Wednesday, August 8, 2018

Nature Communications - 08 August 2018

 
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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 
 
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  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 
 
 

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