Nature Communications - 08 August 2018

Weekly Content Alert Nature Communications is fully open access. Read more. 08 August 2018  Latest content: Articles Author Corrections Publisher Corrections Advertisement   Making data more accessible Ying Sun is a multi-award-winning statistician who is inspired by the value of statistics in solving real-world problems. Discover more about Prof. Sun's latest efforts.  Read more >>  Journal homepage Recommend to library Web feed     Latest Articles View all Articles     Hypermethylation of gene body CpG islands predicts high dosage of functional oncogenes in liver cancer OPEN Maria Arechederra, Fabrice Daian, Annie Yim, Sehrish K. Bazai, Sylvie Richelme, Rosanna Dono, Andrew J. Saurin, Bianca H. Habermann & Flavio Maina Changes in the DNA methylation status are commonly observed in cancer but their impact on cancer development is unclear. Here, combining DNA methylation and expression profiles from a murine model of hepatocellular carcinoma with those from human samples, the authors report an epigenetic reprogramming process ensuring increased dosage of an “oncogene module”. 08 August 2018 | doi: 10.1038/s41467-018-05550-5 Cancer models  Hepatocellular carcinoma  Reduced exposure to extreme precipitation from 0.5 °C less warming in global land monsoon regions OPEN Wenxia Zhang, Tianjun Zhou, Liwei Zou, Lixia Zhang & Xiaolong Chen The populous global land monsoon region has been suffering from extreme precipitation. Here, the authors show that limiting global warming to 1.5 °C instead of 2 °C could reduce areal and population exposures to baseline once-in-20-year rainfall extremes by 25% (18–41%) and 36% (22–46%), respectively. 08 August 2018 | doi: 10.1038/s41467-018-05633-3 Climate change  Climate-change impacts  Environmental impact  Hydrology  γδ T cells control humoral immune response by inducing T follicular helper cell differentiation OPEN Rafael M. Rezende, Amanda J. Lanser, Stephen Rubino, Chantal Kuhn, Nathaniel Skillin, Thais G. Moreira, Shirong Liu, Galina Gabriely, Bruna A. David, Gustavo B. Menezes & Howard L. Weiner Many immune functions have been reported for γδ T cells, including the regulation of antibody responses. Here the authors show that CXCR5+ γδ T cells release Wnt ligands to initiate the T follicular helper cell differentiation program and promote antibody production. 08 August 2018 | doi: 10.1038/s41467-018-05487-9 Adaptive immunity  Antibodies  Autoimmune diseases  Gammadelta T cells  Crystalline polymeric carbon dioxide stable at megabar pressures OPEN Kamil F. Dziubek, Martin Ende, Demetrio Scelta, Roberto Bini, Mohamed Mezouar, Gaston Garbarino & Ronald Miletich The nature and stability of carbon dioxide under extreme conditions relevant to the Earth’s mantle is still under debate, in view of its possible role within the deep carbon cycle. Here, the authors perform high-pressure experiments providing evidence that polymeric crystalline CO2 is stable under megabaric conditions. 08 August 2018 | doi: 10.1038/s41467-018-05593-8 Geochemistry  Materials chemistry  Structure of solids and liquids  Exceptional electrocatalytic oxygen evolution via tunable charge transfer interactions in La0.5Sr1.5Ni1−xFexO4±δ Ruddlesden-Popper oxides OPEN Robin P. Forslund, William G. Hardin, Xi Rong, Artem M. Abakumov, Dmitry Filimonov, Caleb T. Alexander, J. Tyler Mefford, Hrishikesh Iyer, Alexie M. Kolpak, Keith P. Johnston & Keith J. Stevenson Water electrolysis provides a potential means to large-scale renewable fuel generation, although sluggish oxygen evolution kinetics challenges progress. Here, authors report on Ruddlesden–Popper oxides as active oxygen evolution electrocatalysts that provide impetus for overcoming kinetic barriers. 08 August 2018 | doi: 10.1038/s41467-018-05600-y Electrocatalysis  Solid-state chemistry  Forcing the reversibility of a mechanochemical reaction OPEN Amy E. M. Beedle, Marc Mora, Colin T. Davis, Ambrosius P. Snijders, Guillaume Stirnemann & Sergi Garcia-Manyes Mechanical force can facilitate thermodynamically unfavourable reactions. Here, the authors found that a stretching force can promote the SN2 cleavage of a protein disulfide bond by weak nucleophilic thiols, and that removing this force reverses the reaction yielding the original disulfide bond. 08 August 2018 | doi: 10.1038/s41467-018-05115-6 Biocatalysis  Biophysical chemistry  Single-molecule biophysics  Transcriptional and physiological adaptations in nucleus accumbens somatostatin interneurons that regulate behavioral responses to cocaine OPEN Efrain A. Ribeiro, Marine Salery, Joseph R. Scarpa, Erin S. Calipari, Peter J. Hamilton, Stacy M. Ku, Hope Kronman, Immanuel Purushothaman, Barbara Juarez, Mitra Heshmati, Marie Doyle, Casey Lardner, Dominicka Burek, Ana Strat, Stephen Pirpinias, Ezekiell Mouzon, Ming-Hu Han, Rachael L. Neve, Rosemary C. Bagot, Andrew Kasarskis et al. While making up a small percentage of neurons in the nucleus accumbens, somatostatin interneurons may have important function in dopamine- and addiction-related behavior. Here, Ribeiro and colleagues show that somatostatin interneurons regulate behavioral responses to cocaine with physiological and transcriptomic changes. 08 August 2018 | doi: 10.1038/s41467-018-05657-9 Molecular neuroscience  Reward  SENP3 maintains the stability and function of regulatory T cells via BACH2 deSUMOylation OPEN Xiaoyan Yu, Yimin Lao, Xiao-Lu Teng, Song Li, Yan Zhou, Feixiang Wang, Xinwei Guo, Siyu Deng, Yuzhou Chang, Xuefeng Wu, Zhiduo Liu, Lei Chen, Li-Ming Lu, Jinke Cheng, Bin Li, Bing Su, Jin Jiang, Hua-Bing Li, Chuanxin Huang, Jing Yi et al. Regulatory T cells are crucial for the establishment and maintenance of peripheral immune tolerance, yet the mechanisms regulating their stability and function remain to be fully elucidated. Here the authors show SENP3 maintains Treg cell stability and function via BACH2 deSUMOylation. 08 August 2018 | doi: 10.1038/s41467-018-05676-6 Autoimmunity  Regulatory T cells  Tumour immunology  Coherence in carotenoid-to-chlorophyll energy transfer OPEN Elena Meneghin, Andrea Volpato, Lorenzo Cupellini, Luca Bolzonello, Sandro Jurinovich, Vincenzo Mascoli, Donatella Carbonera, Benedetta Mennucci & Elisabetta Collini Energy transfer from carotenoids to chlorophylls in light-harvesting is still not fully understood, especially in the ultrafast regime. Here, the authors investigate the coherent dynamics of this process in peridinin-chlorophyll a-protein complex via 2D electronic spectroscopy and quantum chemical calculations. 08 August 2018 | doi: 10.1038/s41467-018-05596-5 Biochemistry  Optical techniques  Photochemistry  Physical chemistry  Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3 OPEN Luigi Scietti, Antonella Chiapparino, Francesca De Giorgi, Marco Fumagalli, Lela Khoriauli, Solomon Nergadze, Shibom Basu, Vincent Olieric, Lucia Cucca, Blerida Banushi, Antonella Profumo, Elena Giulotto, Paul Gissen & Federico Forneris Lysyl hydroxylase 3 (LH3) catalyzes collagen lysine hydroxylation and their subsequent O-linked glycosylation. Here the authors provide mechanistic insights into the lysyl hydroxylase and glycosyltransferase activities of LH3 by determining the crystal structures of full-length human LH3 bound to cofactors and donor substrates. 08 August 2018 | doi: 10.1038/s41467-018-05631-5 Biochemistry  Enzymes  X-ray crystallography  Conical-intersection dynamics and ground-state chemistry probed by extreme-ultraviolet time-resolved photoelectron spectroscopy OPEN A. von Conta, A. Tehlar, A. Schletter, Y. Arasaki, K. Takatsuka & H. J. Wörner Recent progress in extreme-ultraviolet table-top light sources is enabling advances in ultrafast molecular dynamics. Here the authors demonstrate time-resolved photoelectron spectroscopy with such a source, observing how a molecular wave packet crosses a conical intersection, performs large-amplitude motion and eventually dissociates. 08 August 2018 | doi: 10.1038/s41467-018-05292-4 Attosecond science  Excited states  A biodegradable hybrid inorganic nanoscaffold for advanced stem cell therapy OPEN Letao Yang, Sy-Tsong Dean Chueng, Ying Li, Misaal Patel, Christopher Rathnam, Gangotri Dey, Lu Wang, Li Cai & Ki-Bum Lee The promise of stem cell therapy for treating central nervous system disease is limited by low stem cell transplantation survival rates and poorly controlled cell fate. Here, the authors develop a biodegradable nanoscaffold for spinal cord injury that enhances transplantation and differentiation of neural stem cells and delivers drugs. 08 August 2018 | doi: 10.1038/s41467-018-05599-2 Biomedical engineering  Drug delivery  Stem-cell therapies  Tissue engineering and regenerative medicine  Mapping the energy landscapes of supramolecular assembly by thermal hysteresis OPEN Robert W. Harkness V, Nicole Avakyan, Hanadi F. Sleiman & Anthony K. Mittermaier Complex assembly pathways often involve transient, partly-formed intermediates that are challenging to characterize. Here, the authors present a simple and rapid spectroscopic thermal hysteresis method for mapping the energy landscapes of supramolecular assembly. 08 August 2018 | doi: 10.1038/s41467-018-05502-z Characterization and analytical techniques  DNA and RNA  Self-assembly  Supramolecular assembly  Interphase human chromosome exhibits out of equilibrium glassy dynamics OPEN Guang Shi, Lei Liu, Changbong Hyeon & D. Thirumalai The 3D organization of chromosomes within the nuclear space is important for biological functions. Here the authors model chromosomes as self-avoiding copolymers with distinct epigenetic states, and show that the features of experimentally generated contact maps can be reproduced and their dynamics predicted. 08 August 2018 | doi: 10.1038/s41467-018-05606-6 Biophysics  Chromatin structure  Computational biophysics  Molecular biophysics  Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes OPEN Iker Irisarri, Pooja Singh, Stephan Koblmüller, Julián Torres-Dowdall, Frederico Henning, Paolo Franchini, Christoph Fischer, Alan R. Lemmon, Emily Moriarty Lemmon, Gerhard G. Thallinger, Christian Sturmbauer & Axel Meyer Lake Tanganyika’s cichlid radiation is the main source of East African cichlid diversity. Irisarri et al. resolve its phylogenetic backbone using anchored phylogenomics and identify trans-lineage hybridization prior to major speciation bursts and adaptive loci underlying ecological innovations. 08 August 2018 | doi: 10.1038/s41467-018-05479-9 Adaptive radiation  Molecular evolution  Phylogenetics  Phylogeny  Palladium prompted on-demand cysteine chemistry for the synthesis of challenging and uniquely modified proteins OPEN Muhammad Jbara, Shay Laps, Michael Morgan, Guy Kamnesky, Guy Mann, Cynthia Wolberger & Ashraf Brik Cysteine side chains are reactive sites of protein synthesis and modification. Here, the authors show that tuning palladium chemoselectivity allows for selective removal of several cysteine protection groups, and use their method to synthesize challenging protein analogues. 