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Nature Communications - 31 October 2018

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Following hearts, one cell at a time: recent applications of single-cell RNA sequencing to the understanding of heart disease OPEN
Matthew Ackers-Johnson, Wilson Lek Wen Tan & Roger Sik-Yin Foo
30 October 2018 | doi: 10.1038/s41467-018-06894-8
Cardiovascular diseases  Transcriptomics 
  Latest Articles View all Articles  

Cloaking nanoparticles with protein corona shield for targeted drug delivery OPEN
Jun Yong Oh, Han Sol Kim, L. Palanikumar, Eun Min Go, Batakrishna Jana, Soo Ah Park, Ho Young Kim, Kibeom Kim, Jeong Kon Seo, Sang Kyu Kwak, Chaekyu Kim, Sebyung Kang & Ja-Hyoung Ryu

The efficacy of nanoparticles can be significantly inhibited by serum proteins binding to them. Here, the author developed a supramolecularly constructed protein corona on nanoparticles, which minimises interactions with serum proteins to prevent the clearance of these particles by macrophages.

31 October 2018 | doi: 10.1038/s41467-018-06979-4
Drug delivery  Nanoparticles 

Management of transition dipoles in organic hole-transporting materials under solar irradiation for perovskite solar cells OPEN
Song Ah Ok, Bonghyun Jo, Sivaraman Somasundaram, Hwi Je Woo, Dae Woon Lee, Zijia Li, Bong-Gi Kim, Jong H. Kim, Young Jae Song, Tae Kyu Ahn, Sanghyuk Park & Hui Joon Park

In perovskite solar cells, the excited state property of hole-transport layer is not usually considered for the devices. Here the authors design organic hole-transport materials with high transition dipoles having extended lifetime at the excited states to improve the charge extraction of the devices.

31 October 2018 | doi: 10.1038/s41467-018-06998-1
Solar cells 

All-inorganic cesium lead iodide perovskite solar cells with stabilized efficiency beyond 15% OPEN
Kang Wang, Zhiwen Jin, Lei Liang, Hui Bian, Dongliang Bai, Haoran Wang, Jingru Zhang, Qian Wang & Liu Shengzhong

Black phase cesium lead iodide perovskite is regarded as a promising candidate for solar cells, but it easily transits to undesired yellow phase. Herein, Wang et al. stabilized the black phase using molecular additives to achieve device efficiency beyond 15% with high light soaking stability.

31 October 2018 | doi: 10.1038/s41467-018-06915-6
Electronic devices  Materials science 

Calcium sensing by the STIM1 ER-luminal domain OPEN
Aparna Gudlur, Ana Eliza Zeraik, Nupura Hirve, V. Rajanikanth, Andrey A. Bobkov, Guolin Ma, Sisi Zheng, Youjun Wang, Yubin Zhou, Elizabeth A. Komives & Patrick G. Hogan

Stromal interaction molecule 1 (STIM1) monitors ER-luminal Ca2+ levels to maintain cellular Ca2+ balance. Here the authors find that the STIM1 luminal domain monomer has multiple Ca2+ - binding sites which set the threshold for physiological activation of STIM1 in cells.

31 October 2018 | doi: 10.1038/s41467-018-06816-8
Calcium signalling  Intracellular signalling peptides and proteins 

Structure and pro-toxic mechanism of the human Hsp90/PPIase/Tau complex OPEN
Javier Oroz, Bliss J. Chang, Piotr Wysoczanski, Chung-Tien Lee, Ángel Pérez-Lara, Pijush Chakraborty, Romina V. Hofele, Jeremy D. Baker, Laura J. Blair, Jacek Biernat, Henning Urlaub, Eckhard Mandelkow, Chad A. Dickey & Markus Zweckstetter

The chaperone Hsp90 plays a key role in maintaining cellular homeostasis. Here the authors provide structural insights into substrate recognition and the pro-folding mechanism of Hsp90/co-chaperone complexes by studying the complex of Hsp90 with its co-chaperone FKBP51 and the substrate Tau bound Hsp90/FKBP51 ternary complex using a NMR based integrative approach.

