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woensdag 6 december 2017

Nature Communications -06 December 2017

 
Nature Communications

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06 December 2017 
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Nature Outlook: Women’s health

From common diseases that affect the sexes differently to conditions that affect only women — and from birth, through the menopause, to old age — there are many challenges in women’s health. 

Access the Outlook free online to learn more >>

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Nature Collection: 2017 Nobel Prize in Physics 

Access this collection of articles from Nature Research to celebrate the award of the 2017 Nobel Prize in Physics to Rainer Weiss, Barry Barish and Kip Thorne - who are recognized "for decisive contributions to the LIGO detector and the observation of gravitational waves". 

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Nature Outline: Non-union bone fracture 

Bone fractures that fail to heal with conventional treatment are known as non-union bone fractures. They cause prolonged pain and disability. Work is under way to improve the success rate of surgical repair and to accelerate the bone-healing process. 

Access the Outline >> 

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  Latest Editorial    
 
Safeguarding our soils OPEN
05 December 2017 | doi: 10.1038/s41467-017-02070-6
 
  Latest Correspondence    
 
Correspondence: Reply to ‘Phantom phonon localization in relaxors’ OPEN
Michael E. Manley, Douglas L. Abernathy & John D. Budai
05 December 2017 | doi: 10.1038/s41467-017-01396-5
Actuators  Ferroelectrics and multiferroics 

Correspondence: Phantom phonon localization in relaxors OPEN
Peter M. Gehring, Dan Parshall, Leland Harriger, Chris Stock, Guangyong Xu, Xiaobing Li & Haosu Luo
05 December 2017 | doi: 10.1038/s41467-017-01395-6
Ferroelectrics and multiferroics 
 
  Latest Articles View all Articles  
 

Warhead biosynthesis and the origin of structural diversity in hydroxamate metalloproteinase inhibitors OPEN
Franziska Leipoldt, Javier Santos-Aberturas, Dennis P. Stegmann, Felix Wolf, Andreas Kulik, Rodney Lacret, Désirée Popadić, Daniela Keinhörster, Norbert Kirchner, Paulina Bekiesch, Harald Gross, Andrew W. Truman & Leonard Kaysser

Metalloproteinase inhibitors are leads for drug development, but their biosynthetic pathways are often unknown. Here the authors show that the acyl branched warhead of actinonin and matlystatins derives from an ethylmalonyl-CoA-like pathway and the structural diversity of matlystatins is due to the activity of a decarboxylase-dehydrogenase enzyme.

06 December 2017 | doi: 10.1038/s41467-017-01975-6
Applied microbiology  Metabolic engineering  Multienzyme complexes 

Developmental nonlinearity drives phenotypic robustness OPEN
Rebecca M. Green, Jennifer L. Fish, Nathan M. Young, Francis J. Smith, Benjamin Roberts, Katie Dolan, Irene Choi, Courtney L. Leach, Paul Gordon, James M. Cheverud, Charles C. Roseman, Trevor J. Williams, Ralph S. Marcucio & Benedikt Hallgrímsson

Developmental processes often involve nonlinearities, but the consequences for translating genotype to phenotype are not well characterized. Here, Green et al. vary Fgf8 signaling across allelic series of mice and show that phenotypic robustness in craniofacial shape is explained by a nonlinear effect of Fgf8 expression.

06 December 2017 | doi: 10.1038/s41467-017-02037-7
Evolutionary developmental biology  Evolutionary genetics  Morphogenesis 

Human CD26high T cells elicit tumor immunity against multiple malignancies via enhanced migration and persistence OPEN
Stefanie R. Bailey, Michelle H. Nelson, Kinga Majchrzak, Jacob S. Bowers, Megan M. Wyatt, Aubrey S. Smith, Lillian R. Neal, Keisuke Shirai, Carmine Carpenito, Carl H. June, Michael J. Zilliox & Chrystal M. Paulos

The role of human CD4+ T cell subsets in cancer immunotherapy is still unclear. Here, the authors show that CD26 identifies three CD4+ T cell subsets with distinct immunological properties in both healthy individuals and cancer patients.

06 December 2017 | doi: 10.1038/s41467-017-01867-9
CD4-positive T cells  Immunotherapy  Melanoma  Mesothelioma  Pancreatic cancer 

Intercalation events visualized in single microcrystals of graphite OPEN
Edward R. White, Jared J. Lodico & B. C. Regan

The common lithium-ion battery is re-charged by intercalating its graphite anode, but intercalation remains not well understood. Electron microscope video of intercalating graphite microcrystals reveals that the charge transfer occurs in current pulses that do not match theoretical expectations.

06 December 2017 | doi: 10.1038/s41467-017-01787-8
Batteries  Transmission electron microscopy 

Reversible silencing of lumbar spinal interneurons unmasks a task-specific network for securing hindlimb alternation OPEN
Amanda M. Pocratsky, Darlene A. Burke, Johnny R. Morehouse, Jason E. Beare, Amberly S. Riegler, Pantelis Tsoulfas, Gregory J. R. States, Scott R. Whittemore & David S. K. Magnuson

Intra- and interlimb coordination during locomotion is governed by hierarchically organized lumbar spinal networks. Here, the authors show that reversible silencing of spinal L2–L5 interneurons specifically disrupts hindlimb alternation leading to a continuum of walking to hopping.

06 December 2017 | doi: 10.1038/s41467-017-02033-x
Neuroscience  Spinal cord 

3D microniches reveal the importance of cell size and shape OPEN
Min Bao, Jing Xie, Aigars Piruska & Wilhelm T. S. Huck

Little is known about how geometric cues affect cell function and gene expression in 3D settings. Here the authors use microniches of different geometries to control cell volume and shape, and by extension cell phenotype and lineage.

06 December 2017 | doi: 10.1038/s41467-017-02163-2
Biomaterials – cells  Cell culture  Stem cells 

Allosteric nanobodies uncover a role of hippocampal mGlu2 receptor homodimers in contextual fear consolidation OPEN

G protein-coupled receptors are considered promising therapeutic targets. Here, the authors have identified nanobodies, or single-domain llama antibodies, that specifically enhance agonist-induced activity of a type of G protein-coupled receptor, the mGlu2 receptor.

06 December 2017 | doi: 10.1038/s41467-017-01489-1
Molecular engineering  Molecular medicine  Molecular neuroscience 

Multiplexed computations in retinal ganglion cells of a single type OPEN
Stéphane Deny, Ulisse Ferrari, Emilie Macé, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik & Olivier Marre

Retinal ganglion cell subtypes are traditionally thought to encode a single visual feature across the visual field to form a feature map. Here the authors show that fast OFF ganglion cells in fact respond to two visual features, either object position or speed, depending on the stimulus location.

06 December 2017 | doi: 10.1038/s41467-017-02159-y
Network models  Neural encoding  Retina 

Galectin-3 impacts Cryptococcus neoformans infection through direct antifungal effects OPEN
Fausto Almeida, Julie M. Wolf, Thiago Aparecido da Silva, Carlos M. DeLeon-Rodriguez, Caroline Patini Rezende, André Moreira Pessoni, Fabrício Freitas Fernandes, Rafael Silva-Rocha, Roberto Martinez, Marcio L. Rodrigues, Maria Cristina Roque-Barreira & Arturo Casadevall

The protein Galectin-3 modulates host immunity and plays roles during infections. Here, Almeida et al. show that this protein contributes to host defence against infection with the fungal pathogen Cryptococcus neoformans by inhibiting fungal growth and inducing lysis of fungal extracellular vesicles.

06 December 2017 | doi: 10.1038/s41467-017-02126-7
Antimicrobial responses  Fungal host response  Fungal infection  Pathogens 

Simultaneous representation of a spectrum of dynamically changing value estimates during decision making OPEN
David Meder, Nils Kolling, Lennart Verhagen, Marco K. Wittmann, Jacqueline Scholl, Kristoffer H. Madsen, Oliver J. Hulme, Timothy E.J. Behrens & Matthew F.S. Rushworth

Activity in dorsal anterior cingulate cortex (dACC) dynamically tracks the value of the choice after every outcome. Here the authors report that dACC represents topographic maps of value estimates for different learning rates and interacts with similar maps in other areas at the time of the decision.

05 December 2017 | doi: 10.1038/s41467-017-02169-w
Decision  Learning algorithms 

Neuronal signals regulate obesity induced β-cell proliferation by FoxM1 dependent mechanism OPEN
Junpei Yamamoto, Junta Imai, Tomohito Izumi, Hironori Takahashi, Yohei Kawana, Kei Takahashi, Shinjiro Kodama, Keizo Kaneko, Junhong Gao, Kenji Uno, Shojiro Sawada, Tomoichiro Asano, Vladimir V. Kalinichenko, Etsuo A. Susaki, Makoto Kanzaki, Hiroki R. Ueda, Yasushi Ishigaki, Tetsuya Yamada & Hideki Katagiri

Neuronal signals, in particular those transmitted via the vagal nerve, regulate both β-cell function and proliferation. Here, Yamamoto et al. show that the forkhead box M1 pathway is required for vagal signal-mediated induction of β-cell proliferation during obesity.