08 August 2018 | doi: 10.1038/s41467-018-05628-0 Peptides  Post-translational modifications  Variation in bradyrhizobial NopP effector determines symbiotic incompatibility with Rj2-soybeans via effector-triggered immunity OPEN Masayuki Sugawara, Satoko Takahashi, Yosuke Umehara, Hiroya Iwano, Hirohito Tsurumaru, Haruka Odake, Yuta Suzuki, Hitoshi Kondo, Yuki Konno, Takeo Yamakawa, Shusei Sato, Hisayuki Mitsui & Kiwamu Minamisawa The soybean Rj2 gene encodes a TIR-NBS-LRR protein that confers resistance to nodulation by certain rhizobial strains. Here, the authors show that T3SS effector NopP is an avirulence protein that is necessary for Bradyrhizobium diazoefficiens USDA 122 to trigger Rj2-dependent incompatibility. 07 August 2018 | doi: 10.1038/s41467-018-05663-x Bacterial secretion  Effectors in plant pathology  Rhizobial symbiosis  Precardiac organoids form two heart fields via Bmp/Wnt signaling OPEN Peter Andersen, Emmanouil Tampakakis, Dennisse V. Jimenez, Suraj Kannan, Matthew Miyamoto, Hye Kyung Shin, Amir Saberi, Sean Murphy, Edrick Sulistio, Stephen P. Chelko & Chulan Kwon The heart arises from distinct progenitor cells of both the first and second heart fields (FHF and SHF). Here, the authors generated precardiac organoids from mouse and human pluripotent cells and show that FHF and SHF cells form similarly to their in vivo counterparts in response to BMP and Wnt signalling, respectively. 07 August 2018 | doi: 10.1038/s41467-018-05604-8 Embryonic stem cells  Land-use emissions play a critical role in land-based mitigation for Paris climate targets OPEN Anna B. Harper, Tom Powell, Peter M. Cox, Joanna House, Chris Huntingford, Timothy M. Lenton, Stephen Sitch, Eleanor Burke, Sarah E. Chadburn, William J. Collins, Edward Comyn-Platt, Vassilis Daioglou, Jonathan C. Doelman, Garry Hayman, Eddy Robertson, Detlef van Vuuren, Andy Wiltshire, Christopher P. Webber, Ana Bastos, Lena Boysen et al. Land-based mitigation for meeting the Paris climate target must consider the carbon cycle impacts of land-use change. Here the authors show that when bioenergy crops replace high carbon content ecosystems, forest-based mitigation could be more effective for CO2 removal than bioenergy crops with carbon capture and storage. 07 August 2018 | doi: 10.1038/s41467-018-05340-z Carbon cycle  Climate-change mitigation  Environmental impact  Statin as a novel pharmacotherapy of pulmonary alveolar proteinosis OPEN Cormac McCarthy, Elinor Lee, James P. Bridges, Anthony Sallese, Takuji Suzuki, Jason C. Woods, Brian J. Bartholmai, Tisha Wang, Claudia Chalk, Brenna C. Carey, Paritha Arumugam, Kenjiro Shima, Elizabeth J. Tarling & Bruce C. Trapnell Pulmonary alveolar proteinosis (PAP) is associated with defective macrophage clearance of surfactant. Here, the authors show that patients with PAP have altered cholesterol-to-phospholipid ratio in their surfactant, and that more importantly, statin therapy and reduction of cholesterol accumulation in macrophages can ameliorate PAP in both humans and mice. 07 August 2018 | doi: 10.1038/s41467-018-05491-z Alveolar macrophages  Fat metabolism  Inflammatory diseases  Translational immunology  Tunable inverse spin Hall effect in nanometer-thick platinum films by ionic gating OPEN Sergey Dushenko, Masaya Hokazono, Kohji Nakamura, Yuichiro Ando, Teruya Shinjo & Masashi Shiraishi The ability to electrically control spintronic materials significantly widens their potential for integration into devices, but it is difficult to achieve in metals with high carrier densities. Here the authors demonstrate ionic liquid gated control of the inverse spin Hall effect in platinum. 07 August 2018 | doi: 10.1038/s41467-018-05611-9 Electronic and spintronic devices  Magnetic devices  Spintronics  Surfaces, interfaces and thin films  Inhibition of a K9/K36 demethylase by an H3.3 point mutation found in paediatric glioblastoma OPEN Hsiao P. J. Voon, Maheshi Udugama, Wendi Lin, Linda Hii, Ruby H.P. Law, David L. Steer, Partha P. Das, Jeffrey R. Mann & Lee H. Wong Recent studies have identified a number of oncogenic histone point mutations in different cancers. Here the authors provide evidence that H3.3 G34R substitution mutation, which is found in paediatric gliomas, causes changes in H3K9me3 and H3K36me3 by interfering with the KDM4 family of K9/K36 demethylases. 07 August 2018 | doi: 10.1038/s41467-018-05607-5 Histone post-translational modifications  Histone variants  Persistent structures in a three-dimensional dynamical system with flowing and non-flowing regions OPEN Zafir Zaman, Mengqi Yu, Paul P. Park, Julio M. Ottino, Richard M. Lueptow & Paul B. Umbanhowar Understanding mixing in yield stress materials, such as paint and sand, is complicated due to the coexistence of solid-like and fluid-like regimes. Zaman et al. examine mixing in a granular material in three dimensions and find persistent complex non-mixing structures within the chaotic flowing regime. 07 August 2018 | doi: 10.1038/s41467-018-05508-7 Applied mathematics  Chemical engineering  Fluid dynamics  Nonlinear phenomena  Dietary stearic acid regulates mitochondria in vivo in humans OPEN Deniz Senyilmaz-Tiebe, Daniel H. Pfaff, Sam Virtue, Kathrin V. Schwarz, Thomas Fleming, Sandro Altamura, Martina U. Muckenthaler, Jürgen G. Okun, Antonio Vidal-Puig, Peter Nawroth & Aurelio A. Teleman Dietary fatty acids have different effects on human health. Here, the authors show that ingestion of the fatty acid C18:0, but not of C16:0, rapidly leads to fusion of mitochondria and fatty acid oxidation in humans, possibly explaining the health benefits of C18:0. 07 August 2018 | doi: 10.1038/s41467-018-05614-6 Fatty acids  Metabolism  Mitochondria  Ultra-narrow-band near-infrared thermal exciton radiation in intrinsic one-dimensional semiconductors OPEN Taishi Nishihara, Akira Takakura, Yuhei Miyauchi & Kenichiro Itami Narrow-band thermal emitters are still scarce despite their potential for infrared energy conversion applications. Here the thermal emission of one-dimensional carbon nanotubes up to 2000 K is reported to exhibit very narrow excitonic emission with a full-width at half-maximum of approximately 170 meV. 07 August 2018 | doi: 10.1038/s41467-018-05598-3 Carbon nanotubes and fullerenes  Electronic properties and materials  Differences in age-specific mortality between wild-caught and captive-born Asian elephants OPEN Mirkka Lahdenperä, Khyne U. Mar, Alexandre Courtiol & Virpi Lummaa Wild Asian elephants have been and continue to be captured to supplement captive populations. Here, Lahdenperä et al. use records from Myanmar timber elephants to show that wild-caught elephants have increased mortality compared to captive-born elephants for many years after capture. 07 August 2018 | doi: 10.1038/s41467-018-05515-8 Conservation biology  Evolutionary ecology  Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding OPEN Human leucocyte antigen E (HLA-E) directly engages NK cells but also presents antigen to CD8+ T cells. Here the authors show crystal structures of HLA-E in complex with peptides derived from HIV and Mycobacterium tuberculosis, and describe binding conformations, the positional impact of residues involved and discuss implications for functional presentation to CD8+ T cells. 07 August 2018 | doi: 10.1038/s41467-018-05459-z Antigen-presenting cells  Antigen processing and presentation  Infectious diseases  MHC class I  Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia OPEN Julien Bryois, Melanie E. Garrett, Lingyun Song, Alexias Safi, Paola Giusti-Rodriguez, Graham D. Johnson, Annie W. Shieh, Alfonso Buil, John F. Fullard, Panos Roussos, Pamela Sklar, Schahram Akbarian, Vahram Haroutunian, Craig A. Stockmeier, Gregory A. Wray, Kevin P. White, Chunyu Liu, Timothy E. Reddy, Allison Ashley-Koch, Patrick F. Sullivan et al. Chromatin accessibility may be altered in disease states. Here the authors carry out ATAC-seq on a large number of samples of dorsolateral prefrontal cortex from individuals with schizophrenia, and healthy controls. 07 August 2018 | doi: 10.1038/s41467-018-05379-y Chromatin remodelling  Schizophrenia  Regulation of striatal cells and goal-directed behavior by cerebellar outputs OPEN Le Xiao, Caroline Bornmann, Laetitia Hatstatt-Burklé & Peter Scheiffele Cerebellar outputs contribute to motor as well as cognitive behaviors. Here, the authors elucidate the connectivity between deep cerebellar nuclei and specific cell types in the striatum via the intralaminar thalamic nucleus and the participation of this circuit in striatum-dependent behavior. 07 August 2018 | doi: 10.1038/s41467-018-05565-y Cellular neuroscience  Neural circuits  A mouse model reproducing the pathophysiology of neonatal group B streptococcal infection OPEN Elva Bonifácio Andrade, Ana Magalhães, Ana Puga, Madalena Costa, Joana Bravo, Camila Cabral Portugal, Adília Ribeiro, Margarida Correia-Neves, Augusto Faustino, Arnaud Firon, Patrick Trieu-Cuot, Teresa Summavielle & Paula Ferreira Animal models of group-B streptococcal infections are needed to develop effective therapies. Here, Andrade et al. present a mouse model in which the bacteria are transmitted from vaginally colonised pregnant females to their offspring, causing neonatal meningitis and neurological developmental disabilities. 07 August 2018 | doi: 10.1038/s41467-018-05492-y Bacterial pathogenesis  Meningitis  Structural basis of cell wall anchoring by SLH domains in Paenibacillus alvei OPEN Ryan J. Blackler, Arturo López-Guzmán, Fiona F. Hager, Bettina Janesch, Gudrun Martinz, Susannah M. L. Gagnon, Omid Haji-Ghassemi, Paul Kosma, Paul Messner, Christina Schäffer & Stephen V. Evans Gram-positive bacterial envelopes comprise proteinaceous surface layers (S-layers) important for survival and virulence that are often anchored to the cell wall through secondary cell wall polymers. Here the authors use a structural and biophysical approach to define the molecular mechanism of this important interaction. 07 August 2018 | doi: 10.1038/s41467-018-05471-3 Bacterial structural biology  Glycobiology  X-ray crystallography  Strong whistler mode waves observed in the vicinity of Jupiter’s moons OPEN Y. Y. Shprits, J. D. Menietti, A. Y. Drozdov, R. B. Horne, E. E. Woodfield, J. B. Groene, M. de Soria-Santacruz, T. F. Averkamp, H. Garrett, C. Paranicas & D. A. Gurnett Observations of Jupiter’s magnetosphere provide opportunities to understand how magnetic fields interact with particles. Here, the authors report that the chorus wave power is increased in the vicinity of Europa and Ganymede. The generated waves are able to accelerate particles to very high energy. 07 August 2018 | doi: 10.1038/s41467-018-05431-x Exoplanets  Giant planets  Magnetospheric physics  Rings and moons  Global and Arctic climate sensitivity enhanced by changes in North Pacific heat flux OPEN Summer Praetorius, Maria Rugenstein, Geeta Persad & Ken Caldeira The relative impacts of changes in North Pacific and North Atlantic sea surface temperature on Arctic climate are not well defined. Here the authors find that Arctic surface temperatures are more sensitive to changes in North Pacific heat flux as a result of stronger modulations in poleward moisture and latent heat transport. 