31 October 2018 | doi: 10.1038/s41467-018-06880-0
Chaperones  Solution-state NMR 

Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin OPEN
Cuijun Zhang, Xuan Du, Kai Tang, Zhenlin Yang, Li Pan, Peipei Zhu, Jinyan Luo, Yuwei Jiang, Hui Zhang, Huafang Wan, Xingang Wang, Fengkai Wu, W. Andy Tao, Xin-Jian He, Heng Zhang, Ray A. Bressan, Jiamu Du & Jian-Kang Zhu

DNA methylation and H3K9 dimethylation are two linked epigenetic marks of silenced chromatin in plants that depend on the activity of CMT3/2 and SUVH4/5/6. Here the authors identify AGDP1 as an H3K9me2-binding protein required for heterochromatic non-CG DNA methylation, H3K9 dimethylation, and transcriptional silencing.

31 October 2018 | doi: 10.1038/s41467-018-06965-w
DNA methylation  Histone post-translational modifications  Plant signalling  X-ray crystallography 

Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana OPEN
Dijun Chen, Wenhao Yan, Liang-Yu Fu & Kerstin Kaufmann

Homeotic transcription factors and miRNAs promote floral organ specification. Here Chen et al. reconstruct gene regulatory networks in Arabidopsis flowers and find evidence for feed forward loops between transcription factors, miRNAs and their targets that determine organ-specific gene expression.

31 October 2018 | doi: 10.1038/s41467-018-06772-3
Gene regulatory networks  Plant development 

PRMT2 links histone H3R8 asymmetric dimethylation to oncogenic activation and tumorigenesis of glioblastoma OPEN
Feng Dong, Qian Li, Chao Yang, Dawei Huo, Xing Wang, Chunbo Ai, Yu Kong, Xiaoyu Sun, Wen Wang, Yan Zhou, Xing Liu, Wei Li, Weiwei Gao, Wen Liu, Chunsheng Kang & Xudong Wu

The role of protein arginine methyltransferases (PRMTs) in epigenetic regulation in cancer is still poorly understood. Here, the authors show that PRMT2 is highly expressed in Glioblastoma multiforme (GBM) and provide evidence that PRMT2 acts as a transcriptional co-activator for oncogenic gene expression programs, at least partly dependent on its H3R8me2a activity, in GBM pathogenesis.

31 October 2018 | doi: 10.1038/s41467-018-06968-7
Histone post-translational modifications  Oncogenes 

syn-Selective alkylarylation of terminal alkynes via the combination of photoredox and nickel catalysis OPEN
Lei Guo, Fan Song, Shengqing Zhu, Huan Li & Lingling Chu

Converting alkynes into alkenes with high stereoselectivity via two consecutive C-C bond forming steps is a desirable process, yet very challenging. Here, the authors describe a dual photoredox-nickel catalytic system for the regio- and syn-selective alkylarylation of terminal alkynes with alkyl oxalates and aryl bromides.

31 October 2018 | doi: 10.1038/s41467-018-06904-9
Catalysis  Homogeneous catalysis  Synthetic chemistry methodology  Organic chemistry 

Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif OPEN
Sandip A. Shelke, Yaming Shao, Artur Laski, Deepak Koirala, Benjamin P. Weissman, James R. Fuller, Xiaohong Tan, Tudor P. Constantin, Alan S. Waggoner, Marcel P. Bruchez, Bruce A. Armitage & Joseph A. Piccirilli

The DIR2s RNA aptamer activates the fluorescence of cyanine dyes allowing detection of two well-resolved emission colors. Here authors solve the crystal structures of the apo and OTB-SO3 fluorophore-bound DIR2s and show how the fluorophore ligand is bound.