05 December 2017 | doi: 10.1038/s41467-017-01869-7
Obesity  Type 2 diabetes 

Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection OPEN
Charles-Adrien Arnaud, Grégory Effantin, Corinne Vivès, Sylvain Engilberge, Maria Bacia, Pascale Boulanger, Eric Girard, Guy Schoehn & Cécile Breyton

Host cell recognition is mediated by the phage tail tip proteins, which then triggers viral genome delivery via the phage tail. Here, the authors combine crystallography and cryoEM to structurally characterise the bacteriophage T5 tail tube structure before and after interaction with its host receptor.

05 December 2017 | doi: 10.1038/s41467-017-02049-3
Bacteriophages  Cryoelectron microscopy  Phage biology  X-ray crystallography 

A two-dimensional Fe-doped SnS2 magnetic semiconductor OPEN
Bo Li, Tao Xing, Mianzeng Zhong, Le Huang, Na Lei, Jun Zhang, Jingbo Li & Zhongming Wei

2D materials can be doped with magnetic atoms in order to boost their potential applications in spintronics. Here, the authors fabricate Fe-doped SnS2 monolayers and show that Fe0.021Sn0.979S2 exhibits ferromagnetic behaviour with perpendicular anisotropy at 2 K, and a Curie temperature of 31 K.

05 December 2017 | doi: 10.1038/s41467-017-02077-z
Electronic and spintronic devices  Electronic devices  Two-dimensional materials 

Broad modulus range nanomechanical mapping by magnetic-drive soft probes OPEN
Xianghe Meng, Hao Zhang, Jianmin Song, Xinjian Fan, Lining Sun & Hui Xie

Force-distance curve-based atomic force microscopy can measure material nanomechanics, but only if the probe and material stiffness match, which limits the measurement range. Here, the authors broaden the dynamic range of the probe by up to four orders of magnitude using magnetic drive peak force modulation.

05 December 2017 | doi: 10.1038/s41467-017-02032-y
Atomic force microscopy  Scanning probe microscopy 

Future loss of Arctic sea-ice cover could drive a substantial decrease in California’s rainfall OPEN
Ivana Cvijanovic, Benjamin D. Santer, Céline Bonfils, Donald D. Lucas, John C. H. Chiang & Susan Zimmerman

Persistent atmospheric ridging in the North Pacific steered storms away and led to the California drought of 2012-16. Here the authors use simulations to show that sea-ice changes trigger reorganization of tropical convection resulting in drying over California.

05 December 2017 | doi: 10.1038/s41467-017-01907-4
Atmospheric dynamics  Climate and Earth system modelling  Climate-change impacts  Cryospheric science 

Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions OPEN

Rising rates of peanut allergy pose a public health problem. Here, the authors profile blood transcriptomes during double-blind, placebo-controlled oral challenge in peanut-allergic children to identify gene and cell composition changes, and construct causal networks to detect key allergic reaction drivers.

05 December 2017 | doi: 10.1038/s41467-017-02188-7
Allergy  Bayesian inference  Gene regulatory networks 

Adhesion toughness of multilayer graphene films OPEN
Joseph D. Wood, Christopher M. Harvey & Simon Wang

The reason why the surface adhesion of a graphene monolayer is much greater than that of graphene multilayers remains unclear. Here, the authors build a model to show interlayer sliding and fracture mode mixity cause the decrease in adhesion toughness of multilayer graphene.

05 December 2017 | doi: 10.1038/s41467-017-02115-w
Characterization and analytical techniques  Graphene  Mechanical and structural properties and devices  Theory and computation 

Resolving the spin splitting in the conduction band of monolayer MoS2  OPEN
Kolyo Marinov, Ahmet Avsar, Kenji Watanabe, Takashi Taniguchi & Andras Kis

In monolayer transition-metal dichalcogenides, lack of inversion symmetry results in spin-split valence and conduction bands, but the small conduction band splitting is hard to probe experimentally. Here, the authors extract a sub-band spacing energy of 0.8 meV in the conduction band of monolayer MoS2 via quantum transport measurements.

05 December 2017 | doi: 10.1038/s41467-017-02047-5
Electronic devices  Two-dimensional materials 

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses OPEN
Claire Duvallet, Sean M. Gibbons, Thomas Gurry, Rafael A. Irizarry & Eric J. Alm

Reported associations between the human microbiome and disease are often inconsistent. Here, Duvallet et al. perform a meta-analysis of 28 gut microbiome studies spanning ten diseases, and find associations that are likely not disease-specific but potentially part of a shared response to disease.

05 December 2017 | doi: 10.1038/s41467-017-01973-8
Computational biology and bioinformatics  Microbiome 

Pandemic H1N1 influenza A viruses suppress immunogenic RIPK3-driven dendritic cell death OPEN
Boris M. Hartmann, Randy A. Albrecht, Elena Zaslavsky, German Nudelman, Hanna Pincas, Nada Marjanovic, Michael Schotsaert, Carles Martínez-Romero, Rafael Fenutria, Justin P. Ingram, Irene Ramos, Ana Fernandez-Sesma, Siddharth Balachandran, Adolfo García-Sastre & Stuart C. Sealfon

The differences in virus-host interactions resulting in distinct pathogenicity of seasonal and pandemic influenza A viruses (IAV) are not well understood. Here, the authors show that the hemagglutinin segment from pandemic, but not seasonal, IAV suppresses RIPK3-mediated dendritic cell death, thereby reducing T cell activation.

05 December 2017 | doi: 10.1038/s41467-017-02035-9
Immune cell death  Influenza virus  Necroptosis  Viral immune evasion 

A new stem sarcopterygian illuminates patterns of character evolution in early bony fishes OPEN
Jing Lu, Sam Giles, Matt Friedman & Min Zhu

Terrestrial vertebrates branched from the lobe-finned fish in the Late Devonian. Here, Lu et al. describe the new lobe-finned fish Ptyctolepis brachynotus dating from the Early Devonian, which preserves a novel combination of cranial characters and suggests revision of evolutionary relationships among bony fish.

05 December 2017 | doi: 10.1038/s41467-017-01801-z
Palaeontology  Phylogenetics 

Network dynamics-based cancer panel stratification for systemic prediction of anticancer drug response OPEN
Minsoo Choi, Jue Shi, Yanting Zhu, Ruizhen Yang & Kwang-Hyun Cho

Genomic alterations underlie the variability of drug responses between cancers, but our mechanistic understanding is limited. Here the authors use the p53 network to study how rewiring of signalling networks by genomic alterations impact their dynamic response to pharmacological perturbation.

05 December 2017 | doi: 10.1038/s41467-017-02160-5
Cellular signalling networks  Dynamic networks  Regulatory networks  Systems analysis 

Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine OPEN
Sarah Batson, Cesira de Chiara, Vita Majce, Adrian J. Lloyd, Stanislav Gobec, Dean Rea, Vilmos Fülöp, Christopher W. Thoroughgood, Katie J. Simmons, Christopher G. Dowson, Colin W. G. Fishwick, Luiz Pedro S. de Carvalho & David I. Roper

The antibiotic D-cycloserine (DCS) targets the peptidoglycan biosynthesis enzyme D-Ala-D-Ala ligase (Ddl). Here the authors reveal the DCS inhibitory mechanism by determining the structure of E. coli DdlB with a phosphorylated DCS molecule in the active site that formed in crystallo and mimics the D-alanyl phosphate intermediate.

05 December 2017 | doi: 10.1038/s41467-017-02118-7
Antibiotics  X-ray crystallography 

In vivo transplantation of 3D encapsulated ovarian constructs in rats corrects abnormalities of ovarian failure OPEN
Sivanandane Sittadjody, Justin M. Saul, John P. McQuilling, Sunyoung Joo, Thomas C. Register, James J. Yoo, Anthony Atala & Emmanuel C. Opara

Cell-based hormone replacement therapy (cHRT) may be an alternative therapy to pharmacological (p)HRT. Here, the authors show that implanted 3D bioengineered ovarian constructs of granulosa and theca cells in ovariectomized rats recapitulate native cell interactions and improve efficacy compared to similar doses of pHRT.

05 December 2017 | doi: 10.1038/s41467-017-01851-3
Cell delivery  Hypogonadism 

Mechanistic insight into TRIP13-catalyzed Mad2 structural transition and spindle checkpoint silencing OPEN
Melissa L. Brulotte, Byung-Cheon Jeong, Faxiang Li, Bing Li, Eric B. Yu, Qiong Wu, Chad A. Brautigam, Hongtao Yu & Xuelian Luo

The spindle checkpoint ensures the fidelity of chromosome segregation during mitosis and meiosis. Here the authors use a combination of biochemical and structural biology approaches to show how the TRIP13 ATPase and its adaptor, p31comet, catalyze the conversion of the checkpoint protein Mad2 between latent and active forms

05 December 2017 | doi: 10.1038/s41467-017-02012-2
Chromosome segregation  Enzyme mechanisms  Molecular conformation  Structural biology 

Albumin/vaccine nanocomplexes that assemble in vivo for combination cancer immunotherapy OPEN
Guizhi Zhu, Geoffrey M. Lynn, Orit Jacobson, Kai Chen, Yi Liu, Huimin Zhang, Ying Ma, Fuwu Zhang, Rui Tian, Qianqian Ni, Siyuan Cheng, Zhantong Wang, Nan Lu, Bryant C. Yung, Zhe Wang, Lixin Lang, Xiao Fu, Albert Jin, Ido D. Weiss, Harshad Vishwasrao et al.