07 August 2018 | doi: 10.1038/s41467-018-05337-8 Atmospheric science  Ocean sciences  Dual-template engineering of triple-layered nanoarray electrode of metal chalcogenides sandwiched with hydrogen-substituted graphdiyne OPEN Sifei Zhuo, Yusuf Shi, Lingmei Liu, Renyuan Li, Le Shi, Dalaver H. Anjum, Yu Han & Peng Wang Multi-shelled nanomaterials offer interesting electrochemical properties, but have been limited in composition. Here the authors use dual templating to integrate electroactive metal chalcogenide layers with hydrogen-substituted graphdiyne, achieving electrocatalytic activity for hydrogen evolution. 07 August 2018 | doi: 10.1038/s41467-018-05474-0 Electrocatalysis  Synthesis and processing  Field- and temperature-dependent quantum tunnelling of the magnetisation in a large barrier single-molecule magnet OPEN You-Song Ding, Ke-Xin Yu, Daniel Reta, Fabrizio Ortu, Richard E. P. Winpenny, Yan-Zhen Zheng & Nicholas F. Chilton Understanding quantum tunnelling of the magnetisation in single-molecule magnets is crucial for their potential application in information storage. Here the authors conduct a field- and temperature-dependent study of the magnetisation dynamics of a dysprosium-based SMM, finding four distinct relaxation processes that dominate in different regimes. 07 August 2018 | doi: 10.1038/s41467-018-05587-6 Coordination chemistry  Inorganic chemistry  Magnetic properties and materials  Physical chemistry  Developmental seizures and mortality result from reducing GABAA receptor α2-subunit interaction with collybistin OPEN Rochelle M. Hines, Hans Michael Maric, Dustin J. Hines, Amit Modgil, Patrizia Panzanelli, Yasuko Nakamura, Anna J. Nathanson, Alan Cross, Tarek Deeb, Nicholas J. Brandon, Paul Davies, Jean-Marc Fritschy, Hermann Schindelin & Stephen J. Moss The inhibitory synaptic protein collybistin (CB) and GABAAR-α subunits are thought to interact, but strength and specificity are unclear. Here the authors study the CB–α2 interaction and show that a mouse mutated in the CB-binding region of α2 displays a loss of specific synapses and seizure. 07 August 2018 | doi: 10.1038/s41467-018-05481-1 Cellular neuroscience  Ion channels in the nervous system  Neurotransmitters  Synaptic development  Intrinsic processes drive variability in basal melting of the Totten Glacier Ice Shelf OPEN David E. Gwyther, Terence J. O’Kane, Benjamin K. Galton-Fenzi, Didier P. Monselesan & Jamin S. Greenbaum Low frequency intrinsic ocean variability has an unknown impact on Antarctic ice shelves, yet can arise even in the absence of varying climate forcing. Here, the authors show that this variability significantly affects modelled basal melting under the Totten Ice Shelf, with implications for the attribution of change. 07 August 2018 | doi: 10.1038/s41467-018-05618-2 Cryospheric science  Physical oceanography  Critical role of CD4+ T cells and IFNγ signaling in antibody-mediated resistance to Zika virus infection OPEN Carolina G. O. Lucas, Jamil Z. Kitoko, Fabricio M. Ferreira, Vinicius G. Suzart, Michelle P. Papa, Sharton V. A. Coelho, Cecilia B. Cavazzoni, Heitor A. Paula-Neto, Priscilla C. Olsen, Akiko Iwasaki, Renata M. Pereira, Pedro M. Pimentel-Coelho, Andre M. Vale, Luciana B. de Arruda & Marcelo T. Bozza Characterization of protective immunity to Zika virus has largely focussed on CD8+ T cells and antibody-mediated protection. Here the authors show roles for CD4+ T cells and the associated IFNγ signaling in antibody-mediated resistance to Zika virus infection. 07 August 2018 | doi: 10.1038/s41467-018-05519-4 CD4-positive T cells  Viral host response  Viral infection  A highly reactive precursor in the iron sulfide system OPEN Adriana Matamoros-Veloza, Oscar Cespedes, Benjamin R. G. Johnson, Tomasz M. Stawski, Umberto Terranova, Nora H. de Leeuw & Liane G. Benning Mackinawite is commonly assumed to be the first solid phase in the iron sulfide system. Here, the authors report the existence of a highly reactive nanocrystalline solid phase that is a necessary precursor to the formation of mackinawite. 07 August 2018 | doi: 10.1038/s41467-018-05493-x Element cycles  Nanoparticles  Synthesis and processing  A gate-free monolayer WSe2 pn diode OPEN Jhih-Wei Chen, Shun-Tsung Lo, Sheng-Chin Ho, Sheng-Shong Wong, Thi-Hai-Yen Vu, Xin-Quan Zhang, Yi-De Liu, Yu-You Chiou, Yu-Xun Chen, Jan-Chi Yang, Yi-Chun Chen, Ying-Hao Chu, Yi-Hsien Lee, Chung-Jen Chung, Tse-Ming Chen, Chia-Hao Chen & Chung-Lin Wu Bringing together p- and n-type monolayers of semiconducting transition metal dichalcogenides results in the formation of atomically thin pn junctions. Here, the authors laterally manipulate carrier density to create a WSe2 pn homojunction on a supporting ferroelectric BiFeO3 substrate. 07 August 2018 | doi: 10.1038/s41467-018-05326-x Electronic devices  Two-dimensional materials  Local orthorhombic lattice distortions in the paramagnetic tetragonal phase of superconducting NaFe1−xNixAs OPEN Weiyi Wang, Yu Song, Chongde Cao, Kuo-Feng Tseng, Thomas Keller, Yu Li, L. W. Harriger, Wei Tian, Songxue Chi, Rong Yu, Andriy H. Nevidomskyy & Pengcheng Dai The interplay between nematic, antiferromagnetic order and superconductivity in the iron pnictide superconductors remains obscured. Here, Wang et al. demonstrate well-separated nematic and Neel transition temperatures near optimal superconductivity in NaFe1−xNixAs and uncover local distortions which could account for rotational symmetry breaking common in iron pnictides. 07 August 2018 | doi: 10.1038/s41467-018-05529-2 Electronic properties and materials  Superconducting properties and materials  Monitoring the action of redox-directed cancer therapeutics using a human peroxiredoxin-2-based probe OPEN Troy F. Langford, Beijing K. Huang, Joseph B. Lim, Sun Jin Moon & Hadley D. Sikes Current sensors for intracellular H2O2 are not sensitive enough to detect all biologically relevant H2O2 fluctuations. Here the authors develop a peroxiredoxin-2-based FRET probe that is sensitive enough to measure changes in H2O2 concentration in response to the cancer therapeutic piperlongumine. 07 August 2018 | doi: 10.1038/s41467-018-05557-y Analytical biochemistry  Assay systems  Chemical engineering  Intracellular signalling peptides and proteins  Deep learning to predict the lab-of-origin of engineered DNA OPEN Alec A. K. Nielsen & Christopher A. Voigt The synthetic biology era has seen a rapidly growing number of engineered DNA sequences. Here, the authors develop a deep learning method to predict the lab-of-origin of a DNA sequence based on hidden design signatures. 07 August 2018 | doi: 10.1038/s41467-018-05378-z Biotechnology  Computational biology and bioinformatics  Machine learning  ATP activates bestrophin ion channels through direct interaction OPEN Yu Zhang, Alec Kittredge, Nancy Ward, Changyi Ji, Shoudeng Chen & Tingting Yang Human Bestrophin1 (hBest1), a calcium-activated chloride channel in retinal pigment epithelium (RPE), is essential for retina physiology. Using electrophysiological and structural approaches, the authors uncover an ATP-dependent activation mechanism of hBest1, and identify an ATP-binding motif. 07 August 2018 | doi: 10.1038/s41467-018-05616-4 Chloride channels  Induced pluripotent stem cells  Patch clamp  Single-channel recording  Structural biology  Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation OPEN Francesco Ghini, Carmela Rubolino, Montserrat Climent, Ines Simeone, Matteo J. Marzi & Francesco Nicassio Via the target-directed miRNA degradation process, RNAs can induce degradation of miRNAs by binding with extensive complementarity. Here, the authors show Serpine1 mRNA as one such RNA that can control the levels of the endogenous miRNA miR-30b/c-5p by modulating miRNA degradation. 07 August 2018 | doi: 10.1038/s41467-018-05182-9 CRISPR-Cas9 genome editing  miRNAs  A novel environment-evoked transcriptional signature predicts reactivity in single dentate granule neurons OPEN Baptiste N. Jaeger, Sara B. Linker, Sarah L. Parylak, Jerika J. Barron, Iryna S. Gallina, Christian D. Saavedra, Conor Fitzpatrick, Christina K. Lim, Simon T. Schafer, Benjamin Lacar, Sebastian Jessberger & Fred H. Gage Single nuclei RNA-seq has been used to characterize transcriptional signature of environment-related activity in cells of the dentate gyrus. Here the authors use this approach to show that whether a neuron will be reactivated in response to re-exposure to a previous environment can be predicted by its transcriptional signature. 06 August 2018 | doi: 10.1038/s41467-018-05418-8 Hippocampus  Transcriptomics  Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis OPEN Simon A. Hardwick, Wendy Y. Chen, Ted Wong, Bindu S. Kanakamedala, Ira W. Deveson, Sarah E. Ongley, Nadia S. Santini, Esteban Marcellin, Martin A. Smith, Lars K. Nielsen, Catherine E. Lovelock, Brett A. Neilan & Tim R. Mercer Complex microbial communities pose a challenge to metagenomic analysis. Here the authors develop ‘sequins’, internal DNA standards that represent a synthetic community of artificial genomes. 06 August 2018 | doi: 10.1038/s41467-018-05555-0 Bacterial genomics  Genome informatics  Metagenomics  Standards  Crystalline functionalized endohedral C60 metallofullerides OPEN Ayano Nakagawa, Makiko Nishino, Hiroyuki Niwa, Katsuma Ishino, Zhiyong Wang, Haruka Omachi, Ko Furukawa, Takahisa Yamaguchi, Tatsuhisa Kato, Shunji Bandow, Jeremy Rio, Chris Ewels, Shinobu Aoyagi & Hisanori Shinohara While endohedral metallofullerenes have demonstrated advantageous electronic and magnetic properties, the isolation of monomeric M@C60 remains highly challenging. Here, the authors prepare trifluoromethylated Gd@C60 and La@C60, where the functionalization of C60 allows for the stabilization of these otherwise reactive species. 06 August 2018 | doi: 10.1038/s41467-018-05496-8 Carbon nanotubes and fullerenes  Chemical synthesis  Dipolar cations confer defect tolerance in wide-bandgap metal halide perovskites OPEN Hairen Tan, Fanglin Che, Mingyang Wei, Yicheng Zhao, Makhsud I. Saidaminov, Petar Todorović, Danny Broberg, Grant Walters, Furui Tan, Taotao Zhuang, Bin Sun, Zhiqin Liang, Haifeng Yuan, Eduard Fron, Junghwan Kim, Zhenyu Yang, Oleksandr Voznyy, Mark Asta & Edward H. Sargent The performance of wide-bandgap perovskite photovoltaics is limited by the undesired phase transition and high density of deep level traps. Here, Tan et al. incorporate dipolar methylammonium cation to make the material defect-tolerant and achieve a high power conversion efficiency of 20.7%. 06 August 2018 | doi: 10.1038/s41467-018-05531-8 Devices for energy harvesting  Solar cells  A dynamic and multi-responsive porous flexible metal–organic material OPEN Mohana Shivanna, Qing-Yuan Yang, Alankriti Bajpai, Ewa Patyk-Kazmierczak & Michael J. Zaworotko Stimuli-responsive porous materials are attractive for a range of applications, but each material typically exhibits only one type of transformation. Here, the authors report on a metal–organic material that exhibits six distinct phases as a result of four types of structural transformation in response to different stimuli. 