliazkov, Shourya S. Roy Burman, Louise Fairall, Charles Milano, Abdulkerim Eroglu, Charlotte M. Proby et al.

Alteration of the epigenetic landscape has been implicated in several disease processes, where targeting histone modifiers may have therapeutic applications. Here the authors report a bifunctional small molecule inhibitor that simultaneously targets the deacetylase (HDAC1) and demethylase (LSD1) activities of the CoREST complex.

04 January 2018 | doi: 10.1038/s41467-017-02242-4
Chemical tools  Histone post-translational modifications  Multienzyme complexes 

Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors OPEN
Ye Chen, Joanne M. L. Ho, David L. Shis, Chinmaya Gupta, James Long, Daniel S. Wagner, William Ott, Krešimir Josić & Matthew R. Bennett

For synthetic gene circuits to behave as designed, ligand-inducible promoters should display predictable ON/OFF characteristics. Here the authors design multi-input hybrid promoters to build transcriptional logic gates.

04 January 2018 | doi: 10.1038/s41467-017-02473-5
Expression systems  Synthetic biology 

APRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients OPEN
Jean-Louis Guéant, Céline Chéry, Abderrahim Oussalah, Javad Nadaf, David Coelho, Thomas Josse, Justine Flayac, Aurélie Robert, Isabelle Koscinski, Isabelle Gastin, Pierre Filhine-Tresarrieu, Mihaela Pupavac, Alison Brebner, David Watkins, Tomi Pastinen, Alexandre Montpetit, Fadi Hariri, David Tregouët, Benjamin A Raby, Wendy K. Chung et al.

Inborn errors of vitamin B12 metabolism of the cblC class are caused by mutations in the MMACHC gene. Here, Guéant et al. report epi-cblC, a class of cblC in which patients are compound heterozygous for a genetic mutation and a secondary epimutation at the MMACHC locus.

04 January 2018 | doi: 10.1038/s41467-017-02306-5
Disease genetics  DNA methylation  Genetics research  Molecular medicine 

Controlling protein activity by dynamic recruitment on a supramolecular polymer platform OPEN
Sjors P. W. Wijnands, Wouter Engelen, René P. M. Lafleur, E. W. Meijer & Maarten Merkx

DNA-origami allows the precise recruitment of DNA-protein conjugates but lacks the dynamics found in natural protein assemblies. Here the authors present a synthetic polymer platform that combines the dynamics of supramolecular polymers with the programmability of DNA-mediated protein recruitment.

04 January 2018 | doi: 10.1038/s41467-017-02559-0
Nanostructures  Self-assembly  Supramolecular polymers  Synthetic biology 

Short-chain fatty acids regulate systemic bone mass and protect from pathological bone loss OPEN
Sébastien Lucas, Yasunori Omata, Jörg Hofmann, Martin Böttcher, Aida Iljazovic, Kerstin Sarter, Olivia Albrecht, Oscar Schulz, Brenda Krishnacoumar, Gerhard Krönke, Martin Herrmann, Dimitrios Mougiakakos, Till Strowig, Georg Schett & Mario M. Zaiss

Short-chain fatty acids (SCFA) are a main class of metabolites derived from fermentation of dietary fibre in the intestine. Here, the authors show that dietary administration of SCFA is associated with inhibition of osteoclast differentiation, increased bone mass, and reduced pathological bone loss in mice.

04 January 2018 | doi: 10.1038/s41467-017-02490-4
Bone  Fatty acids  Microbiota  Osteoclasts 

C9ORF72 GGGGCC repeat-associated non-AUG translation is upregulated by stress through eIF2α phosphorylation OPEN
Weiwei Cheng, Shaopeng Wang, Alexander A. Mestre, Chenglai Fu, Andres Makarem, Fengfan Xian, Lindsey R. Hayes, Rodrigo Lopez-Gonzalez, Kevin Drenner, Jie Jiang, Don W. Cleveland & Shuying Sun

Hexanucleotide GGGGCC repeat expansion in C9ORF72 is the most frequent cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here the authors show that (GGGGCC) n translation can initiate without a 5′-cap, and this cap-independent translation is upregulated by stress mediated through eIF2α phosphorylation.