31 October 2018 | doi: 10.1038/s41467-018-06942-3
Chemical biology  RNA  Structural biology 

Fluidity onset in graphene OPEN
Denis A. Bandurin, Andrey V. Shytov, Leonid S. Levitov, Roshan Krishna Kumar, Alexey I. Berdyugin, Moshe Ben Shalom, Irina V. Grigorieva, Andre K. Geim & Gregory Falkovich

Experimental demonstrations of materials supporting electron fluids have been elusive so far. Here, the authors investigate nonlocal transport in bilayer graphene across the ballistic-to-hydrodynamic crossover, and identify a sharp maximum of negative resistance at the transition between the two regimes.

31 October 2018 | doi: 10.1038/s41467-018-07004-4
Electronic properties and materials  Fluid dynamics 

Dual-gate organic phototransistor with high-gain and linear photoresponse OPEN
Philip C. Y. Chow, Naoji Matsuhisa, Peter Zalar, Mari Koizumi, Tomoyuki Yokota & Takao Someya

High-resolution imaging technologies call for photodetectors with high-gain and linear response over a large dynamic range. Chow et al. show a dual-gate structure that combines the operation of photodiodes and phototransistors to enable both amplified and linear response without external circuitry.

31 October 2018 | doi: 10.1038/s41467-018-06907-6
Engineering  Nanoscience and technology 

MiR-584-5p potentiates vincristine and radiation response by inducing spindle defects and DNA damage in medulloblastoma OPEN
Nourhan Abdelfattah, Subapriya Rajamanickam, Subbarayalu Panneerdoss, Santosh Timilsina, Pooja Yadav, Benjamin C. Onyeagucha, Michael Garcia, Ratna Vadlamudi, Yidong Chen, Andrew Brenner, Peter Houghton & Manjeet K. Rao

The radiation and chemotherapy used for treating medulloblastoma patients cause debilitating side effects. Here, the authors show that miR-584 acts as a therapeutic adjuvant as it sensitizes medulloblastoma to radiation and chemotherapy by targeting HDAC1 or eIF4E3 to enhance spindle defects and DNA damage.

31 October 2018 | doi: 10.1038/s41467-018-06808-8
Cell biology  CNS cancer  Paediatric cancer 

Interfacing nickel nitride and nickel boosts both electrocatalytic hydrogen evolution and oxidation reactions OPEN
Fuzhan Song, Wei Li, Jiaqi Yang, Guanqun Han, Peilin Liao & Yujie Sun

Efficient hydrogen production and utilization materials will be crucial in order to compete with fossil fuel technologies. Here, authors report nickel and nickel nitride interfaces as effected catalysts for hydrogen evolution and oxidation in water.

31 October 2018 | doi: 10.1038/s41467-018-06728-7
Electrocatalysis  Electronic properties and materials  Hydrogen fuel 

In situ strain tuning of the metal-insulator-transition of Ca2RuO4 in angle-resolved photoemission experiments OPEN
S. Riccò, M. Kim, A. Tamai, S. McKeown Walker, F. Y. Bruno, I. Cucchi, E. Cappelli, C. Besnard, T. K. Kim, P. Dudin, M. Hoesch, M. J. Gutmann, A. Georges, R. S. Perry & F. Baumberger

The role of the lattice in the correlated metal-insulator transition of Ca2RuO4 has led to significant interest but experiments that are at the same time sensitive to crystal and electronic structure are difficult. Riccò et al. successfully combine ARPES measurements with in situ strain tuning across the Mott transition.

31 October 2018 | doi: 10.1038/s41467-018-06945-0
Electronic properties and materials  Phase transitions and critical phenomena 

Induced-fit expansion and contraction of a self-assembled nanocube finely responding to neutral and anionic guests OPEN
Yi-Yang Zhan, Tatsuo Kojima, Takashi Nakamura, Toshihiro Takahashi, Satoshi Takahashi, Yohei Haketa, Yoshiaki Shoji, Hiromitsu Maeda, Takanori Fukushima & Shuichi Hiraoka

Induced-fit binding, common in biological systems, is still relatively rare in artificial hosts. Here, the authors assemble a molecular cube from six gear-shaped faces, whose interdigitated design allows the cube to expand and contract in response to the size, shape, and charge of a guest molecule.