06 August 2018 | doi: 10.1038/s41467-018-05503-y Coordination chemistry  Metal–organic frameworks  Porous materials  Probe exciplex structure of highly efficient thermally activated delayed fluorescence organic light emitting diodes OPEN Tzu-Chieh Lin, Monima Sarma, Yi-Ting Chen, Shih-Hung Liu, Ke-Ting Lin, Pin-Yi Chiang, Wei-Tsung Chuang, Yi-Chen Liu, Hsiu-Fu Hsu, Wen-Yi Hung, Wei-Chieh Tang, Ken-Tsung Wong & Pi-Tai Chou The development of exciplex-type hosts for thermally activated delayed fluorescence organic light-emitting diodes is hindered by a lack of structural information for these donor:acceptor blends. Here, the authors report the pump-probe Step-Scan Fourier transform IR spectra for a D:A exciplex host. 06 August 2018 | doi: 10.1038/s41467-018-05527-4 Organic LEDs  An atmospheric chronology for the glacial-deglacial Eastern Equatorial Pacific OPEN Ning Zhao & Lloyd D. Keigwin Chronological assumptions in marine sediment records can result in uncertainties in paleoenvironmental reconstructions. Here, using computed tomography to identify in situ woody debris, the authors construct a robust 14C chronology and reassess ventilation ages in the Eastern Equatorial Pacific during the LGM. 06 August 2018 | doi: 10.1038/s41467-018-05574-x Palaeoceanography  Palaeoclimate  The identification of carbon dioxide mediated protein post-translational modifications OPEN Victoria L. Linthwaite, Joanna M. Janus, Adrian P. Brown, David Wong-Pascua, AnnMarie C. O’Donoghue, Andrew Porter, Achim Treumann, David R. W. Hodgson & Martin J. Cann Carbon dioxide can interact with proteins to form carbamate post-translational modifications. Here, the authors developed a strategy to identify carbamate post-translational modifications by trapping carbon dioxide and subsequently identifying the carbamylated proteins. 06 August 2018 | doi: 10.1038/s41467-018-05475-z Chemical modification  Post-translational modifications  Proteomic analysis  Genome-wide association study results for educational attainment aid in identifying genetic heterogeneity of schizophrenia OPEN V. Bansal, M. Mitjans, C. A. P. Burik, R. K. Linnér, A. Okbay, C. A. Rietveld, M. Begemann, S. Bonn, S. Ripke, R. de Vlaming, M. G. Nivard, H. Ehrenreich & P. D. Koellinger Educational attainment and schizophrenia have a negative phenotypic relationship but show positive genetic correlation. Here, the authors study genetic dependence between the two traits and find that multiple genes have pleiotropic effects on both without a systematic pattern of sign concordance. 06 August 2018 | doi: 10.1038/s41467-018-05510-z Genome-wide association studies  Intelligence  Psychiatric disorders  Schizophrenia  Myeloid apolipoprotein E controls dendritic cell antigen presentation and T cell activation OPEN Fabrizia Bonacina, David Coe, Guosu Wang, Maria P. Longhi, Andrea Baragetti, Annalisa Moregola, Katia Garlaschelli, Patrizia Uboldi, Fabio Pellegatta, Liliana Grigore, Lorenzo Da Dalt, Andrea Annoni, Silvia Gregori, Qingzhong Xiao, Donatella Caruso, Nico Mitro, Alberico L. Catapano, Federica M. Marelli-Berg & Giuseppe D. Norata Cholesterol homeostasis can modulate immunity via multiple pathways. Here the authors show that apolipoprotein E, an important regulator of cholesterol, produced by myeloid cells can regulate T cell activation by controlling the antigen presentation activity of dendritic cells in both humans and mice. 06 August 2018 | doi: 10.1038/s41467-018-05322-1 Antigen processing and presentation  Fat metabolism  Conventional dendritic cells  Translational immunology  Development of MPFC function mediates shifts in self-protective behavior provoked by social feedback OPEN Leehyun Yoon, Leah H. Somerville & Hackjin Kim People insulate themselves against negative social feedback via self-protective behaviors. Here, the authors show that early adolescents react against immediate social feedback, but adults also consider accumulated past negative evaluations, a function mediated by the rostromedial prefrontal cortex (RMPFC). 06 August 2018 | doi: 10.1038/s41467-018-05553-2 Emotion  Human behaviour  Motivation  Social behaviour  Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit OPEN Dominique Ray-Gallet, M. Daniel Ricketts, Yukari Sato, Kushol Gupta, Ekaterina Boyarchuk, Toshiya Senda, Ronen Marmorstein & Geneviève Almouzni The HIRA histone chaperone complex is involved in the deposition of the histone variant H3.3. Here the authors, by using biochemical and crystallographic approaches, report the homotrimerization of the HIRA subunit which is critical for the functional activity of the complex. 06 August 2018 | doi: 10.1038/s41467-018-05581-y Histone variants  Nucleosomes  AND-1 fork protection function prevents fork resection and is essential for proliferation OPEN Takuya Abe, Ryotaro Kawasumi, Michele Giannattasio, Sabrina Dusi, Yui Yoshimoto, Keiji Miyata, Koyuki Umemura, Kouji Hirota & Dana Branzei AND-1, the vertebrate orthologue of Ctf4, is a critical player during DNA replication and for maintenance of genome integrity. Here the authors use a conditional AND-1 depletion system in avian DT40 cells to reveal the consequences of the lack of AND-1 on cell proliferation and DNA replication. 06 August 2018 | doi: 10.1038/s41467-018-05586-7 Cellular imaging  Genetic association study  Replisome  Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer OPEN Jingying Nong, Yuhua Gong, Yanfang Guan, Xin Yi, Yuting Yi, Lianpeng Chang, Ling Yang, Jialin Lv, Zhirong Guo, Hongyan Jia, Yuxing Chu, Tao Liu, Ming Chen, Lauren Byers, Emily Roarty, Vincent K. Lam, Vassiliki A. Papadimitrakopoulou, Ignacio Wistuba, John V. Heymach, Bonnie Glisson et al. Small cell lung cancer (SCLC) may evolve under treatment. But tumor tissues are often not available to study evolution of SCLC. Here, the authors utilize circulating tumor DNA to investigate the genomic evolution and subclonal architecture of SCLC during therapy. 06 August 2018 | doi: 10.1038/s41467-018-05327-w Cancer genomics  Cancer therapeutic resistance  Small-cell lung cancer  Tumour biomarkers  Tumour heterogeneity  Phosphatidylserine exposure mediated by ABC transporter activates the integrin signaling pathway promoting axon regeneration OPEN Naoki Hisamoto, Anna Tsuge, Strahil Iv. Pastuhov, Tatsuhiro Shimizu, Hiroshi Hanafusa & Kunihiro Matsumoto Apoptotic cells display surface signals such as phosphatidlyserines that are recognized by phagocytes via engulfment signal receptors. Here, the authors show how one such receptor, transthyretin-like protein 11, plays a role in initiating axon regeneration in the peripheral nervous system. 06 August 2018 | doi: 10.1038/s41467-018-05478-w Extracellular signalling molecules  Regeneration and repair in the nervous system  Elastic pseudospin transport for integratable topological phononic circuits OPEN Si-Yuan Yu, Cheng He, Zhen Wang, Fu-Kang Liu, Xiao-Chen Sun, Zheng Li, Hai-Zhou Lu, Ming-Hui Lu, Xiao-Ping Liu & Yan-Feng Chen Precise control of elastic waves is of great use in current technologies. Here, Yu et al. realize the analogue of quantum spin Hall effects for the elastic waves in a plain plate consisting of identical perforated holes in wavelength scales. 06 August 2018 | doi: 10.1038/s41467-018-05461-5 Acoustics  Topological insulators  Sleep-dependent reconsolidation after memory destabilization in starlings OPEN Timothy P. Brawn, Howard C. Nusbaum & Daniel Margoliash Sleep is important for memory consolidation but its role in reconsolidation is not known. Here, the authors show in starlings that an auditory memory consolidated by sleep can be destabilized by retrieval and impaired by subsequent interference, but the memory recovers and stabilizes after a night of sleep-dependent reconsolidation. 06 August 2018 | doi: 10.1038/s41467-018-05518-5 Circadian rhythms and sleep  Learning and memory  Psychology  Salvage of the 5-deoxyribose byproduct of radical SAM enzymes OPEN Guillaume A. W. Beaudoin, Qiang Li, Jacob Folz, Oliver Fiehn, Justin L. Goodsell, Alexander Angerhofer, Steven D. Bruner & Andrew D. Hanson 5-Deoxyribose is formed from 5′-deoxyadenosine, a toxic byproduct of radical S-adenosylmethionine enzymes. Here, the authors identify and biochemically characterize a bacterial salvage pathway for 5-deoxyribose, consisting of three enzymes, and solve the crystal structure of the key aldolase. 06 August 2018 | doi: 10.1038/s41467-018-05589-4 Bacteria  Enzymes  Metabolic pathways  UV radiation limited the expansion of cyanobacteria in early marine photic environments OPEN Aleksandra M. Mloszewska, Devon B. Cole, Noah J. Planavsky, Andreas Kappler, Denise S. Whitford, George W. Owttrim & Kurt. O Konhauser The means by which planktonic cyanobacteria were able to persist through the Archean despite high fluxes of UV radiation are unclear. Here, the authors show that Fe(III)-Si rich precipitates in the Archean photic zone could have provided early planktonic cyanobacteria an effective shield against UV-C radiation. 06 August 2018 | doi: 10.1038/s41467-018-05520-x Element cycles  Microbial ecology  Ocean sciences  Biosensor libraries harness large classes of binding domains for construction of allosteric transcriptional regulators OPEN Javier F. Juárez, Begoña Lecube-Azpeitia, Stuart L. Brown, Christopher D. Johnston & George M. Church Bacterially encoded environmental sensor proteins are potentially a rich source of transcriptional control but only a few have been harnessed for biotechnological applications. Here the authors develop a general strategy for designing custom-made monogenic synthetic sensors and validate the approach by designing two sense-and-respond regulators for benzoate. 06 August 2018 | doi: 10.1038/s41467-018-05525-6 Environmental microbiology  Sensors and probes  Synthetic biology  Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte OPEN Maelenn Chevreuil, Didier Law-Hine, Jingzhi Chen, Stéphane Bressanelli, Sophie Combet, Doru Constantin, Jéril Degrouard, Johannes Möller, Mehdi Zeghal & Guillaume Tresset The mechanism by which virus capsules assemble around RNA to package their genetic material is not clear. Here, the authors observed the assembly of the cowpea chlorotic mottle virus capsid around viral RNA or poly(styrene sulfonic acid) using time-resolved small-angle X-ray scattering measurements. 06 August 2018 | doi: 10.1038/s41467-018-05426-8 Biological physics  Nanoscale biophysics  Virus structures  Potential-induced nanoclustering of metallic catalysts during electrochemical CO2 reduction OPEN Jianfeng Huang, Nicolas Hörmann, Emad Oveisi, Anna Loiudice, Gian Luca De Gregorio, Oliviero Andreussi, Nicola Marzari & Raffaella Buonsanti While the degradation of materials during usage is crucial in understanding their performance, it is challenging to understand the corrosion processes. Here, authors find copper nanoparticles to undergo an unusual potential-driven nanoclustering degradation pathway during carbon dioxide reduction. 06 August 2018 | doi: 10.1038/s41467-018-05544-3 Electrocatalysis  Heterogeneous catalysis  Nanoparticles  Structure of the mouse TRPC4 ion channel OPEN Jingjing Duan, Jian Li, Bo Zeng, Gui-Lan Chen, Xiaogang Peng, Yixing Zhang, Jianbin Wang, David E. Clapham, Zongli Li & Jin Zhang Members of the transient receptor potential (TRP) ion channels conduct cations into cells upon activation by a variety of signals. Here authors present the cryo-EM structure of TRPC4 in its unliganded (apo) state, which provides molecular insights into TRPC4's ion selectivity and TPR channel evolution. 