Albumin conjugates can enhance drug delivery. Here, the authors repurpose albumin-binding Evans blue to develop nanovaccines that co-deliver adjuvants and tumor neoantigens to antigen-presenting cells in lymph nodes, resulting in potent and durable antitumour immunity in combination immunotherapy.

05 December 2017 | doi: 10.1038/s41467-017-02191-y
Cancer immunotherapy  Nanoparticles  Tumour vaccines 

Exploration of pyrazine-embedded antiaromatic polycyclic hydrocarbons generated by solution and on-surface azomethine ylide homocoupling OPEN
Xiao-Ye Wang, Marcus Richter, Yuanqin He, Jonas Björk, Alexander Riss, Raju Rajesh, Manuela Garnica, Felix Hennersdorf, Jan J. Weigand, Akimitsu Narita, Reinhard Berger, Xinliang Feng, Willi Auwärter, Johannes V. Barth, Carlos-Andres Palma & Klaus Müllen

Polyaromatic hydrocarbons can be precisely manipulated to yield ever more complex and discrete graphene analogs, such as nanographenes. Here, the authors use azomethine ylide homocoupling to insert an antiaromatic pyrazine ring into the core of a nanographene, and characterize the molecule’s unique electronic character.

05 December 2017 | doi: 10.1038/s41467-017-01934-1
Nanoscale materials  Organic chemistry  Surface chemistry 

Sumatran tiger survival threatened by deforestation despite increasing densities in parks OPEN
Matthew Scott Luskin, Wido Rizki Albert & Mathias W. Tobler

Determining the conservation status and populations trends for elusive predators has been impeded by discrepancies in how densities are calculated. Here, Luskin et al. introduce a means to standardize previous density estimates and assess the threats to the Sumatran tiger.

05 December 2017 | doi: 10.1038/s41467-017-01656-4
Biogeography  Conservation biology  Population dynamics 

Geochemical and mineralogical evidence that Rodinian assembly was unique OPEN
Chao Liu, Andrew H. Knoll & Robert M. Hazen

The supercontinent Rodinia has been hypothesised to have formed in a different manner from other supercontinents. Here, the authors report geochemical and mineralogical evidence for prevalence of non-arc magmatism and enhanced erosion of volcanic arcs and orogens during Rodinian assembly.

05 December 2017 | doi: 10.1038/s41467-017-02095-x
Geochemistry  Mineralogy  Precambrian geology 

Cooperation and the evolution of hunter-gatherer storytelling OPEN
Daniel Smith, Philip Schlaepfer, Katie Major, Mark Dyble, Abigail E. Page, James Thompson, Nikhil Chaudhary, Gul Deniz Salali, Ruth Mace, Leonora Astete, Marilyn Ngales, Lucio Vinicius & Andrea Bamberg Migliano

Storytelling entails costs in terms of time and effort, yet it is a ubiquitous feature of human society. Here, Smith et al. show benefits of storytelling in Agta hunter-gatherer communities, as storytellers have higher reproductive success and storytelling is associated with higher cooperation in the group.

05 December 2017 | doi: 10.1038/s41467-017-02036-8
Behavioural ecology  Biological anthropology  Cultural evolution  Social anthropology 

Discrete and continuous mechanisms of temporal selection in rapid visual streams OPEN
Sébastien Marti & Stanislas Dehaene

Humans can identify a target picture even when presented within a rapid stream of stimuli. Here the authors report that the neural activity initially supports parallel processing of multiple stimuli around the target in ventral visual areas followed later by isolated activation of reported images in parietal areas.

05 December 2017 | doi: 10.1038/s41467-017-02079-x
Attention  Consciousness  Human behaviour 

Existence of multi-radical and closed-shell semiconducting states in post-graphene organic Dirac materials OPEN
Isaac Alcón, Francesc Viñes, Iberio de P. R. Moreira & Stefan T. Bromley

The lack of band gap controllability in graphene severely restricts its use in nanoelectronics. Here, the authors predict that post-graphene organic Dirac materials should allow for exceptional electronic tunability between graphene-like semimetallicity and multi-radical and/or closed-shell semiconducting states.

05 December 2017 | doi: 10.1038/s41467-017-01977-4
Electronic materials  Electronic properties and devices  Electronic structure 

3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations OPEN
Pengze Wu, Tingting Li, Ruifeng Li, Lumeng Jia, Ping Zhu, Yifang Liu, Qing Chen, Daiwei Tang, Yuezhou Yu & Cheng Li

Chromosome conformation capture techniques enable the study of genome organization in cancer cells. Here, the authors use Hi-C, WGS, and RNA-seq to study the 3D genome of multiple myeloma and find that genome disorganization is associated with copy number variations and changes in gene expression.

05 December 2017 | doi: 10.1038/s41467-017-01793-w
Cancer genomics  Structural variation 

The interdomain flexible linker of the polypeptide GalNAc transferases dictates their long-range glycosylation preferences OPEN
Matilde de las Rivas, Erandi Lira-Navarrete, Earnest James Paul Daniel, Ismael Compañón, Helena Coelho, Ana Diniz, Jesús Jiménez-Barbero, Jesús M. Peregrina, Henrik Clausen, Francisco Corzana, Filipa Marcelo, Gonzalo Jiménez-Osés, Thomas A. Gerken & Ramon Hurtado-Guerrero

GalNAc transferases’ (GalNAc-Ts) catalytic domains are connected to a lectin domain through a flexible linker. Here the authors present a structural analysis of GalNAc-T4 that implicates the linker region as modulator of the orientations of the lectin domain, which in turn imparts substrate specificity.

05 December 2017 | doi: 10.1038/s41467-017-02006-0
Enzyme mechanisms  Glycobiology  Kinetics 

Impact-induced changes in source depth and volume of magmatism on Mercury and their observational signatures OPEN
Sebastiano Padovan, Nicola Tosi, Ana-Catalina Plesa & Thomas Ruedas

Mantle partial melting produced the volcanic crust of Mercury. Here, the authors numerically model the formation of post-impact melt sheets and find that mantle convection was weak at around 3.7–3.8 Ga and that the melt sheets of Caloris and Rembrandt may contain partial melting of pristine mantle material.

05 December 2017 | doi: 10.1038/s41467-017-01692-0
Geodynamics  Inner planets 

Generation of photonic entanglement in green fluorescent proteins OPEN
Siyuan Shi, Prem Kumar & Kim Fook Lee

Quantum-enhanced applications such as quantum spectroscopy of biological samples could take advantage from in situ generation of quantum states of light. Here, the authors characterize polarization-entangled photon states generated through spontaneous four-wave mixing in enhanced green fluorescent proteins.

05 December 2017 | doi: 10.1038/s41467-017-02027-9
Biomaterials – proteins  Nonlinear optics  Quantum optics 

Polη O-GlcNAcylation governs genome integrity during translesion DNA synthesis OPEN
Xiaolu Ma, Hongmei Liu, Jing Li, Yihao Wang, Yue-He Ding, Hongyan Shen, Yeran Yang, Chenyi Sun, Min Huang, Yingfeng Tu, Yang Liu, Yongliang Zhao, Meng-Qiu Dong, Ping Xu, Tie-Shan Tang & Caixia Guo

Polη is a key player in translesion DNA synthesis. Here, the authors uncover that, in response to DNA damage, Polη undergoes O-GlcNAcylation at threonine 457 by O-GlcNAc transferase to facilitate the timely disassembly of Polη after DNA lesion bypass.

05 December 2017 | doi: 10.1038/s41467-017-02164-1
Glycosylation  Translesion synthesis  Ubiquitylation 

Diffusion of treatment in social networks and mass drug administration OPEN
Goylette F. Chami, Andreas A. Kontoleon, Erwin Bulte, Alan Fenwick, Narcis B. Kabatereine, Edridah M. Tukahebwa & David W. Dunne

Mass drug administration depends on the distributors’ contact with community members. Using data of deworming treatment distribution from Ugandan villages, the authors show that community medicine distributors with tightly-knit friendship connections achieve the greatest reach and speed of coverage.

05 December 2017 | doi: 10.1038/s41467-017-01499-z
Complex networks  Infectious diseases  Public health 

The anthelmintic praziquantel is a human serotoninergic G-protein-coupled receptor ligand OPEN
John D. Chan, Pauline M. Cupit, Gihan S. Gunaratne, John D. McCorvy, Yang Yang, Kristen Stoltz, Thomas R. Webb, Peter I. Dosa, Bryan L. Roth, Ruben Abagyan, Charles Cunningham & Jonathan S. Marchant

Schistosomiasis is caused by infection with the flatworm Schistosoma, and praziquantel is the drug of choice for its treatment. Here, Chan and colleagues identify praziquantel as a ligand for the human serotoninergic 5-HT2B G-protein-coupled receptor, and reveal a function for praziquantel as a regulator of vascular tone in treated hosts.

05 December 2017 | doi: 10.1038/s41467-017-02084-0
Parasite host response  Parasitic infection  Receptor pharmacology 

Three distinct developmental pathways for adaptive and two IFN-γ-producing γδ T subsets in adult thymus OPEN
Terkild Brink Buus, Niels Ødum, Carsten Geisler & Jens Peter Holst Lauritsen

Mouse γδ T cells have diverse functional subsets, but how these subsets are programmed during their development is still unclear. Here the authors show that three surface markers, CD117, CD200 and CD371, refine the development of γδ T cells in the thymus into three pathways programming distinct γδ T cell subsets.