04 January 2018 | doi: 10.1038/s41467-017-02495-z
Neurodegenerative diseases  Translation 

A non-cell-autonomous role for Pml in the maintenance of leukemia from the niche OPEN
Jlenia Guarnerio, Lourdes Maria Mendez, Noboru Asada, Archita Venugopal Menon, Jacqueline Fung, Kelsey Berry, Paul S. Frenette, Keisuke Ito & Pier Paolo Pandolfi

Persistence of resistant leukemic cells after therapy is the main cause of relapse. Here, the authors show that mesenchymal stem cells-derived PML is involved in the maintenance of leukemia cells through Cxcl1 and IL6 and that PML inhibition enhances sensitivity to chemotherapy.

04 January 2018 | doi: 10.1038/s41467-017-02427-x
Cancer microenvironment  Cancer stem cells  Haematological cancer 

Human macrophages differentially produce specific resolvin or leukotriene signals that depend on bacterial pathogenicity OPEN
Oliver Werz, Jana Gerstmeier, Stephania Libreros, Xavier De la Rosa, Markus Werner, Paul C. Norris, Nan Chiang & Charles N. Serhan

M1 and M2 cells are representative of proinflammatory versus resolving macrophages, respectively. Here the authors characterize the lipid mediator response to bacterial infection by these cells and show that differing panels of leukotrienes and specialized pro-resolving mediators contribute to control of the dichotomy.

04 January 2018 | doi: 10.1038/s41467-017-02538-5
Acute inflammation  Bacterial pathogenesis  Monocytes and macrophages 

Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts OPEN
Gregory W. Goldberg, Elizabeth A. McMillan, Andrew Varble, Joshua W. Modell, Poulami Samai, Wenyan Jiang & Luciano A. Marraffini

CRISPR-Cas systems, such as type III-A CRISPR-Cas, provide an immune mechanism for prokaryotic hosts to resist parasites, including phages. Here, the authors show that maintenance of conditionally tolerant type III-A systems can affect the fitness of Staphylococcus aureus lysogens.

04 January 2018 | doi: 10.1038/s41467-017-02557-2
Bacteriophages  CRISPR-Cas9 genome editing  CRISPR-Cas systems  Pathogens 

Profiling the lymphoid-resident T cell pool reveals modulation by age and microbiota OPEN
Aurélie Durand, Alexandra Audemard-Verger, Vincent Guichard, Raphaël Mattiuz, Arnaud Delpoux, Pauline Hamon, Nelly Bonilla, Matthieu Rivière, Jérôme Delon, Bruno Martin, Cédric Auffray, Alexandre Boissonnas & Bruno Lucas

Non-circulating, tissue-resident T cells have been reported for non-lymphoid organs, but their characterization and regulation in secondary lymphoid organs (SLO) are still lacking. Here the authors show that age and microbiota both exert SLO-specific effects for the various tissue-resident T cell subsets.

04 January 2018 | doi: 10.1038/s41467-017-02458-4
Ageing  Lymphoid tissues  Peripheral tolerance  T cells 

Phenotypic memory in Bacillus subtilis links dormancy entry and exit by a spore quantity-quality tradeoff OPEN
Alper Mutlu, Stephanie Trauth, Marika Ziesack, Katja Nagler, Jan-Philip Bergeest, Karl Rohr, Nils Becker, Thomas Höfer & Ilka B. Bischofs

Bacillus subtilis withstands starvation by forming dormant spores that revive when nutrients become available. Here, Mutlu et al. show that sporulation timing controls spore revival through a phenotypic ‘memory’ that arises from the carry-over of a metabolic enzyme from the vegetative cell into the spore.