06 August 2018 | doi: 10.1038/s41467-018-05247-9 Cryoelectron microscopy  Permeation and transport  Differential dynamics of cortical neuron dendritic trees revealed by long-term in vivo imaging in neonates OPEN Shingo Nakazawa, Hidenobu Mizuno & Takuji Iwasato Layer 4 stellate neurons in barrel cortex have a characteristic dendritic pattern. Here, the authors conduct long-term imaging from postnatal day 3–6 to show that an orientation bias is established through dendritic tree turnover and selective elaboration, which may be induced by biased thalamocortical inputs. 06 August 2018 | doi: 10.1038/s41467-018-05563-0 Barrel cortex  Development of the nervous system  Low irradiance multiphoton imaging with alloyed lanthanide nanocrystals OPEN Bining Tian, Angel Fernandez-Bravo, Hossein Najafiaghdam, Nicole A. Torquato, M. Virginia P. Altoe, Ayelet Teitelboim, Cheryl A. Tajon, Yue Tian, Nicholas J. Borys, Edward S. Barnard, Mekhail Anwar, Emory M. Chan, P. James Schuck & Bruce E. Cohen By using a near-IR optical excitation, upconverting nanoparticles may enable high-resolution imaging deep in tissue. Here, Tian et al. introduce alloyed upconverting nanoparticles with improved brightness due to newly described energy transfer pathways. 06 August 2018 | doi: 10.1038/s41467-018-05577-8 Materials for optics  Nanoparticles  Nonlinear optics  Azole-induced cell wall carbohydrate patches kill Aspergillus fumigatus OPEN Bernadette Geißel, Veronika Loiko, Isabel Klugherz, Zhaojun Zhu, Nikola Wagener, Oliver Kurzai, Cees A. M. J. J. van den Hondel & Johannes Wagener Azole antifungals inhibit fungal ergosterol biosynthesis. Here, Geißel et al. show that the fungicidal activity of azoles involves excessive synthesis of cell wall carbohydrates at defined spots along the hyphae, leading to formation of membrane invaginations and eventually rupture of the plasma membrane. 06 August 2018 | doi: 10.1038/s41467-018-05497-7 Antifungal agents  Antimicrobials  Fungal infection  Network enhancement as a general method to denoise weighted biological networks OPEN Bo Wang, Armin Pourshafeie, Marinka Zitnik, Junjie Zhu, Carlos D. Bustamante, Serafim Batzoglou & Jure Leskovec Technical noise in experiments is unavoidable, but it introduces inaccuracies into the biological networks we infer from the data. Here, the authors introduce a diffusion-based method for denoising undirected, weighted networks, and show that it improves the performances of downstream analyses. 06 August 2018 | doi: 10.1038/s41467-018-05469-x Computational models  Data mining  Machine learning  Network topology  Molecular insights into antibiotic resistance - how a binding protein traps albicidin OPEN Lida Rostock, Ronja Driller, Stefan Grätz, Dennis Kerwat, Leonard von Eckardstein, Daniel Petras, Maria Kunert, Claudia Alings, Franz-Josef Schmitt, Thomas Friedrich, Markus C. Wahl, Bernhard Loll, Andi Mainz & Roderich D. Süssmuth The potent antibacterial compound albicidin is synthesized by the plant-pathogenic bacterium Xanthomonas albilineans. Here the authors employ a multidisciplinary approach and provide structural and mechanistic insights into how the drug-binding protein AlbA confers albicidin resistance to Klebsiella oxytoca. 06 August 2018 | doi: 10.1038/s41467-018-05551-4 Biochemistry  Biophysical chemistry  DNA-binding proteins  Proteins  Structural biology  Genome-wide identification of directed gene networks using large-scale population genomics data OPEN René Luijk, Koen F. Dekkers, Maarten van Iterson, Wibowo Arindrarto, Annique Claringbould, Paul Hop, Marian Beekman, Ruud van der Breggen, Joris Deelen, Nico Lakenberg, Matthijs Moed, H. Eka D. Suchiman, Wibowo Arindrarto, Peter van ’t Hof, Marc Jan Bonder, Patrick Deelen, Ettje F. Tigchelaar, Alexandra Zhernakova, Dasha V. Zhernakova, Jenny van Dongen et al. Identification of causal drivers behind expression is essential for understanding gene function. Here authors develop a method for the large-scale inference of gene–gene interactions in observational population genomics data and characterize a network of trans-effects for 6600 genes. 06 August 2018 | doi: 10.1038/s41467-018-05452-6 Gene regulatory networks  Genomics  Anion stabilised hypercloso-hexaalane Al6H6 OPEN Simon J. Bonyhady, David Collis, Nicole Holzmann, Alison J. Edwards, Ross O. Piltz, Gernot Frenking, Andreas Stasch & Cameron Jones While polyhedral boron hydride complexes have found application in a number of diverse fields, the isolation of stable aluminium analogues remains highly challenging. Here, Jones and colleagues demonstrate that reduction of an amidinato-aluminum(III) hydride complex with magnesium(I) dimers affords stable aluminium(I) hydride compounds. 06 August 2018 | doi: 10.1038/s41467-018-05504-x Chemical bonding  Organometallic chemistry  A novel probe to assess cytosolic entry of exogenous proteins OPEN Qiao Lu, Jeff E. Grotzke & Peter Cresswell The mechanism of protein dislocation into the cytosol during antigen cross-presentation is poorly understood. Here the authors engineer a dislocation reporter fusing a glycosylated luciferase variant to the Fc region of IgG1, and find that dislocation is the rate limiting step in cross-presentation. 06 August 2018 | doi: 10.1038/s41467-018-05556-z Antigen processing and presentation  Cell biology  Sensors and probes  Ba3Mg3(BO3)3F3 polymorphs with reversible phase transition and high performances as ultraviolet nonlinear optical materials OPEN Miriding Mutailipu, Min Zhang, Hongping Wu, Zhihua Yang, Yihan Shen, Junliang Sun & Shilie Pan Nonlinear optical crystals suitable for the UV spectral region could simplify short-wavelength generation and make it more efficient. Here, the authors design and demonstrate that one of two asymmetric borate polymorphs exhibits promising optical and mechanical properties for generating UV light. 06 August 2018 | doi: 10.1038/s41467-018-05575-w Nonlinear optics  Optical materials  NOVA1 regulates hTERT splicing and cell growth in non-small cell lung cancer OPEN Andrew T. Ludlow, Mandy Sze Wong, Jerome D. Robin, Kimberly Batten, Laura Yuan, Tsung-Po Lai, Nicole Dahlson, Lu Zhang, Ilgen Mender, Enzo Tedone, Mohammed E. Sayed, Woodring E. Wright & Jerry W. Shay Splicing of the telomerase transcript, hTERT, can be altered in cancer cells. Here the authors report NOVA1, as a splicing regulator that directly interacts with hTERT pre-mRNA enhancing the number of full-length transcripts and thus telomerase activity in lung cancer cells. 06 August 2018 | doi: 10.1038/s41467-018-05582-x Cancer  Cell biology  Molecular biology  Dynamic weakening during earthquakes controlled by fluid thermodynamics OPEN M. Acosta, F. X. Passelègue, A. Schubnel & M. Violay Understanding the physics of fault lubrication during earthquake propagation can help assess seismic hazard. In this study, by replicating earthquakes in the laboratory at upper-crustal conditions, the authors show that fluid thermodynamics control fault lubrication, specifically at man-made earthquake depths. 06 August 2018 | doi: 10.1038/s41467-018-05603-9 Geophysics  Materials science  Solid Earth sciences  A metabolic interplay coordinated by HLX regulates myeloid differentiation and AML through partly overlapping pathways OPEN Indre Piragyte, Thomas Clapes, Aikaterini Polyzou, Ramon I. Klein Geltink, Stylianos Lefkopoulos, Na Yin, Pierre Cauchy, Jonathan D. Curtis, Lhéanna Klaeylé, Xavier Langa, Cora C. A. Beckmann, Marcin W. Wlodarski, Patrick Müller, Dominic Van Essen, Angelika Rambold, Friedrich G. Kapp, Marina Mione, Joerg M. Buescher, Erika L. Pearce, Alexander Polyzos et al. HLX transcription factor regulates haematopoietic stem and progenitor cell (HSPC) differentiation and is overexpressed in acute myeloid leukemia. Here the authors show that HLX overexpression leads to myeloid differentiation block in zebrafish and human HSPCs by direct regulation of metabolic pathways. 06 August 2018 | doi: 10.1038/s41467-018-05311-4 Differentiation  Haematopoietic stem cells  Myelopoiesis  Transcription  Transcriptional regulatory elements  Ultrafast switch-on dynamics of frequency-tuneable semiconductor lasers OPEN Iman Kundu, Feihu Wang, Xiaoqiong Qi, Hanond Nong, Paul Dean, Joshua R. Freeman, Alexander Valavanis, Gary Agnew, Andrew T. Grier, Thomas Taimre, Lianhe Li, Dragan Indjin, Juliette Mangeney, Jérôme Tignon, Sukhdeep S. Dhillon, Aleksandar D. Rakić, John E. Cunningham, Edmund H. Linfield & A. Giles Davies Single-mode, tuneable monolithic semiconductor lasers are important light sources for integrated photonics. Here, Kundu et al. observe the switch-on dynamics and mode competition of a terahertz quantum cascade laser and explain the behaviour with a carrier and photon transport model. 06 August 2018 | doi: 10.1038/s41467-018-05601-x Quantum cascade lasers  Semiconductor lasers  TRPS1 shapes YAP/TEAD-dependent transcription in breast cancer cells OPEN Dana Elster, Marie Tollot, Karin Schlegelmilch, Alessandro Ori, Andreas Rosenwald, Erik Sahai & Björn von Eyss YAP is a transcriptional co-activator downstream of Hippo pathway that displays oncogenic but also tumour suppressive functions. Here, the authors perform an unbiased genome wide CRISPR screen and identify Trichorhinophalangeal syndrome 1 (TRPS1) that represses YAP/TEAD activity independently of Hippo pathway in breast cancer. 06 August 2018 | doi: 10.1038/s41467-018-05370-7 Breast cancer  Mechanisms of disease  Transcriptomics  Bipolar dispersal of red-snow algae OPEN Takahiro Segawa, Ryo Matsuzaki, Nozomu Takeuchi, Ayumi Akiyoshi, Francisco Navarro, Shin Sugiyama, Takahiro Yonezawa & Hiroshi Mori Red-snow algae are red-pigmented unicellular algae that appear seasonally on the surface of thawing snow worldwide. Here, Segawa et al. analyse nuclear ITS2 sequences from snow algae from the Arctic and Antarctica, identifying dominant phylotypes present in both poles as well as endemic organisms. 06 August 2018 | doi: 10.1038/s41467-018-05521-w Biogeography  Environmental microbiology  Social interactions impact on the dopaminergic system and drive individuality OPEN N. Torquet, F. Marti, C. Campart, S. Tolu, C. Nguyen, V. Oberto, M. Benallaoua, J. Naudé, S. Didienne, N. Debray, S. Jezequel, L. Le Gouestre, B. Hannesse, J. Mariani, A. Mourot & P. Faure Individual animals differ in behavioral traits, but the mechanisms underlying individuation are unclear. Here, the authors show that mice living in a ‘city’ develop individual behavior differences, associated with changes in dopamine cell firing, that can be reversed on moving them to a different social environment. 06 August 2018 | doi: 10.1038/s41467-018-05526-5 Neural circuits  Neuroscience  Reward  Social behaviour  SLC10A7 mutations cause a skeletal dysplasia with amelogenesis imperfecta mediated by GAG biosynthesis defects OPEN Johanne Dubail, Céline Huber, Sandrine Chantepie, Stephan Sonntag, Beyhan Tüysüz, Ercan Mihci, Christopher T. Gordon, Elisabeth Steichen-Gersdorf, Jeanne Amiel, Banu Nur, Irene Stolte-Dijkstra, Albertien M. van Eerde, Koen L. van Gassen, Corstiaan C. Breugem, Alexander Stegmann, Caroline Lekszas, Reza Maroofian, Ehsan Ghayoor Karimiani, Arnaud Bruneel, Nathalie Seta et al. The majority of skeletal dysplasia are caused by pathogenic variants in genes required for glycosaminoglycan (GAG) metabolism. Here, Dubail et al. identify genetic variants in the solute carrier family protein SLC10A7 in families with skeletal dysplasia and amelogenesis imperfecta that disrupt GAG synthesis. 