04 December 2017 | doi: 10.1038/s41467-017-01963-w
Gammadelta T cells  Immunogenetics  Lymphocyte differentiation  Thymus 

Complete 3-Qubit Grover search on a programmable quantum computer OPEN
C. Figgatt, D. Maslov, K. A. Landsman, N. M. Linke, S. Debnath & C. Monroe

Grover’s algorithm provides a quantum speedup when searching through an unsorted database. Here, the authors perform it on 3 qubits using trapped ions, demonstrating two methods for marking the correct result in the algorithm’s oracle and providing data for searches yielding 1 or 2 solutions.

04 December 2017 | doi: 10.1038/s41467-017-01904-7
Information theory and computation  Quantum information  Qubits 

Alu-dependent RNA editing of GLI1 promotes malignant regeneration in multiple myeloma OPEN
Elisa Lazzari, Phoebe K. Mondala, Nathaniel Delos Santos, Amber C. Miller, Gabriel Pineda, Qingfei Jiang, Heather Leu, Shawn A. Ali, Anusha-Preethi Ganesan, Christina N. Wu, Caitlin Costello, Mark Minden, Raffaella Chiaramonte, A.  Keith Stewart, Leslie A. Crews & Catriona H. M. Jamieson

The treatment of multiple myeloma is challenging due to high relapse rates. Here the authors show that expression of ADAR1 correlates with poor patient outcomes, and that ADAR1-mediated editing of GLI1 is a mechanism relevant in the context of multiple myeloma progression and drug resistance.

04 December 2017 | doi: 10.1038/s41467-017-01890-w
Cancer stem cells  Myeloma  Transcriptomics 

Lysosomal integral membrane protein-2 as a phospholipid receptor revealed by biophysical and cellular studies OPEN
Karen S. Conrad, Ting-Wen Cheng, Daniel Ysselstein, Saskia Heybrock, Lise R. Hoth, Boris A. Chrunyk, Christopher W. am Ende, Dimitri Krainc, Michael Schwake, Paul Saftig, Shenping Liu, Xiayang Qiu & Michael D. Ehlers

Lysosomal integral membrane protein-2 (LIMP-2) is a glucocerebrosidase receptor, which is linked to kidney failure and other diseases. Here the authors show that LIMP-2 is also a phospholipid receptor and present the lipid-bound structure of the LIMP-2 luminal domain dimer and discuss its lipid trafficking mechanism.

04 December 2017 | doi: 10.1038/s41467-017-02044-8
Membrane trafficking  X-ray crystallography 

ORAI channels are critical for receptor-mediated endocytosis of albumin OPEN
Bo Zeng, Gui-Lan Chen, Eliana Garcia-Vaz, Sunil Bhandari, Nikoleta Daskoulidou, Lisa M. Berglund, Hongni Jiang, Thomas Hallett, Lu-Ping Zhou, Li Huang, Zi-Hao Xu, Viji Nair, Robert G. Nelson, Wenjun Ju, Matthias Kretzler, Stephen L. Atkin, Maria F. Gomez & Shang-Zhong Xu

Patients with diabetic nephropathy suffer from impaired albumin reabsorption by proximal tubular epithelial cells. Here authors use diabetic and transgenic mouse models and in vitro models to show the cause for this lies in the down regulation and internalization of the ion channels, ORAI1-3.

04 December 2017 | doi: 10.1038/s41467-017-02094-y
Kidney  Nephrons  Physiology 

IFT proteins spatially control the geometry of cleavage furrow ingression and lumen positioning OPEN
Nicolas Taulet, Benjamin Vitre, Christelle Anguille, Audrey Douanier, Murielle Rocancourt, Michael Taschner, Esben Lorentzen, Arnaud Echard & Benedicte Delaval

Cytokinesis relies on central spindle organization and provides a spatial landmark for lumen formation. Here, the authors show that intraflagellar transport proteins are required for the localization of the cytokinetic regulator Aurora B and subsequent cleavage furrow ingression and lumen positioning.

04 December 2017 | doi: 10.1038/s41467-017-01479-3
Cytokinesis  Motor proteins 

Distributed neural representation of saliency controlled value and category during anticipation of rewards and punishments OPEN
Zhihao Zhang, Jennifer Fanning, Daniel B. Ehrlich, Wenting Chen, Daeyeol Lee & Ifat Levy

Stimulus category, saliency and value all affect the subjective value estimates that guide our decisions. Here, the authors systematically vary their stimuli along these three dimensions in humans and report category independent encoding of values and saliency in the vmPFC and striatum.

04 December 2017 | doi: 10.1038/s41467-017-02080-4
Decision  Neural encoding  Reward 

Crystal plasticity as an indicator of the viscous-brittle transition in magmas OPEN
J. E. Kendrick, Y. Lavallée, E. Mariani, D. B. Dingwell, J. Wheeler & N. R. Varley

The rheological behaviour of magma in shallow conditions may help determine a volcano’s eruptive style. Here, the authors perform deformation experiments on lava from Volcán de Colima to demonstrate that crystal plasticity may preclude failure at certain shallow magmatic conditions.

04 December 2017 | doi: 10.1038/s41467-017-01931-4
Mineralogy  Petrology  Volcanology 

Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells OPEN
Timo A. Lehti, Maria I. Pajunen, Maria S. Skog & Jukka Finne

Eukaryotic organisms are continuously exposed to bacteriophages, but these are not thought to enter non-phagocytic cells. Here, Lehti et al. show that a bacteriophage can bind to a specific receptor on the surface of human neuroblastoma cells in vitro, and be internalized via the endolysosomal route.

04 December 2017 | doi: 10.1038/s41467-017-02057-3
Bacteriophages  Cell biology  Phage biology 

Multiyne chains chelating osmium via three metal-carbon σ bonds OPEN
Qingde Zhuo, Jianfeng Lin, Yuhui Hua, Xiaoxi Zhou, Yifan Shao, Shiyan Chen, Zhixin Chen, Jun Zhu, Hong Zhang & Haiping Xia

Metal-carbon σ bonds mark the basis of organometallic chemistry, but the formation of multiple such bonds between single organic and metal entities remains a challenge. Here, the authors report a one-pot aromaticity-driven method to construct osmium-based multidentate complexes containing three metal-carbon σ bonds from multiyn chains.

04 December 2017 | doi: 10.1038/s41467-017-02120-z
Organic chemistry  Organometallic chemistry  Reaction mechanisms 

Dendrogenin A drives LXR to trigger lethal autophagy in cancers OPEN
Gregory Segala, Marion David, Philippe de Medina, Mathias C. Poirot, Nizar Serhan, François Vergez, Aurelie Mougel, Estelle Saland, Kevin Carayon, Julie Leignadier, Nicolas Caron, Maud Voisin, Julia Cherier, Laetitia Ligat, Frederic Lopez, Emmanuel Noguer, Arnaud Rives, Bruno Payré, Talal al Saati, Antonin Lamaziere et al.

Dendrogenin A, cholesterol metabolite, has tumor suppressive properties but the mechanisms are unknown. Here the authors show that Dendrogenin A can induce autophagy-mediated cell death in both melanoma and acute myeloid leukaemia.

04 December 2017 | doi: 10.1038/s41467-017-01948-9
Acute myeloid leukaemia  Drug development  Macroautophagy  Melanoma  Receptor pharmacology 

Dissipatively coupled waveguide networks for coherent diffusive photonics OPEN
Sebabrata Mukherjee, Dmitri Mogilevtsev, Gregory Ya. Slepyan, Thomas H. Doherty, Robert R. Thomson & Natalia Korolkova

Diffusive light propagation represents a valuable additional tool for integrated photonic technologies. As an example, here the authors experimentally demonstrate optical equalisation of coherent light propagating in a femtosecond laser written circuit which simulates a dissipatively-coupled quantum chain.

04 December 2017 | doi: 10.1038/s41467-017-02048-4
Integrated optics  Quantum simulation  Theoretical physics 

Harnessing heterogeneous nucleation to control tin orientations in electronic interconnections OPEN
Z. L. Ma, S. A. Belyakov, K. Sweatman, T. Nishimura, T. Nishimura & C. M. Gourlay

Control over the crystallographic orientation of solder joints based on βSn will improve the reliability of electronic interconnects. Using a technique based on droplet solidification and lattice matching, Ma et al. are able to control the βSn nucleation events, hence control the grain orientation.

04 December 2017 | doi: 10.1038/s41467-017-01727-6
Applied physics  Electronic devices 

Interleukin-13 receptor alpha 2 cooperates with EGFRvIII signaling to promote glioblastoma multiforme OPEN
Jennifer P. Newman, Grace Y. Wang, Kazuhiko Arima, Shou P. Guan, Michael R. Waters, Webster K. Cavenee, Edward Pan, Edita Aliwarga, Siao T. Chong, Catherine Y. L. Kok, Berwini B. Endaya, Amyn A. Habib, Tomohisa Horibe, Wai H. Ng, Ivy A. W. Ho, Kam M. Hui, Tomasz Kordula & Paula Y. P. Lam

Interleukin-13 receptor alpha 2 is highly expressed in glioblastoma multiforme but its role in this malignancy is unclear. Here the authors show that this receptor interacts with mutant EGFR, stimulating its kinase activity, thus inducing proliferation.