31 October 2018 | doi: 10.1038/s41467-018-06874-y
Molecular capsules  Self-assembly 

Lévy-like movement patterns of metastatic cancer cells revealed in microfabricated systems and implicated in vivo OPEN
Sabil Huda, Bettina Weigelin, Katarina Wolf, Konstantin V. Tretiakov, Konstantin Polev, Gary Wilk, Masatomo Iwasa, Fateme S. Emami, Jakub W. Narojczyk, Michal Banaszak, Siowling Soh, Didzis Pilans, Amir Vahid, Monika Makurath, Peter Friedl, Gary G. Borisy, Kristiana Kandere-Grzybowska & Bartosz A. Grzybowski
31 October 2018 | doi: 10.1038/s41467-018-06563-w
Cellular motility  Metastasis 

Establishing the effects of mesoporous silica nanoparticle properties on in vivo disposition using imaging-based pharmacokinetics OPEN
Prashant Dogra, Natalie L. Adolphi, Zhihui Wang, Yu-Shen Lin, Kimberly S. Butler, Paul N. Durfee, Jonas G. Croissant, Achraf Noureddine, Eric N. Coker, Elaine L. Bearer, Vittorio Cristini & C. Jeffrey Brinker

Nanoparticle applications are limited by insufficient understanding of physiochemical properties on in vivo disposition. Here, the authors explore the influence of size, surface chemistry and administration on the biodisposition of mesoporous silica nanoparticles using image-based pharmacokinetics.

31 October 2018 | doi: 10.1038/s41467-018-06730-z
Drug delivery  Imaging techniques and agents  Nanoparticles  Nanotechnology in cancer  Scientific data 

Anomalous X-ray diffraction studies of ion transport in K+ channels OPEN
Patricia S. Langan, Venu Gopal Vandavasi, Kevin L. Weiss, Pavel V. Afonine, Kamel el Omari, Ramona Duman, Armin Wagner & Leighton Coates

The number of K+ occupied binding sites in the selectivity filter of potassium ion channels is still under debate. Here, the authors collect diffraction data on the K+ selective NaK channel NaK2K at a wavelength of 3.35 Å, close to the K absorption edge, revealing that all four binding sites in the selectivity filter are fully occupied by K+ ions.

31 October 2018 | doi: 10.1038/s41467-018-06957-w
Potassium channels  X-ray crystallography 

Single-cell barcode analysis provides a rapid readout of cellular signaling pathways in clinical specimens OPEN
Randy J. Giedt, Divya Pathania, Jonathan C. T. Carlson, Philip J. McFarland, Andres Fernandez del Castillo, Dejan Juric & Ralph Weissleder

Diagnostic tests need optimization to avoid invasive and costly repeated biopsies. Here the authors present an antibody-DNA barcoding approach where harvested single cells can be re-stained through custom oligonucleotide-fluorophore conjugates, enabling multiplexed analysis of cancer pathways.

31 October 2018 | doi: 10.1038/s41467-018-07002-6
Biomarkers  Breast cancer  Single-cell imaging  Targeted therapies  Tumour heterogeneity 

Redox regulation of EGFR steers migration of hypoxic mammary cells towards oxygen OPEN
Mathieu Deygas, Rudy Gadet, Germain Gillet, Ruth Rimokh, Philippe Gonzalo & Ivan Mikaelian

Aerotaxis, chemotaxis towards oxygen, occurs in bacteria and likely in cancer cells. Here the authors find that confined cells from different tissues escape hypoxia by aerotaxis, a process independent of mitochondria and the HIF pathway, and dependent on EGF receptor interpretation of a ROS gradient in mammary cells.