06 August 2018 | doi: 10.1038/s41467-018-05191-8 Bone development  Disease genetics  Medical genetics  Calcium is an essential cofactor for metal efflux by the ferroportin transporter family OPEN Chandrika N. Deshpande, T. Alex Ruwe, Ali Shawki, Vicky Xin, Kyle R. Vieth, Erika V. Valore, Bo Qiao, Tomas Ganz, Elizabeta Nemeth, Bryan Mackenzie & Mika Jormakka Ferroportin (Fpn) is essential for mammalian iron homeostasis as it exports iron from cells into blood circulation, but the molecular mechanisms of Fpn-mediated iron transport remain obscure. Here the authors use biophysical approaches to reveal that Ca2+ is a required cofactor for Fpn transport activity. 06 August 2018 | doi: 10.1038/s41467-018-05446-4 Calcium  Permeation and transport  X-ray crystallography  A PDGFRα-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine OPEN Hyun Jung Jun, Vicky A. Appleman, Hua-Jun Wu, Christopher M. Rose, Javier J. Pineda, Alan T. Yeo, Bethany Delcuze, Charlotte Lee, Aron Gyuris, Haihao Zhu, Steve Woolfenden, Agnieszka Bronisz, Ichiro Nakano, Ennio A. Chiocca, Roderick T. Bronson, Keith L. Ligon, Jann N. Sarkaria, Steve P. Gygi, Franziska Michor, Timothy J. Mitchison et al. Amplification of PDGFRα is a common alteration in glioblastoma. In this study, the authors develop a genetically engineered mouse model of GBM based on autocrine, chronic stimulation of overexpressed PDGFR and discover Stathmin1 as an important PDGFRα regulated-protein involved in the response to vinstabline. 06 August 2018 | doi: 10.1038/s41467-018-05036-4 Cancer models  Chemotherapy  CNS cancer  Optical imaging of metabolic dynamics in animals OPEN Lingyan Shi, Chaogu Zheng, Yihui Shen, Zhixing Chen, Edilson S. Silveira, Luyuan Zhang, Mian Wei, Chang Liu, Carmen de Sena-Tomas, Kimara Targoff & Wei Min Non-destructive methods to image metabolism in situ in living tissues are limited. Here the authors combine deuterium oxide probing and stimulated Raman scattering microscopy to image lipid metabolic dynamics and protein synthesis in cells and in vivo in mice, C. elegans, and zebrafish. 06 August 2018 | doi: 10.1038/s41467-018-05401-3 Optical imaging  Raman spectroscopy  Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate OPEN Shin-Fu Chen, Nan-Lan Huang, Jung-Hsin Lin, Chyuan-Chuan Wu, Ying-Ren Wang, Yu-Jen Yu, Michael K. Gilson & Nei-Li Chan Type II DNA topoisomerases (Top2s) direct the passage of one DNA duplex through another, which is important for resolving DNA entanglements. Here the authors combine X-ray crystallography and MD simulations and present the structure of the human Top2 DNA-gate in an open conformation and discuss mechanistic implications. 06 August 2018 | doi: 10.1038/s41467-018-05406-y Computational biophysics  Structural biology  X-ray crystallography  Gating of miRNA movement at defined cell-cell interfaces governs their impact as positional signals OPEN Damianos S. Skopelitis, Kristine Hill, Simon Klesen, Cristina F. Marco, Patrick von Born, Daniel H. Chitwood & Marja C. P. Timmermans Movement of small RNA between cells is critical to plant development and stress responses. Here the authors uncover a gate-keeping mechanism that can restrict small RNA movement at cell-cell interfaces, providing selectivity in long-distance signalling and limiting the scope of local mobility. 06 August 2018 | doi: 10.1038/s41467-018-05571-0 Patterning  Plant development  Plant sciences  Small RNAs  Self-assembly directed one-step synthesis of [4]radialene on Cu(100) surfaces OPEN Qing Li, Jianzhi Gao, Youyong Li, Miguel Fuentes-Cabrera, Mengxi Liu, Xiaohui Qiu, Haiping Lin, Lifeng Chi & Minghu Pan Radialenes have distinct structural, electronic and chemical properties from other hydrocarbons, but their synthesis remains a challenge. Here, the authors report a copper catalyzed one-step synthetic protocol of [4]radialene via the cyclotetramerization of phenylacetylene molecules upon thermal activation. 06 August 2018 | doi: 10.1038/s41467-018-05472-2 Density functional theory  Scanning probe microscopy  Surface assembly  Directed evolution of CRISPR-Cas9 to increase its specificity OPEN Jungjoon K. Lee, Euihwan Jeong, Joonsun Lee, Minhee Jung, Eunji Shin, Young-hoon Kim, Kangin Lee, Inyoung Jung, Daesik Kim, Seokjoong Kim & Jin-Soo Kim Undesired off-target effects can hamper the use of CRISPR-Cas9 in therapeutic applications. Here the authors use a directed evolution approach to develop Sniper-Cas9 which combines high specificity with no loss of on-target activity. 06 August 2018 | doi: 10.1038/s41467-018-05477-x CRISPR-Cas9 genome editing  Drug development  High-throughput screening  Molecular evolution  Automated single-molecule imaging in living cells OPEN Masato Yasui, Michio Hiroshima, Jun Kozuka, Yasushi Sako & Masahiro Ueda Large scale live cell screens often lack single-molecule resolution. Here the authors present an artificial intelligence-assisted TIRF microscope with automated cell searching and focusing, and use it for high-throughput single-molecule imaging of EGFR dynamics in response to various stimuli. 03 August 2018 | doi: 10.1038/s41467-018-05524-7 Fluorescence imaging  Growth factor signalling  Single-molecule biophysics  Non plasmonic semiconductor quantum SERS probe as a pathway for in vitro cancer detection OPEN Rupa Haldavnekar, Krishnan Venkatakrishnan & Bo Tan Surface enhanced Raman scattering is a bio-analytical tool and the development and optimisation of probes is an active area of investigation. Here, the authors report on the development and testing of biocompatible semiconductor zinc oxide quantum probes on a platform for cell adhesion and analysis. 03 August 2018 | doi: 10.1038/s41467-018-05237-x Biomedical materials  Nanostructures  Surface plasmon resonance  A widespread alternate form of cap-dependent mRNA translation initiation OPEN Columba de la Parra, Amanda Ernlund, Amandine Alard, Kelly Ruggles, Beatrix Ueberheide & Robert J. Schneider Binding of eIF4E to the 5′ cap of mRNAs is a key early step in canonical translation initiation, but the requirement for eIF4E is not universal. Here the authors show that the eIF4G homolog DAP5 interacts with eIF3 to promote cap-dependent translation of a significant number of mRNA in an eIF4E-independent manner. 03 August 2018 | doi: 10.1038/s41467-018-05539-0 RNA  Translation  In situ formation of catalytically active graphene in ethylene photo-epoxidation OPEN Xueqiang Zhang, Gayatri Kumari, Jaeyoung Heo & Prashant K. Jain In situ studies under working conditions are important in atomic-level elucidation, design, and optimization of industrially relevant catalysts. Here, the authors report an in situ study of an Ag ethylene photo-epoxidation catalyst using surface enhanced Raman scattering, which uncovers an unconventional mechanism. 03 August 2018 | doi: 10.1038/s41467-018-05352-9 Graphene  Nanoscale materials  Photocatalysis  Global rewiring of cellular metabolism renders Saccharomyces cerevisiae Crabtree negative OPEN Zongjie Dai, Mingtao Huang, Yun Chen, Verena Siewers & Jens Nielsen Reducing aerobic ethanol production, a phenomenon referred to as the Crabtree effect, may open up new perspectives for using yeast as a cell factory. Here, the authors turn the Crabtree-positive yeast into Crabtree negative by combined engineering of cytosolic acetyl-CoA metabolism and mutating the RNA polymerase II mediator complex. 03 August 2018 | doi: 10.1038/s41467-018-05409-9 Metabolic engineering  Synthetic biology  The chimeric TAC receptor co-opts the T cell receptor yielding robust anti-tumor activity without toxicity OPEN Christopher W. Helsen, Joanne A. Hammill, Vivian W. C. Lau, Kenneth A. Mwawasi, Arya Afsahi, Ksenia Bezverbnaya, Lisa Newhook, Danielle L. Hayes, Craig Aarts, Bojana Bojovic, Galina F. Denisova, Jacek M. Kwiecien, Ian Brain, Heather Derocher, Katy Milne, Brad H. Nelson & Jonathan L. Bramson Chimeric antigen receptors (CARs) are effective tools for directing T cell killing of tumors, but may cause adverse side effects. Here the authors show that coupling of antigen-recognition and CD3-binding in a modular format induces more efficient anti-tumour responses but reduced toxicity when compared with current CARs. 03 August 2018 | doi: 10.1038/s41467-018-05395-y Cancer immunotherapy  Cellular immunity  Translational immunology  Tumour immunology  Uniaxial stress flips the natural quantization axis of a quantum dot for integrated quantum photonics OPEN Xueyong Yuan, Fritz Weyhausen-Brinkmann, Javier Martín-Sánchez, Giovanni Piredda, Vlastimil Křápek, Yongheng Huo, Huiying Huang, Christian Schimpf, Oliver G. Schmidt, Johannes Edlinger, Gabriel Bester, Rinaldo Trotta & Armando Rastelli The natural quantization axis in quantum dots, which is usually parallel to the growth direction, is not ideal for planar photonic circuits. Here Yuan et al. show that for gallium arsenide dots, the quantization axis can be flipped to lie in the growth plane via moderate in-plane uniaxial stress. 03 August 2018 | doi: 10.1038/s41467-018-05499-5 Quantum dots  Quantum optics  Single photons and quantum effects  Locomotor recovery following contusive spinal cord injury does not require oligodendrocyte remyelination OPEN Greg J. Duncan, Sohrab B. Manesh, Brett J. Hilton, Peggy Assinck, Jie Liu, Aaron Moulson, Jason R. Plemel & Wolfram Tetzlaff The contribution of oligodendrocytes to remyelination in functional recovery after spinal cord injury is not fully understood. Here, the authors show that oligodendrocyte progenitor cell differentiation is not required for functional recovery after spinal cord injury in mice. 03 August 2018 | doi: 10.1038/s41467-018-05473-1 Myelin biology and repair  Oligodendrocyte  Spinal cord  Spinal cord injury  A stochastic assembly model for Nipah virus revealed by super-resolution microscopy OPEN Qian Liu, Lei Chen, Hector C. Aguilar & Keng C. Chou The current model for Nipah virus assembly suggests that packaging is orchestrated by the matrix protein at the plasma membrane. Here, using super-resolution microscopy and Nipah virus-like particles, Liu et al. show that Nipah virus assembly is stochastic. 03 August 2018 | doi: 10.1038/s41467-018-05480-2 Super-resolution microscopy  Virology  Dynamic anticrack propagation in snow OPEN J. Gaume, T. Gast, J. Teran, A. van Herwijnen & C. Jiang Anticrack propagation in snow results from the mixed-mode failure and collapse of a buried weak layer and can lead to slab avalanches. Here, authors reproduce the complex dynamics of anticrack propagation observed in field experiments using a Material Point Method with large strain elastoplasticity. 03 August 2018 | doi: 10.1038/s41467-018-05181-w Applied mathematics  Mechanical engineering  Natural hazards  Genomic instability in mutant p53 cancer cells upon entotic engulfment OPEN Hannah L. Mackay, David Moore, Callum Hall, Nicolai J. Birkbak, Mariam Jamal-Hanjani, Saadia A. Karim, Vinaya M. Phatak, Lucia Piñon, Jennifer P. Morton, Charles Swanton, John Le Quesne & Patricia A. J. Muller Cell-in-cell (CIC) structures are frequently observed in cancers; however, it is unclear how their formation contributes to tumorigenesis. Here, the authors show that the high frequency of CIC is linked to mutant p53 status and CIC containing p53 mutant cancer cells are pro-tumorigenic due to enhanced genomic instability. 