04 December 2017 | doi: 10.1038/s41467-017-01392-9
CNS cancer  Growth factor signalling 

Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B OPEN
Yongjian Qiu, Elise K. Pasoreck, Amit K. Reddy, Akira Nagatani, Wenxiu Ma, Joanne Chory & Meng Chen

Plant phytochromes mediate the degradation of PIF transcription factors to transduce light signaling. Here, contrary to previous models, Qiu et al. show that degradation of PIF3 does not require the N-terminal photosensory module of PHYB but can instead be mediated by the C-terminal output module.

04 December 2017 | doi: 10.1038/s41467-017-02062-6
Light responses  Plant signalling 

ATM and CDK2 control chromatin remodeler CSB to inhibit RIF1 in DSB repair pathway choice OPEN
Nicole L. Batenburg, John R. Walker, Sylvie M. Noordermeer, Nathalie Moatti, Daniel Durocher & Xu-Dong Zhu

Cockayne syndrome group B protein (CSB) is a multifunctional chromatin remodeler involved in double-strand break repair. Here the authors investigate the molecular post-translational signals regulating CSB activity.

04 December 2017 | doi: 10.1038/s41467-017-02114-x
Chromatin remodelling  Double-strand DNA breaks  Homologous recombination  Non-homologous-end joining  Phosphorylation 

The transcript cleavage factor paralogue TFS4 is a potent RNA polymerase inhibitor OPEN
Thomas Fouqueau, Fabian Blombach, Ross Hartman, Alan C. M. Cheung, Mark J. Young & Finn Werner

Transcript cleavage factors such as eukaryotic TFIIS assist the resumption of transcription following RNA pol II backtracking. Here the authors find that one of the Sulfolobus solfataricus TFIIS homolog—TFS4—has evolved into a potent RNA polymerase inhibitor potentially involved in antiviral defense.

04 December 2017 | doi: 10.1038/s41467-017-02081-3
Archaeal biology  Enzyme mechanisms  Transcriptional regulatory elements 

TRPM7 kinase activity is essential for T cell colonization and alloreactivity in the gut OPEN
Andrea Romagnani, Valentina Vettore, Tanja Rezzonico-Jost, Sarah Hampe, Elsa Rottoli, Wiebke Nadolni, Michela Perotti, Melanie A. Meier, Constanze Hermanns, Sheila Geiger, Gunther Wennemuth, Camilla Recordati, Masayuki Matsushita, Susanne Muehlich, Michele Proietti, Vladimir Chubanov, Thomas Gudermann, Fabio Grassi & Susanna Zierler

Gut-homing and colonization of T cells are important for maintaining local immune homoeostasis and protective immunity. Here the authors show that the kinase activity of TRPM7 regulates Th17 differentiation and T cell alloreactivity in the gut by modulating SMAD2 activation and CD103 expression in T cells

04 December 2017 | doi: 10.1038/s41467-017-01960-z
Allotransplantation  Mucosal immunology  Signal transduction  T-helper 17 cells 

Direct evidence of hidden local spin polarization in a centrosymmetric superconductor LaO0.55 F0.45BiS2  OPEN
Shi-Long Wu, Kazuki Sumida, Koji Miyamoto, Kazuaki Taguchi, Tomoki Yoshikawa, Akio Kimura, Yoshifumi Ueda, Masashi Arita, Masanori Nagao, Satoshi Watauchi, Isao Tanaka & Taichi Okuda

The local broken symmetry induced spin-splitting in centrosymmetric materials has been predicted previously. Here the authors provide spectroscopic evidence for the coexistence of Rashba-like and Dresselhaus-like spin textures in centrosymmetric electron doped superconductor La(O,F)BiS2.

04 December 2017 | doi: 10.1038/s41467-017-02058-2
Electronic properties and materials  Spintronics  Superconducting properties and materials  Topological insulators 

Random access quantum information processors using multimode circuit quantum electrodynamics OPEN
R. K. Naik, N. Leung, S. Chakram, Peter Groszkowski, Y. Lu, N. Earnest, D. C. McKay, Jens Koch & D. I. Schuster

Despite their versatility, superconducting qubits such as transmons still have limited coherence times compared to resonators. Here, the authors show how to use a single transmon to implement universal one-qubit and two-qubit operations among nine qubits encoded in superconducting resonators’ eigenmodes.

04 December 2017 | doi: 10.1038/s41467-017-02046-6
Quantum information  Qubits  Superconducting devices 

Van der Waals epitaxial growth and optoelectronics of large-scale WSe2/SnS2 vertical bilayer p–n junctions OPEN
Tiefeng Yang, Biyuan Zheng, Zhen Wang, Tao Xu, Chen Pan, Juan Zou, Xuehong Zhang, Zhaoyang Qi, Hongjun Liu, Yexin Feng, Weida Hu, Feng Miao, Litao Sun, Xiangfeng Duan & Anlian Pan

Growth of large area and defect-free two-dimensional semiconductor layers for high-performance p–n junction applications has been a great challenge. Yang et al. prepare millimeter-scaled WSe2/SnS2 vertical heterojunctions by two-step van der Waals epitaxy, which show excellent optoelectronic properties.

04 December 2017 | doi: 10.1038/s41467-017-02093-z
Materials science  Nanoscale materials  Two-dimensional materials 

Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility OPEN
Amit Sud, Hauke Thomsen, Philip J. Law, Asta Försti, Miguel Inacio da Silva Filho, Amy Holroyd, Peter Broderick, Giulia Orlando, Oleg Lenive, Lauren Wright, Rosie Cooke, Douglas Easton, Paul Pharoah, Alison Dunning, Julian Peto, Federico Canzian, Rosalind Eeles, ZSofia Kote-Jarai, Kenneth Muir, Nora Pashayan et al.

Classical Hodgkin lymphoma is a cancer that originates in lymph nodes. Little is known about its genetic susceptibility. Here, the authors combined existing and new genome-wide association studies to identify risk loci for classical Hodgkin lymphoma at 6q22.33, and nodular sclerosis Hodgkin lymphoma at 3q28, 6q23.3, 10p14, 13q34, 16p13.13.

01 December 2017 | doi: 10.1038/s41467-017-00320-1
Cancer genetics  Genome-wide association studies  Hodgkin lymphoma  Immunogenetics 

Directed self-assembly of fluorescence responsive nanoparticles and their use for real-time surface and cellular imaging OPEN
Shane Cheung & Donal F. O’Shea

Polymer nanoparticles that have an in-built capacity to elicit an output during drug delivery are highly desirable. Here the authors describe the self-assembly of an amphiphilic tri-block co-polymer that shows particle fluorescence in response to temperature, surface adsorption and cellular uptake.

01 December 2017 | doi: 10.1038/s41467-017-02060-8
Biophysical chemistry  Drug delivery  Imaging techniques and agents  Supramolecular polymers 

Magnesium uptake by connecting fluid-phase endocytosis to an intracellular inorganic cation filter OPEN
Sandra H. Klompmaker, Kid Kohl, Nicolas Fasel & Andreas Mayer

Metal bioavailability is frequently limited by sequestering agents which makes them inaccessible to cells. Here the authors show that cells can increase Mg2+ uptake via fluid phase endocytosis and accumulate this metal in their vacuole loaded with polyphosphate, and later can be exported to the cytosol.

01 December 2017 | doi: 10.1038/s41467-017-01930-5
Endocytosis  Magnesium  Organelles 

Small molecule screen in embryonic zebrafish using modular variations to target segmentation OPEN
Sandra Richter, Ulrike Schulze, Pavel Tomançak & Andrew C. Oates

Chemical screens can identify small molecules that affect biological development, with potential therapeutic value. Here, the authors use a modular approach in a screen in zebrafish embryos, varying concentration, genotype and timing to target segmentation disorders, birth defects that affect the spinal column.

01 December 2017 | doi: 10.1038/s41467-017-01469-5
Musculoskeletal development  Phenotypic screening  Zebrafish 

Nematic superconducting state in iron pnictide superconductors OPEN
Jun Li, Paulo J. Pereira, Jie Yuan, Yang-Yang Lv, Mei-Ping Jiang, Dachuan Lu, Zi-Quan Lin, Yong-Jie Liu, Jun-Feng Wang, Liang Li, Xiaoxing Ke, Gustaaf Van Tendeloo, Meng-Yue Li, Hai-Luke Feng, Takeshi Hatano, Hua-Bing Wang, Pei-Heng Wu, Kazunari Yamaura, Eiji Takayama-Muromachi, Johan Vanacken et al.

Nematic electronic order is rare and its onset often indicates a phase transition. Here, Li et al. report a nematic superconducting state in Ba0.5K0.5Fe2As2 by measuring the angular dependence of the in-plane and out-of-plane magnetoresistivity.

01 December 2017 | doi: 10.1038/s41467-017-02016-y
Superconducting devices  Superconducting properties and materials 

Retarding oxidation of copper nanoparticles without electrical isolation and the size dependence of work function OPEN
G. Dinesha M.R. Dabera, Marc Walker, Ana M. Sanchez, H. Jessica Pereira, Richard Beanland & Ross A. Hatton

Copper nanoparticles are susceptible to oxidation in air, which limits their applications. Here, the authors reveal correlations between the stability of a Cu nanoparticle and the structure of its passivating ligand, finding that short chain thiols are surprisingly more effective at retarding oxidation than longer chain ones.