04 January 2018 | doi: 10.1038/s41467-017-02477-1
Bacteriology  Cellular microbiology  Microbial ecology 

Trithorax dependent changes in chromatin landscape at enhancer and promoter regions drive female puberty OPEN
Carlos A. Toro, Hollis Wright, Carlos F. Aylwin, Sergio R. Ojeda & Alejandro Lomniczi

Before the onset of puberty, Polycomb proteins repress the expression of Kiss1 in KNDy neurons of the arcuate nucleus. Here, by CRISPR-Cas9-directed epigenome editing and RNAi, the authors show that coordinated action of Mll proteins at the Kiss1 promoter and enhancer is required for correct timing of puberty.

04 January 2018 | doi: 10.1038/s41467-017-02512-1
CRISPR-Cas9 genome editing  Developmental biology  Epigenetics  Epigenetics in the nervous system 

Importance of the 1+7 configuration of ribonucleoprotein complexes for influenza A virus genome packaging OPEN
Takeshi Noda, Shin Murakami, Sumiho Nakatsu, Hirotaka Imai, Yukiko Muramoto, Keiko Shindo, Hiroshi Sagara & Yoshihiro Kawaoka

Influenza A virus (IAV) packages its eight genomic RNA segments in a specific “1+7” pattern. Here, the authors generate IAV that lack one RNA segment and show that ribosomal RNA is packaged in place of the eighth segment, suggesting that the 1+7 pattern is important for particle production.

04 January 2018 | doi: 10.1038/s41467-017-02517-w
Electron microscopy  Influenza virus  Virus structures 

Sleeping sickness is a circadian disorder OPEN
Filipa Rijo-Ferreira, Tânia Carvalho, Cristina Afonso, Margarida Sanches-Vaz, Rui M Costa, Luísa M. Figueiredo & Joseph S. Takahashi

African sleeping sickness is well known for the alterations of sleeping patterns, but it is not known how circadian biology is altered by the causative pathogen Trypanosoma brucei. Here the authors show T. brucei causes a disorder of the cellular circadian clock that is unrelated to the immune response to the parasite.

04 January 2018 | doi: 10.1038/s41467-017-02484-2
Circadian regulation  Pathogens 

How to probe the spin contribution to momentum relaxation in topological insulators OPEN
Moon-Sun Nam, Benjamin H. Willams, Yulin Chen, Sonia Contera, Shuhua Yao, Minghui Lu, Yan-Feng Chen, Grigore A. Timco, Christopher A. Muryn, Richard E. P. Winpenny & Arzhang Ardavan

Magnetic scattering may profoundly modify the electronic properties of a topological insulator. Here, Nam et al. report a method enabling separation of the effects of magnetic and non-magnetic scattering by decorating the surface of topological insulators with molecules.

04 January 2018 | doi: 10.1038/s41467-017-02420-4
Magnetic properties and materials  Topological insulators 

Loss of mtDNA activates astrocytes and leads to spongiotic encephalopathy OPEN
Olesia Ignatenko, Dmitri Chilov, Ilse Paetau, Elena de Miguel, Christopher B. Jackson, Gabrielle Capin, Anders Paetau, Mugen Terzioglu, Liliya Euro & Anu Suomalainen

Astrocytes in the brain are metabolically dynamic. Here, Ignatenko, Chilov and colleagues delete mitochondrial DNA (mtDNA) in a cell type specific manner, and show that inactivation of mtDNA helicase Twinkle in astrocytes leads to spongiotic encephalopathy.

04 January 2018 | doi: 10.1038/s41467-017-01859-9
Astrocyte  Energy metabolism  Neurodegenerative diseases 

Iron diapirs entrain silicates to the core and initiate thermochemical plumes OPEN
J. R. Fleck, C. L. Rains, D. S. Weeraratne, C. T. Nguyen, D. M. Brand, S. M. Klein, J. M. McGehee, J. M. Rincon, C. Martinez & P. L. Olson

During planetary formation segregation of an iron core from rocky silicates takes place. Here, the authors use analogue fluid experiments show that iron diapirs entrain volatiles and silicates to the Earth’s core and initiate buoyant thermochemical plumes to reoxidize and hydrate the upper mantle and atmosphere.

04 January 2018 | doi: 10.1038/s41467-017-02503-2
Core processes 
 
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