03 August 2018 | doi: 10.1038/s41467-018-05368-1 Cell biology  Non-small-cell lung cancer  Vibration hotspots reveal longitudinal funneling of sound-evoked motion in the mammalian cochlea OPEN Nigel P. Cooper, Anna Vavakou & Marcel van der Heijden Locations along the cochlea are tuned to different sound frequencies, and the individual vibration components are dynamically compressed before being converted to neural activity for further auditory processing. Here, the authors use optical coherence tomography to map sound-evoked vibrations and find a “hotspot” region with larger vibrations. 03 August 2018 | doi: 10.1038/s41467-018-05483-z Neuroscience  Physiology  A Zika virus vaccine expressing premembrane-envelope-NS1 polyprotein OPEN Anzhong Li, Jingyou Yu, Mijia Lu, Yuanmei Ma, Zayed Attia, Chao Shan, Miaoge Xue, Xueya Liang, Kelsey Craig, Nirajkumar Makadiya, Jennifer J. He, Ryan Jennings, Pei-Yong Shi, Mark E. Peeples, Shan-Lu Liu, Prosper N. Boyaka & Jianrong Li Current Zika virus (ZIKV) subunit vaccine development largely focuses on prM and E proteins, and the role of NS1 for immune response and protection is unclear. Here, Li et al. develop an attenuated VSV-based vaccine expressing a ZIKV prM-E-NS1 polyprotein and characterize immune response and protection in mice. 03 August 2018 | doi: 10.1038/s41467-018-05276-4 Live attenuated vaccines  Viral infection  Direct imaging of structural changes induced by ionic liquid gating leading to engineered three-dimensional meso-structures OPEN Bin Cui, Peter Werner, Tianping Ma, Xiaoyan Zhong, Zechao Wang, James Mark Taylor, Yuechen Zhuang & Stuart S. P. Parkin Local and reversible oxidation is used to exploit the very different properties of oxygen and vacancy ordered oxides. Here the authors directly image and make use of anisotropic migration velocities of oxygen in SrCoOx to create 3D meso-structures of those two phases by ionic liquid gating. 03 August 2018 | doi: 10.1038/s41467-018-05330-1 Electronic properties and materials  Surfaces, interfaces and thin films  Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1 OPEN Michael Graf, Paul Huter, Cristina Maracci, Miroslav Peterek, Marina V. Rodnina & Daniel N. Wilson In bacteria, the process of translation termination is performed by three termination release factors RF1, RF2 and RF3. Here the authors provide detailed structural insights into the mechanism by which RF1 is dissociated from the ribosome by RF3 during termination. 03 August 2018 | doi: 10.1038/s41467-018-05465-1 Cryoelectron microscopy  Ribosome  Dynamic contrast enhancement and flexible odor codes OPEN Srinath Nizampatnam, Debajit Saha, Rishabh Chandak & Baranidharan Raman Sensory stimuli are encountered in multiple ways necessitating a flexible and adaptive neural population code for identification. Here, the authors show that the dynamics of odor coding in the locust antennal lobe varies with stimulus context so as to enhance the target stimulus representation. 03 August 2018 | doi: 10.1038/s41467-018-05533-6 Olfactory bulb  Sensory processing  Regulation of miR-181a expression in T cell aging OPEN Zhongde Ye, Guangjin Li, Chulwoo Kim, Bin Hu, Rohit R. Jadhav, Cornelia M. Weyand & Jörg J. Goronzy MicroRNA miR-181a has been implicated in the regulation of T cell activation and development. Here the authors show that miR-181a is regulated by a transcription factor, YY1, with reduced YY1 expression linked to reduced miR-181a in old individuals, while silencing YY1 impairs T cell functions largely through influencing the expression of miR-181a targets. 03 August 2018 | doi: 10.1038/s41467-018-05552-3 Lymphocyte activation  miRNA in immune cells  Senescence  T cells  Viral regulation of host cell biology by hijacking of the nucleolar DNA-damage response OPEN Stephen M. Rawlinson, Tianyue Zhao, Ashley M. Rozario, Christina L. Rootes, Paul J. McMillan, Anthony W. Purcell, Amanda Woon, Glenn A. Marsh, Kim G. Lieu, Lin-Fa Wang, Hans J. Netter, Toby D. M. Bell, Cameron R. Stewart & Gregory W. Moseley Many RNA viruses that replicate in the cytoplasm express proteins that localize to nucleoli, but the nucleolar functions remain largely unknown. Here, the authors show that the Henipavirus matrix protein mimics an endogenous Treacle partner of the DNA-damage response, resulting in suppression of rRNA biogenesis. 03 August 2018 | doi: 10.1038/s41467-018-05354-7 DNA damage response  Nucleolus  Super-resolution microscopy  Virus–host interactions  Discovering privileged topologies of molecular knots with self-assembling models OPEN Mattia Marenda, Enzo Orlandini & Cristian Micheletti Only a few different types of supramolecular knots have been synthesized so far. Here the authors use Monte Carlo sampling, molecular dynamics and combinatorics to discover new knot types made of identical templates. 03 August 2018 | doi: 10.1038/s41467-018-05413-z Computational methods  Self-assembly  Statistical physics  Supramolecular chemistry  Sensing of cytosolic LPS through caspy2 pyrin domain mediates noncanonical inflammasome activation in zebrafish OPEN Dahai Yang, Xin Zheng, Shouwen Chen, Zhuang Wang, Wenting Xu, Jinchao Tan, Tianjian Hu, Mingyu Hou, Wenhui Wang, Zhaoyan Gu, Qiyao Wang, Ruilin Zhang, Yuanxing Zhang & Qin Liu In humans, caspase-5 is an LPS sensor that can induce gasdermin D cleavage and pyroptosis. Here, the authors show that zebrafish caspy2 is a functional homolog as it also senses cytosolic LPS to activate the noncanonical inflammasome and to protect against bacterial infection, but it does so via pyrin death domain interactions. 03 August 2018 | doi: 10.1038/s41467-018-04984-1 Antimicrobial responses  Evolutionary developmental biology  Inflammasome  Molecular evolution  Sepsis  Sensor-regulator and RNAi based bifunctional dynamic control network for engineered microbial synthesis OPEN Yaping Yang, Yuheng Lin, Jian Wang, Yifei Wu, Ruihua Zhang, Mengyin Cheng, Xiaolin Shen, Jia Wang, Zhenya Chen, Chenyi Li, Qipeng Yuan & Yajun Yan Engineering dynamic control can improve microbial production of target chemicals. Here, the authors design a sensor-regulator and RNAi based bifunctional dynamic control network that can simultaneously and independently turn up and down cellular metabolism for engineered muconic acid production in E. coli. 02 August 2018 | doi: 10.1038/s41467-018-05466-0 Metabolic engineering  Synthetic biology  Silica-rich volcanism in the early solar system dated at 4.565 Ga OPEN Poorna Srinivasan, Daniel R. Dunlap, Carl B. Agee, Meenakshi Wadhwa, Daniel Coleff, Karen Ziegler, Ryan Zeigler & Francis M. McCubbin Achondritic meteorites can record volcanism and crust formation on planetesimals in the early Solar System. Here, the authors date the Northwest Africa 11119 meteorite with an Al-Mg age of 4564.8 ± 0.3 Ma indicating that this is the earliest evidence of silicic volcanism in the Solar System to date. 02 August 2018 | doi: 10.1038/s41467-018-05501-0 Asteroids, comets and Kuiper belt  Early solar system  Geochemistry  Meteoritics  Planetary science  De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations OPEN Karen H. Y. Wong, Michal Levy-Sakin & Pui-Yan Kwok The majority of the human reference genome assembly is represented as a single consensus haplotype. Here, Wong et al. analyze de novo assemblies of 17 diverse, haplotype-resolved genomes to gain insights into the structure of genetic diversity and compile a list of alternative haplotypes across populations. 02 August 2018 | doi: 10.1038/s41467-018-05513-w Genome assembly algorithms  Genome informatics  Haplotypes  Structural variation  Developing China’s Ecological Redline Policy using ecosystem services assessments for land use planning OPEN Yang Bai, Christina P. Wong, Bo Jiang, Alice C. Hughes, Min Wang & Qing Wang Ecosystem services, though a prominent ecological concept, have yet to be considered in major land use policy changes. Here, the authors demonstrate how the Ecological Redline Policy implemented in Shanghai utilized ecosystem services science and stakeholder engagement. 02 August 2018 | doi: 10.1038/s41467-018-05306-1 Ecosystem services  Sustainability  Wildfire as a major driver of recent permafrost thaw in boreal peatlands OPEN Carolyn M. Gibson, Laura E. Chasmer, Dan K. Thompson, William L. Quinton, Mike D. Flannigan & David Olefeldt Future permafrost thaw may be underestimated unless effects of wildfire are considered. Here the authors show that wildfires in boreal permafrost peatlands influence soil temperature and seasonal thaw depth for several decades, and increase the rate of complete permafrost thaw along permafrost edges. 02 August 2018 | doi: 10.1038/s41467-018-05457-1 Boreal ecology  Cryospheric science  Fire ecology  Wetlands ecology  Carbon losses from deforestation and widespread degradation offset by extensive growth in African woodlands OPEN Iain M. McNicol, Casey M. Ryan & Edward T. A. Mitchard Degradation—the loss of carbon stored in intact woodland—is very difficult to measure over large areas. Here, the authors show that carbon emissions from degradation in African woodlands greatly exceed those from deforestation, but are happening alongside widespread increases in biomass in remote areas. 02 August 2018 | doi: 10.1038/s41467-018-05386-z Attribution  Climate-change ecology  Developing world  Ecosystem ecology  Tropical ecology  A phase-stable dual-comb interferometer OPEN Zaijun Chen, Ming Yan, Theodor W. Hänsch & Nathalie Picqué Dual-comb interferometry promises to be a high-precision metrology technique, but is hindered by short coherence times that limit the maximum number of averages. Here, Chen et al. achieve mutual coherence times of almost 2000 s by feed-forward stabilization of the carrier-envelope offsets. 02 August 2018 | doi: 10.1038/s41467-018-05509-6 Frequency combs  Near-infrared spectroscopy  Highly sensitive switching of solid-state luminescence by controlling intersystem crossing OPEN Weijun Zhao, Zikai He, Qian Peng, Jacky W. Y. Lam, Huili Ma, Zijie Qiu, Yuncong Chen, Zheng Zhao, Zhigang Shuai, Yongqiang Dong & Ben Zhong Tang The development of intelligent materials, in particular those showing the highly sensitive mechanoresponsive luminescence (MRL), remains challenging. Here the authors report a strategy for constructing high performance On-Off MRL materials by introducing nitrophenyl groups to molecules with aggregation-induced emission characteristic. 02 August 2018 | doi: 10.1038/s41467-018-05476-y Materials for optics  Mechanical properties  Optical materials and structures  Soil bacterial networks are less stable under drought than fungal networks OPEN Franciska T. de Vries, Rob I. Griffiths, Mark Bailey, Hayley Craig, Mariangela Girlanda, Hyun Soon Gweon, Sara Hallin, Aurore Kaisermann, Aidan M. Keith, Marina Kretzschmar, Philippe Lemanceau, Erica Lumini, Kelly E. Mason, Anna Oliver, Nick Ostle, James I. Prosser, Cecile Thion, Bruce Thomson & Richard D. Bardgett Drought conditions can alter the composition of soil microbial communities, but the effects of drought on network properties have not been tested. Here, de Vries and colleagues show that co-occurrence networks are destabilised under drought for bacteria but not fungi. 