01 December 2017 | doi: 10.1038/s41467-017-01735-6
Chemical physics  Nanoparticles 

Evidence for single metal two electron oxidative addition and reductive elimination at uranium OPEN
Benedict M. Gardner, Christos E. Kefalidis, Erli Lu, Dipti Patel, Eric J. L. McInnes, Floriana Tuna, Ashley J. Wooles, Laurent Maron & Stephen T. Liddle

The reactivity of f-block complexes is primarily defined by single-electron oxidations and σ-bond metathesis. Here, Liddle and co-workers provide evidence that a uranium complex can undergo reversible oxidative addition and reductive elimination, demonstrating transition metal-like reactivity within f-block chemistry.

01 December 2017 | doi: 10.1038/s41467-017-01363-0
Catalysis  Coordination chemistry  Organometallic chemistry 

Alternative activation generates IL-10 producing type 2 innate lymphoid cells OPEN
Corey R. Seehus, Asha Kadavallore, Brian de la Torre, Alyson R. Yeckes, Yizhou Wang, Jie Tang & Jonathan Kaye

Type 2 innate lymphoid cells (ILC2) are thought to be a uniform population of effector cells that produce IL-5 and IL-13. Here, the authors shown that, in mice, IL-33 can alternatively activate these cells to generate a molecularly distinct IL-10-producing subset designated ILC210.

01 December 2017 | doi: 10.1038/s41467-017-02023-z
Innate immunity  Innate lymphoid cells 

Unusual scaling laws for plasmonic nanolasers beyond the diffraction limit OPEN
Suo Wang, Xing-Yuan Wang, Bo Li, Hua-Zhou Chen, Yi-Lun Wang, Lun Dai, Rupert F. Oulton & Ren-Min Ma

Since the first proposal for plasmonic nanolasers there has been a debate about the limitations on performance posed by the inherent losses in metallic systems. Here, the authors compare over 100 plasmonic and photonic laser devices and find sub-wavelength plasmonic lasers to be advantageous.

01 December 2017 | doi: 10.1038/s41467-017-01662-6
Nanophotonics and plasmonics  Semiconductor lasers 

Remodelling of the gut microbiota by hyperactive NLRP3 induces regulatory T cells to maintain homeostasis OPEN
Xiaomin Yao, Chenhong Zhang, Yue Xing, Guang Xue, Qianpeng Zhang, Fengwei Pan, Guojun Wu, Yingxin Hu, Qiuhong Guo, Ailing Lu, Xiaoming Zhang, Rongbin Zhou, Zhigang Tian, Benhua Zeng, Hong Wei, Warren Strober, Liping Zhao & Guangxun Meng

Inflammasomes are involved in gut homeostasis and inflammatory pathologies. The authors show that a hyperactive NLRP3 inflammasome maintains gut homeostasis through remodelling of the gut microbiota and induction of regulatory T cells.

01 December 2017 | doi: 10.1038/s41467-017-01917-2
Inflammasome  Microbiome  T cells 

Metric clusters in evolutionary games on scale-free networks OPEN
Kaj-Kolja Kleineberg

Heterogeneous complex networks tend to be a more realistic representation of social networks than homogenous ones. Here Kleineberg investigates the role of network heterogeneity in the emergence of cooperation in social dilemmas and shows that it can sometimes hinder it.

01 December 2017 | doi: 10.1038/s41467-017-02078-y
Complex networks  Social evolution 

Multiplex single-cell visualization of nucleic acids and protein during HIV infection OPEN
Maritza Puray-Chavez, Philip R. Tedbury, Andrew D. Huber, Obiaara B. Ukah, Vincent Yapo, Dandan Liu, Juan Ji, Jennifer J. Wolf, Alan N. Engelman & Stefan G. Sarafianos

Technical limitations in simultaneous microscopic visualization of HIV transcription from individual integration sites have curtailed progress in the field. Here the authors report a branched DNA in situ hybridization method for direct single-cell visualization of HIV DNA, RNA, and protein.

01 December 2017 | doi: 10.1038/s41467-017-01693-z
Fluorescence imaging  Retrovirus 

Opposite effects of Activin type 2 receptor ligands on cardiomyocyte proliferation during development and repair OPEN
Deepika Dogra, Suchit Ahuja, Hyun-Taek Kim, S. Javad Rasouli, Didier Y. R. Stainier & Sven Reischauer

Zebrafish can regenerate damaged myocardial tissue but it is unclear how this is regulated. Here, the authors show that two TGF-β family members, Mstnb and Inhbaa, have opposite effects in regeneration, with mstnb overexpression or inhbaa loss-of-function causing cardiac scarring after injury.

01 December 2017 | doi: 10.1038/s41467-017-01950-1
Cardiac regeneration  Cell proliferation  Growth factor signalling  Mitosis 

Bending and breaking of stripes in a charge ordered manganite OPEN
Benjamin H. Savitzky, Ismail El Baggari, Alemayehu S. Admasu, Jaewook Kim, Sang-Wook Cheong, Robert Hovden & Lena F. Kourkoutis

Charge-lattice coupling plays a central role in the exotic behaviors of multiferroic complex oxides, such as manganites, however, obtaining a microscopic picture is challenging. Here, Savitzky et al. map periodic lattice displacement fields at the picometer scale to study local order-disorder competition.

01 December 2017 | doi: 10.1038/s41467-017-02156-1
Characterization and analytical techniques  Electronic properties and materials  Nanoscale materials  Phase transitions and critical phenomena 

Fine control of metal concentrations is necessary for cells to discern zinc from cobalt OPEN
Deenah Osman, Andrew W. Foster, Junjun Chen, Kotryna Svedaite, Jonathan W. Steed, Elena Lurie-Luke, Thomas G. Huggins & Nigel J. Robinson

Bacteria possess transcription factors whose DNA-binding activity is altered upon binding to specific metals, but the binding of metals is not specific in vitro. Here, Osman et al. show that tight regulation of buffered intracellular metal concentrations is a prerequisite for metal specificity.

01 December 2017 | doi: 10.1038/s41467-017-02085-z
Cellular microbiology  Metalloproteins 

Energetic instability of passive states in thermodynamics OPEN
Carlo Sparaciari, David Jennings & Jonathan Oppenheim

Is it possible to single out the thermal state from all the passive states even when not operating in the thermodynamic limit? Here, the authors show that an optimal amount of energy can be extracted from any athermal quantum state when using a machine that operates in a reversible cycle.

01 December 2017 | doi: 10.1038/s41467-017-01505-4
Quantum information  Theoretical physics  Thermodynamics 

Environmental conditions limit attractiveness of a complex sexual signal in the túngara frog OPEN
Wouter Halfwerk, Judith A. H. Smit, Hugo Loning, Amanda M. Lea, Inga Geipel, Jacintha Ellers & Michael J. Ryan

Animal sexual signals should be conspicuous to mates but not to enemies. Here, the authors show that call site properties can set limits on the attractiveness of male frogs' advertisement call, but that males may balance sexual success over predation risk by digging deeper puddles.

01 December 2017 | doi: 10.1038/s41467-017-02067-1
Behavioural ecology  Sexual selection 

Schwann cell TRPA1 mediates neuroinflammation that sustains macrophage-dependent neuropathic pain in mice OPEN
Francesco De Logu, Romina Nassini, Serena Materazzi, Muryel Carvalho Gonçalves, Daniele Nosi, Duccio Rossi Degl’Innocenti, Ilaria M. Marone, Juliano Ferreira, Simone Li Puma, Silvia Benemei, Gabriela Trevisan, Daniel Souza Monteiro de Araújo, Riccardo Patacchini, Nigel W. Bunnett & Pierangelo Geppetti

Following peripheral nerve injury, influx of immune cells to the site may contribute to the development of chronic pain. Here the authors show that TRPA1 is expressed on Schwann cells and contributes to immune cell influx in a mouse model of neuropathic pain.

01 December 2017 | doi: 10.1038/s41467-017-01739-2
Chronic pain  Schwann cell 

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism OPEN
Xiaohan Yang, Rongbin Hu, Hengfu Yin, Jerry Jenkins, Shengqiang Shu, Haibao Tang, Degao Liu, Deborah A. Weighill, Won Cheol Yim, Jungmin Ha, Karolina Heyduk, David M. Goodstein, Hao-Bo Guo, Robert C. Moseley, Elisabeth Fitzek, Sara Jawdy, Zhihao Zhang, Meng Xie, James Hartwell, Jane Grimwood et al.

Crassulacean acid metabolism (CAM) is a metabolic adaptation of photosynthesis that enhances water use efficiency. Here, via genomic analysis of Kalanchoë, the authors provide evidence for convergent evolution of protein sequence and temporal gene expression underpinning the multiple independent emergences of CAM.

01 December 2017 | doi: 10.1038/s41467-017-01491-7
Photosynthesis  Plant evolution  Sequencing 

Expressed fusion gene landscape and its impact in multiple myeloma OPEN
A. Cleynen, R. Szalat, M. Kemal Samur, S. Robiou du Pont, L. Buisson, E. Boyle, M. L. Chretien, K. Anderson, S. Minvielle, P. Moreau, M. Attal, G. Parmigiani, J. Corre, N. Munshi & H. Avet-Loiseau

Multiple myeloma is a malignancy of plasma cells in the blood. Here, the authors establish the landscape of fusion genes within this disease, identifying novel recurrent fusion genes that impact survival and may drive disease progression.

01 December 2017 | doi: 10.1038/s41467-017-00638-w
Cancer genomics  Myeloma 

Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories OPEN
Supratik Sen Mojumdar, Zackary N. Scholl, Derek R. Dee, Logan Rouleau, Uttam Anand, Craig Garen & Michael T. Woodside

Misfolding of superoxide dismutase 1 (SOD1) is linked to amyotrophic lateral sclerosis. Here the authors characterize the unfolding/refolding of single SOD1 molecules using optical tweezers, identifying partially folded intermediates that lead to misfolding after the formation of a native-like core.

01 December 2017 | doi: 10.1038/s41467-017-01996-1
Biological physics  Protein folding  Single-molecule biophysics 

Inverted activity patterns in ventromedial prefrontal cortex during value-guided decision-making in a less-is-more task OPEN
Georgios K. Papageorgiou, Jerome Sallet, Marco K. Wittmann, Bolton K. H. Chau, Urs Schüffelgen, Mark J. Buckley & Matthew F. S. Rushworth

Ventromedial prefrontal cortex in humans shows functional magnetic resonance imaging signals related to the subjective values of choices that are taken during decision-making as well as task-negative signals. Here, the authors report that in macaque ventromedial prefrontal cortex both activity patterns are inverted and lesions of this area disrupt subjective choice evaluation.

01 December 2017 | doi: 10.1038/s41467-017-01833-5
Decision  Reward 

Thin single crystal perovskite solar cells to harvest below-bandgap light absorption OPEN
Zhaolai Chen, Qingfeng Dong, Ye Liu, Chunxiong Bao, Yanjun Fang, Yun Lin, Shi Tang, Qi Wang, Xun Xiao, Yang Bai, Yehao Deng & Jinsong Huang

Thin films of halide perovskites are promising for solar cell technology but they do not perform well at the band edge due to the low optical absorption. Herein, Chen et al. fabricate a high efficiency single crystal perovskite solar cell with thicker single crystals to harvest the below-bandgap photons.

01 December 2017 | doi: 10.1038/s41467-017-02039-5
Solar cells 

Proton gradients and pH oscillations emerge from heat flow at the microscale OPEN
Lorenz M. R. Keil, Friederike M. Möller, Michael Kieß, Patrick W. Kudella & Christof B. Mast

Proton motive forces are central for life but it is not well understood how these pH gradients emerged at the beginning of life. Here the authors show that heat flow across a water-filled chamber forms and sustains stable pH gradients and support their experimental findings with simulations.

01 December 2017 | doi: 10.1038/s41467-017-02065-3
Biophysical chemistry  Reaction kinetics and dynamics  Chemical origin of life 

Discovery of naturally occurring ESR1 mutations in breast cancer cell lines modelling endocrine resistance OPEN
Lesley-Ann Martin, Ricardo Ribas, Nikiana Simigdala, Eugene Schuster, Sunil Pancholi, Tencho Tenev, Pascal Gellert, Laki Buluwela, Alison Harrod, Allan Thornhill, Joanna Nikitorowicz-Buniak, Amandeep Bhamra, Marc-Olivier Turgeon, George Poulogiannis, Qiong Gao, Vera Martins, Margaret Hills, Isaac Garcia-Murillas, Charlotte Fribbens, Neill Patani et al.

ESR1 mutations occur in endocrine-resistant patients but have not yet been reported in in vitro models of breast cancer. Here, the authors report the discovery of naturally occurring ESR1 Y537Cand ESR1 Y537S mutations in two breast cancer cell lines after acquisition of resistance to long-term-estrogen-deprivation.

30 November 2017 | doi: 10.1038/s41467-017-01864-y
Breast cancer  Hormone receptors 

Colloidal shuttles for programmable cargo transport OPEN
Ahmet F. Demirörs, Fritz Eichenseher, Martin J. Loessner & André R. Studart

Biological shuttles efficiently traffic molecules in cells, inspiring the development of synthetic analogs. Here, the authors create colloidal shuttles that collect, transport, and deliver cargo particles and cells under the control of external electrical and magnetic fields.

30 November 2017 | doi: 10.1038/s41467-017-01956-9
Colloids  Fluidics  Magnetic devices  Self-assembly 

Super-radiance reveals infinite-range dipole interactions through a nanofiber OPEN
P. Solano, P. Barberis-Blostein, F. K. Fatemi, L. A. Orozco & S. L. Rolston

The confinement of electromagnetic field in one dimension is known to allow peculiar effects such as infinite-range coupling. Here, the authors report on the observation of light-mediated infinite-range interactions between spatially separated atomic clouds mediated by an optical nanofiber.

30 November 2017 | doi: 10.1038/s41467-017-01994-3
Quantum optics  Single photons and quantum effects 

Contributions of Zea mays subspecies mexicana haplotypes to modern maize OPEN
Ning Yang, Xi-Wen Xu, Rui-Ru Wang, Wen-Lei Peng, Lichun Cai, Jia-Ming Song, Wenqiang Li, Xin Luo, Luyao Niu, Yuebin Wang, Min Jin, Lu Chen, Jingyun Luo, Min Deng, Long Wang, Qingchun Pan, Feng Liu, David Jackson, Xiaohong Yang, Ling-Ling Chen et al.

Maize was domesticated from wild lowland progenitors that co-existed with upland subspecies in Southwestern Mexico. Here Yang et al. use a meta-assembly approach to assemble an upland mexicana genome and find evidence of introgression suggesting it contributed to modern maize adaptation

30 November 2017 | doi: 10.1038/s41467-017-02063-5
Genome  Plant domestication  Plant genetics 

Fruit fracture biomechanics and the release of Lepidium didymum pericarp-imposed mechanical dormancy by fungi OPEN
Katja Sperber, Tina Steinbrecher, Kai Graeber, Gwydion Scherer, Simon Clausing, Nils Wiegand, James E. Hourston, Rainer Kurre, Gerhard Leubner-Metzger & Klaus Mummenhoff

Mechanical dormancy imposed by a hard fruit pericarp prevents premature seed germination. Here, the authors show that the pericarp of Lepidium didymum prevents germination by limiting water uptake and that dormancy can be released by fungal activity that weakens predetermined breaking zones in the fruit coat.

30 November 2017 | doi: 10.1038/s41467-017-02051-9
Seed distribution 

Multi-scale magnetic mapping of serpentinite carbonation OPEN
Masako Tominaga, Andreas Beinlich, Eduardo A. Lima, Maurice A. Tivey, Brian A. Hampton, Benjamin Weiss & Yumiko Harigane

Peridotite carbonation plays an important role in the carbon cycle. Here, the authors present a geophysical characterization of serpentinite carbonation from km to mm scale and confirm that the abundance of magnetic minerals provides a strong correlation with the overall carbonation reaction process.

30 November 2017 | doi: 10.1038/s41467-017-01610-4
Geochemistry  Geomagnetism 

Structural basis of respiratory syncytial virus subtype-dependent neutralization by an antibody targeting the fusion glycoprotein OPEN
Daiyin Tian, Michael B. Battles, Syed M. Moin, Man Chen, Kayvon Modjarrad, Azad Kumar, Masaru Kanekiyo, Kevin W. Graepel, Noor M. Taher, Anne L. Hotard, Martin L. Moore, Min Zhao, Zi-Zheng Zheng, Ning-Shao Xia, Jason S. McLellan & Barney S. Graham

Monoclonal antibodies to prevent respiratory syncytial virus (RSV) disease are under development, but the molecular requirements for cross-subtype neutralization are unclear. Here, the authors show that residue 201 in RSV fusion protein determines subtype specific neutralization for the clinically-relevant monoclonal antibody, 5C4.

30 November 2017 | doi: 10.1038/s41467-017-01858-w
Antibody therapy  Vaccines  Viral immune evasion  Virus structures 

Inference of differentiation time for single cell transcriptomes using cell population reference data OPEN
Na Sun, Xiaoming Yu, Fang Li, Denghui Liu, Shengbao Suo, Weiyang Chen, Shirui Chen, Lu Song, Christopher D. Green, Joseph McDermott, Qin Shen, Naihe Jing & Jing-Dong J. Han

Single cell transcriptome data can be used to determine developmental lineage trajectories. Here the authors map single cell transcriptomes onto a differentiation trajectory defined by cell population transcriptomes and show that cell cycle regulators have a role in differentiation timing.

30 November 2017 | doi: 10.1038/s41467-017-01860-2
Data integration  Differentiation  Embryonic stem cells  Stem-cell differentiation 

Observed positive vegetation-rainfall feedbacks in the Sahel dominated by a moisture recycling mechanism OPEN
Yan Yu, Michael Notaro, Fuyao Wang, Jiafu Mao, Xiaoying Shi & Yaxing Wei

Vegetation-rainfall feedbacks in the Sahel are thought to be positive, but the precise mechanisms for this are unclear. Here the authors analyse observations to show that a moisture recycling mechanism drives this feedback.

30 November 2017 | doi: 10.1038/s41467-017-02021-1
Atmospheric dynamics  Hydrology 

Downregulation of myostatin pathway in neuromuscular diseases may explain challenges of anti-myostatin therapeutic approaches OPEN
Virginie Mariot, Romain Joubert, Christophe Hourdé, Léonard Féasson, Michael Hanna, Francesco Muntoni, Thierry Maisonobe, Laurent Servais, Caroline Bogni, Rozen Le Panse, Olivier Benvensite, Tanya Stojkovic, Pedro M. Machado, Thomas Voit, Ana Buj-Bello & Julie Dumonceaux

Drugs targeting myostatin reverse muscle wasting in animal models, but have limited efficacy in patients. The authors show that the myostatin pathway is downregulated in patients, possibly explaining the poor outcome of anti-myostatin approaches, and that it can be reactivated by correcting disease-causing mutations in mice.