02 August 2018 | doi: 10.1038/s41467-018-05516-7 Climate-change ecology  Ecological networks  Ecosystem ecology  Microbial ecology  Generating high-order optical and spin harmonics from ferromagnetic monolayers OPEN G. P. Zhang, M. S. Si, M. Murakami, Y. H. Bai & Thomas F. George High-order harmonic generation (HHG) has been explored in different kinds of solids except magnetic materials. Here the authors theoretically predict that the HHG in ferromagnetic Fe thin films is sensitive to the spin–orbit coupling and carries band structure information. 02 August 2018 | doi: 10.1038/s41467-018-05535-4 High-harmonic generation  Magnetic properties and materials  Pseudo-spin–valley coupled edge states in a photonic topological insulator OPEN Yuhao Kang, Xiang Ni, Xiaojun Cheng, Alexander B. Khanikaev & Azriel Z. Genack Valleys in the photonic band structure provide an additional degree of freedom to engineer topological photonic structures and devices. Here, Kang et al. demonstrate that inter-valley scattering is inhibited at a Y-junction between three sections with different valley topology. 02 August 2018 | doi: 10.1038/s41467-018-05408-w Optical physics  Photonic crystals  Topological matter  Energy-efficient CO2 hydrogenation with fast response using photoexcitation of CO2 adsorbed on metal catalysts OPEN Chanyeon Kim, Seokwon Hyeon, Jonghyeok Lee, Whi Dong Kim, Doh C. Lee, Jihan Kim & Hyunjoo Lee While many heterogeneous chemical transformations require high temperatures, such conditions are costly and corrosive to the catalysts. Here, authors enhance CO2 hydrogenation over metal nanoparticles by light irradiation via an unusual mechanism and reduce the reaction’s energetic demands. 02 August 2018 | doi: 10.1038/s41467-018-05542-5 Chemical engineering  Heterogeneous catalysis  Photocatalysis  Global cooling and enhanced Eocene Asian mid-latitude interior aridity OPEN J. X. Li, L. P. Yue, A. P. Roberts, A. M. Hirt, F. Pan, Lin Guo, Y. Xu, R. G. Xi, Lei Guo, X. K. Qiang, C. C. Gai, Z. X. Jiang, Z. M. Sun & Q. S. Liu The role Tibetan Plateau uplift played in Asian inland aridification remains unclear due to a paucity of accurately dated records. Here, the authors present a continuous aeolian sequence for the period >51–39 Ma, analysis of which indicates that aridification was driven by global climatic forcing rather than uplift. 02 August 2018 | doi: 10.1038/s41467-018-05415-x Palaeomagnetism  Tectonics  Spontaneous Hall effect in the Weyl semimetal candidate of all-in all-out pyrochlore iridate OPEN Kentaro Ueda, Ryoma Kaneko, Hiroaki Ishizuka, Jun Fujioka, Naoto Nagaosa & Yoshinori Tokura Material with both topological state and magnetic order remains rare. Here, Ueda et al. observe a sizable spontaneous Hall conductivity with minimal magnetization at a few Kelvin below the all-in-all-out magnetic ordering temperature in the predicted magnetic Weyl semimetal R2Ir2O7. 02 August 2018 | doi: 10.1038/s41467-018-05530-9 Electronic properties and materials  Magnetic properties and materials  Topological insulators  JNK regulates muscle remodeling via myostatin/SMAD inhibition OPEN Sarah J. Lessard, Tara L. MacDonald, Prerana Pathak, Myoung Sook Han, Vernon G. Coffey, Johann Edge, Donato A. Rivas, Michael F. Hirshman, Roger J. Davis & Laurie J. Goodyear Endurance and resistance exercise have different effects on skeletal muscle phenotype. Using mouse models and human subjects, the authors show that JNK/Smad2 signaling acts as molecular switch that when activated by resistance exercise leads to hypertrophy, and when inhibited promotes endurance adaptations in muscle. 02 August 2018 | doi: 10.1038/s41467-018-05439-3 Cell signalling  Muscle  Interleukin-2 induces the in vitro maturation of human pluripotent stem cell-derived intestinal organoids OPEN Kwang Bo Jung, Hana Lee, Ye Seul Son, Mi-Ok Lee, Young-Dae Kim, Soo Jin Oh, Ohman Kwon, Sunwha Cho, Hyun-Soo Cho, Dae-Soo Kim, Jung-Hwa Oh, Matthias Zilbauer, Jeong-Ki Min, Cho-Rok Jung, Janghwan Kim & Mi-Young Son Human pluripotent stem cell-derived intestinal organoids (hIOs) are a useful model with which to study intestinal development and disease, but they require in vivo maturation to resemble adult tissue. Here, the authors show that T lymphocyte-derived IL-2 induces hIO maturation in vitro through the activation of STAT3. 02 August 2018 | doi: 10.1038/s41467-018-05450-8 Stem-cell biotechnology  Stem-cell differentiation  Cross-reactive Dengue virus-specific CD8+ T cells protect against Zika virus during pregnancy OPEN Jose Angel Regla-Nava, Annie Elong Ngono, Karla M. Viramontes, Anh-Thy Huynh, Ying-Ting Wang, Anh-Viet T. Nguyen, Rebecca Salgado, Anila Mamidi, Kenneth Kim, Michael S. Diamond & Sujan Shresta Heterologous immunity can confer protection between related viruses. Here the authors show that prior exposure to Dengue virus can protect against subsequent infection with Zika virus in the context of pregnancy, and crucially can prevent demise of the fetus in murine models of infection. 02 August 2018 | doi: 10.1038/s41467-018-05458-0 CD8-positive T cells  Immunological memory  Infection  Viral infection  An isolable catenane consisting of two Möbius conjugated nanohoops OPEN Yang-Yang Fan, Dandan Chen, Ze-Ao Huang, Jun Zhu, Chen-Ho Tung, Li-Zhu Wu & Huan Cong Molecules exhibiting Möbius topology are fascinating but challenging synthetic targets. Here, the authors report the elegant synthesis and crystal structure of a catenane formed from two fully conjugated, interlocked Möbius nanohoops, and use theoretical calculations to understand its conformational stability and aromaticity. 02 August 2018 | doi: 10.1038/s41467-018-05498-6 Interlocked molecules  Synthetic chemistry methodology  Organic chemistry  Targeting myelin lipid metabolism as a potential therapeutic strategy in a model of CMT1A neuropathy OPEN R. Fledrich, T. Abdelaal, L. Rasch, V. Bansal, V. Schütza, B. Brügger, C. Lüchtenborg, T. Prukop, J. Stenzel, R. U. Rahman, D. Hermes, D. Ewers, W. Möbius, T. Ruhwedel, I. Katona, J. Weis, D. Klein, R. Martini, W. Brück, W. C. Müller et al. Charcot–Marie–Tooth disease 1A (CMT1A) is a peripheral demyelinating disease. Here, the authors demonstrate in a rodent model of CMT1A that Schwann cells have impairments in lipid biosynthesis, and that restoring lipids via diet can reverse the dysmyelinating phenotype in these animals. 02 August 2018 | doi: 10.1038/s41467-018-05420-0 Diseases of the nervous system  Myelin biology and repair  Schwann cell  Cysteine-mediated decyanation of vitamin B12 by the predicted membrane transporter BtuM OPEN S. Rempel, E. Colucci, J. W. de Gier, A. Guskov & D. J. Slotboom Uptake of vitamin B12 is essential for many prokaryotes, but in most cases the membrane proteins involved are yet to be identified. Here, the authors use X-ray crystallography and spectroscopy to characterize BtuM, a predicted bacterial substrate-modifying vitamin B12 transporter. 02 August 2018 | doi: 10.1038/s41467-018-05441-9 Membrane proteins  X-ray crystallography  Multimodal neuromarkers in schizophrenia via cognition-guided MRI fusion OPEN Jing Sui, Shile Qi, Theo G. M. van Erp, Juan Bustillo, Rongtao Jiang, Dongdong Lin, Jessica A. Turner, Eswar Damaraju, Andrew R. Mayer, Yue Cui, Zening Fu, Yuhui Du, Jiayu Chen, Steven G. Potkin, Adrian Preda, Daniel H. Mathalon, Judith M. Ford, James Voyvodic, Bryon A. Mueller, Aysenil Belger et al. Cognitive impairment is a feature of many psychiatric diseases. Here the authors aimed to identify multimodal neuromarkers that can be used to quantify and predict cognitive performance in individuals with schizophrenia using three different features of MRI and three independent cohorts. 02 August 2018 | doi: 10.1038/s41467-018-05432-w Cognitive control  Schizophrenia    Nature Communications JOBS of the week Associate Professorship in Precision Medicine of Chronic Lung Disease Charité - Universitätsmedizin Berlin Dekanat Postdoctoral Research Scientist Cancer Research Beatson Institute Sr. Research Scientist Memorial Sloan Kettering Cancer Center (MSKCC) Bioinformatician Institute of Molecular Biology (IMB) Mainz Associate Scientist St. Jude Children's Research Hospital (SJCRH) Staff Scientist Position RNA Bioinformatics National Cancer Institute - Center for Cancer Research Postdoc Associate Trustees of Boston University Medical Campus Associate Research Scientist Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University Faculty Positions at the SUSTech Medical School for Advanced Study Southern University of Science and Technology (SUSTech) Research Specialist II Princeton University More Science jobs from Nature Communications EVENT 18th International Symposium on Staphylococci and Staphylococcal Infections 23.08.18 Kobenhavn, Denmark More science events from     Latest Author Corrections       Author Correction: Interfacial photochemistry at the ocean surface is a global source of organic vapors and aerosols OPEN Martin Brüggemann, Nathalie Hayeck & Christian George 08 August 2018 | doi: 10.1038/s41467-018-05687-3 Atmospheric chemistry  Environmental impact  Author Correction: Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes OPEN Bruce A. Rheaume, Amyeo Jereen, Mohan Bolisetty, Muhammad S. Sajid, Yue Yang, Kathleen Renna, Lili Sun, Paul Robson & Ephraim F. Trakhtenberg 07 August 2018 | doi: 10.1038/s41467-018-05792-3 Cellular neuroscience  Retina  Transcriptomics  Author Correction: P53 and mTOR signalling determine fitness selection through cell competition during early mouse embryonic development OPEN Sarah Bowling, Aida Di Gregorio, Margarida Sancho, Sara Pozzi, Marieke Aarts, Massimo Signore, Michael D. Schneider, Juan Pedro Martinez-Barbera, Jesús Gil & Tristan A. Rodríguez 02 August 2018 | doi: 10.1038/s41467-018-05718-z Embryology  Embryonic stem cells  Gastrulation  Pluripotency      Latest Publisher Corrections       Publisher Correction: Bistable and photoswitchable states of matter OPEN Brady T. Worrell, Matthew K. McBride, Gayla B. Lyon, Lewis M. Cox, Chen Wang, Sudheendran Mavila, Chern-Hooi Lim, Hannah M. Coley, Charles B. Musgrave, Yifu Ding & Christopher N. Bowman 07 August 2018 | doi: 10.1038/s41467-018-05789-y Mechanical properties  Organic molecules in materials science  Polymers  Publisher Correction: Sensory overamplification in layer 5 auditory corticofugal projection neurons following cochlear nerve synaptic damage OPEN Meenakshi M. Asokan, Ross S. Williamson, Kenneth E. Hancock & Daniel B. Polley 03 August 2018 | doi: 10.1038/s41467-018-05333-y Cortex  Sensory processing  Publisher Correction: Finding influential nodes for integration in brain networks using optimal percolation theory OPEN Gino Del Ferraro, Andrea Moreno, Byungjoon Min, Flaviano Morone, Úrsula Pérez-Ramírez, Laura Pérez-Cervera, Lucas C. Parra, Andrei Holodny, Santiago Canals & Hernán A. Makse 03 August 2018 | doi: 10.1038/s41467-018-05686-4 Complex networks  Hippocampus      Advertisement Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. 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