30 November 2017 | doi: 10.1038/s41467-017-01486-4
Neuromuscular disease  Skeletal muscle 

BEX1 is an RNA-dependent mediator of cardiomyopathy OPEN
Federica Accornero, Tobias G. Schips, Jennifer M. Petrosino, Shan-Qing Gu, Onur Kanisicak, Jop H. van Berlo & Jeffery D. Molkentin

Little is known about the changes in mRNA splicing, processing and stability that can alter gene expression during heart failure. Here, the authors show that BEX1 is induced during heart failure and is part of a ribonucleoprotein complex enhancing the expression and stability of proinflammatory genes.

30 November 2017 | doi: 10.1038/s41467-017-02005-1
Cardiac hypertrophy  RNA metabolism 

O-GlcNAcylation is required for B cell homeostasis and antibody responses OPEN
Jung-Lin Wu, Ming-Feng Chiang, Pan-Hung Hsu, Dong-Yen Tsai, Kuo-Hsuan Hung, Ying-Hsiu Wang, Takashi Angata & Kuo-I Lin

Post-translational modification has a variety of regulatory functions for important immune molecules. Here the authors use B-cell specific knockout mice to show how O-GlcNAcylation is required for functional B cell responses and humoral immunity.

30 November 2017 | doi: 10.1038/s41467-017-01677-z
B cells  Humoral immunity  Post-translational modifications 

Restoration of patterned vision with an engineered photoactivatable G protein-coupled receptor OPEN
Michael H. Berry, Amy Holt, Joshua Levitz, Johannes Broichhagen, Benjamin M. Gaub, Meike Visel, Cherise Stanley, Krishan Aghi, Yang Joon Kim, Dirk Trauner, John Flannery & Ehud Y. Isacoff

To restore sight after retinal degeneration, one approach is to express light-sensitive proteins in remaining cells. Here the authors combine a light-sensitive engineered G protein-coupled receptor and ion channels to restore ON and OFF responses as well as superior visual pattern discrimination.

30 November 2017 | doi: 10.1038/s41467-017-01990-7
Molecular neuroscience  Protein design  Retina 

Inhibiting Rho kinase promotes goal-directed decision making and blocks habitual responding for cocaine OPEN
Andrew M. Swanson, Lauren M. DePoy & Shannon L. Gourley

Action-outcome learning requires the prelimbic prefrontal cortex. Here the authors report that fasudil, a Rho kinase inhibitor, reduces dendritic spine densities on prelimbic neurons in an activity-dependent manner, stimulating goal-directed actions, and reducing habitual responding for cocaine.

30 November 2017 | doi: 10.1038/s41467-017-01915-4
Operant learning  Reward 

Developmental YAPdeltaC determines adult pathology in a model of spinocerebellar ataxia type 1 OPEN
Kyota Fujita, Ying Mao, Shigenori Uchida, Xigui Chen, Hiroki Shiwaku, Takuya Tamura, Hikaru Ito, Kei Watase, Hidenori Homma, Kazuhiko Tagawa, Marius Sudol & Hitoshi Okazawa

Ataxin-1, linked to spinocerebellar ataxia type 1, is known to interact with the orphan nuclear receptor RORα. Here, Fujita and colleagues show that genetic supplementation of RORα-interacting protein YAPdeltaC during early development can rescue the adult pathologies of SCA1 mouse model.

30 November 2017 | doi: 10.1038/s41467-017-01790-z
Spinocerebellar ataxia  Transcriptional regulatory elements 

Optical charge state control of spin defects in 4H-SiC OPEN
Gary Wolfowicz, Christopher P. Anderson, Andrew L. Yeats, Samuel J. Whiteley, Jens Niklas, Oleg G. Poluektov, F. Joseph Heremans & David D. Awschalom

Defects in silicon carbide represent a viable candidate for realization of spin qubits. Here, the authors show stable bidirectional charge state conversion for the silicon vacancy and divacancy, improving the photoluminescence intensity by up to three orders of magnitude with no effect on spin coherence.

30 November 2017 | doi: 10.1038/s41467-017-01993-4
Qubits  Semiconductors  Spintronics 

Synthesis of structurally controlled hyperbranched polymers using a monomer having hierarchical reactivity OPEN
Yangtian Lu, Takashi Nemoto, Masatoshi Tosaka & Shigeru Yamago

Hyperbranched polymers are used in many applications due to their advantageous properties such as low intrinsic viscosity, low glass transition temperature, and large number of terminal groups. Here the authors show a one-step synthesis of structurally well-controlled dendritic hyperbranched polymers.

30 November 2017 | doi: 10.1038/s41467-017-01838-0
Dendrimers  Synthetic chemistry methodology  Polymer synthesis  Polymerization mechanisms 

Controlling thermal reactivity with different colors of light OPEN
Hannes A. Houck, Filip E. Du Prez & Christopher Barner-Kowollik

The ability to switch between thermally and photochemically activated reaction channels with an external stimulus constitutes a key frontier within the realm of chemical reaction control. Here, the authors describe how the thermal reactivity of molecules can completely be switched off by visible light to provide UV light-induced selectivity of the reaction outcome.

30 November 2017 | doi: 10.1038/s41467-017-02022-0
Photochemistry  Polymer chemistry 

NDP52 activates nuclear myosin VI to enhance RNA polymerase II transcription OPEN
Natalia Fili, Yukti Hari-Gupta, Ália dos Santos, Alexander Cook, Simon Poland, Simon M. Ameer-Beg, Maddy Parsons & Christopher P. Toseland

Myosin VI (MVI) is known to interact with RNA Polymerase II and to play non-cytoplasmic roles in cells. Here, the authors provide evidence that the transcription co-activator NDP52 regulates MVI binding to DNA and that MVI interacts with nuclear receptors to drive gene expression.

30 November 2017 | doi: 10.1038/s41467-017-02050-w
Biological fluorescence  Cytoskeletal proteins  DNA  Kinetics 

Hepatic Crtc2 controls whole body energy metabolism via a miR-34a-Fgf21 axis OPEN
Hye-Sook Han, Byeong Hun Choi, Jun Seok Kim, Geon Kang & Seung-Hoi Koo

CREB-regulated transcription coactivator 2, CRTC2, has been associated with regulation of glucose and lipid homeostasis. Here Han et al. show that Creb/Crtc2 modulates lipid and glucose metabolism by inhibiting the expression of mi-R34 that, in turn, represses the expression of Sirt1 and PPARα and consequently Fgf21 levels.

30 November 2017 | doi: 10.1038/s41467-017-01878-6
Mechanisms of disease  Metabolic disorders 

Graphene-edge dielectrophoretic tweezers for trapping of biomolecules OPEN
Avijit Barik, Yao Zhang, Roberto Grassi, Binoy Paulose Nadappuram, Joshua B. Edel, Tony Low, Steven J. Koester & Sang-Hyun Oh

The capability of positioning target molecules onto the edges of patterned graphene nanostructures is highly desirable. Here, the authors demonstrate that the atomically sharp edges of graphene can be used as dielectrophoretic tweezers for gradient-force-based trapping applications.

30 November 2017 | doi: 10.1038/s41467-017-01635-9
Electronic properties and devices  Nanosensors  Nanostructures 

Demonstration of chemistry at a point through restructuring and catalytic activation at anchored nanoparticles OPEN
Dragos Neagu, Evangelos I. Papaioannou, Wan K. W. Ramli, David N. Miller, Billy J. Murdoch, Hervé Ménard, Ahmed Umar, Anders J. Barlow, Peter J. Cumpson, John T. S. Irvine & Ian S. Metcalfe

Metal nanoparticles prepared by exsolution at the surface of perovskite oxides are key species in catalysis and energy fields. Here, the authors develop a chemistry at a point concept by tracking individual nanoparticles with excellent activity and stability throughout various chemical transformations.

30 November 2017 | doi: 10.1038/s41467-017-01880-y
Catalyst synthesis  Heterogeneous catalysis  Nanoparticles 

Hydrodenitrogenation of pyridines and quinolines at a multinuclear titanium hydride framework OPEN
Shaowei Hu, Gen Luo, Takanori Shima, Yi Luo & Zhaomin Hou

Hydrodenitrogenation is a fundamental process in the petroleum refinery context. Here, the authors report the mild ring-opening and denitrogenation of pyridines and quinolines with a titanium hydride cluster and the unusual formation of denitrogenated cyclic hydrocarbon products.

30 November 2017 | doi: 10.1038/s41467-017-01607-z
Organic chemistry  Organometallic chemistry 

Symbionts protect aphids from parasitic wasps by attenuating herbivore-induced plant volatiles OPEN
Enric Frago, Mukta Mala, Berhane T. Weldegergis, Chenjiao Yang, Ailsa McLean, H. Charles J. Godfray, Rieta Gols & Marcel Dicke

Bacterial symbionts are increasingly known to influence behaviour and fitness in insects. Here, Frago et al. show that plants fed on by aphids with symbionts have altered volatile chemical profiles, leading to reduced parasitoid attack of aphids.

30 November 2017 | doi: 10.1038/s41467-017-01935-0
Behavioural ecology  Community ecology  Entomology 
 
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