31 October 2018 | doi: 10.1038/s41467-018-06988-3
Chemotaxis  Metastasis 

Interactions between callose and cellulose revealed through the analysis of biopolymer mixtures OPEN
Radwa H. Abou-Saleh, Mercedes C. Hernandez-Gomez, Sam Amsbury, Candelas Paniagua, Matthieu Bourdon, Shunsuke Miyashima, Ykä Helariutta, Martin Fuller, Tatiana Budtova, Simon D. Connell, Michael E. Ries & Yoselin Benitez-Alfonso

Despite their importance in plant development and defence the properties of (1,3)-β-glucan remain largely unknown. Here, the authors find that addition of (1,3)-β-glucans increases the flexibility of cellulose and its resilience to high strain, an effect originating in molecular level interactions.

31 October 2018 | doi: 10.1038/s41467-018-06820-y
Biological physics  Biopolymers in vivo  Cell wall  Soft materials 

Identification and characterization of a large family of superbinding bacterial SH2 domains OPEN
Tomonori Kaneko, Peter J. Stogios, Xiang Ruan, Courtney Voss, Elena Evdokimova, Tatiana Skarina, Amy Chung, Xiaoling Liu, Lei Li, Alexei Savchenko, Alexander W. Ensminger & Shawn S.-C. Li

SH2 domains bind to tyrosine-phosphorylated proteins and play crucial roles in signal transduction in mammalian cells. Here, Kaneko et al. identify a large family of SH2 domains in the bacterial pathogen Legionella that bind to mammalian phosphorylated proteins, in some cases with very high affinity.

31 October 2018 | doi: 10.1038/s41467-018-06943-2
Bacterial structural biology  Cell signalling  Pathogens  X-ray crystallography 

Direct cysteine sulfenylation drives activation of the Src kinase OPEN
David E. Heppner, Christopher M. Dustin, Chenyi Liao, Milena Hristova, Carmen Veith, Andrew C. Little, Bethany A. Ahlers, Sheryl L. White, Bin Deng, Ying-Wai Lam, Jianing Li & Albert van der Vliet

The activity of several protein kinases is increased upon cellular production of reactive oxygen species, which can cause cysteine oxidation. Here the authors show that sulfenylation of specific cysteine residues within Src induce local structural changes that directly impact its activation.

30 October 2018 | doi: 10.1038/s41467-018-06790-1
Enzyme mechanisms  Kinases  Molecular modelling  Post-translational modifications 

M-Phase Phosphoprotein 9 regulates ciliogenesis by modulating CP110-CEP97 complex localization at the mother centriole OPEN
Ning Huang, Donghui Zhang, Fangyuan Li, Peiyuan Chai, Song Wang, Junlin Teng & Jianguo Chen

Ciliogenesis is negatively regulated by the CP110-CEP97 complex, although the mechanism controlling mother centriole localization is poorly understood. Here, Huang et al. show that KIF24 recruits MMP9 to the mother centriole, where it regulates ciliogenesis by controlling CP110-CEP97 recruitment.

30 October 2018 | doi: 10.1038/s41467-018-06990-9
Centrosome  Cilia 

Biologically relevant laminin as chemically defined and fully human platform for human epidermal keratinocyte culture OPEN
Monica Suryana Tjin, Alvin Wen Choong Chua, Aida Moreno-Moral, Li Yen Chong, Po Yin Tang, Nathan Peter Harmston, Zuhua Cai, Enrico Petretto, Bien Keem Tan & Karl Tryggvason

In vitro expansion of human epidermal keratinocytes to resurface severe wound defects still relies on a human/mouse xenograft culture system. Here the authors develop a fully human, xeno-free culture system using skin-associated laminins, normally present in vivo, to replace mouse feeder cells.

30 October 2018 | doi: 10.1038/s41467-018-06934-3
Skin stem cells  Stem-cell research  Translational research 

Adrenal hormones mediate disease tolerance in malaria OPEN
Leen Vandermosten, Thao-Thy Pham, Sofie Knoops, Charlotte De Geest, Natacha Lays, Kristof Van der Molen, Christopher J. Kenyon, Manu Verma, Karen E. Chapman, Frans Schuit, Karolien De Bosscher, Ghislain Opdenakker & Philippe E. Van den Steen

Disease tolerance mechanisms counter the negative effects of infection without decreasing the pathogen load. Here, the authors show that in mouse models of malaria, such disease tolerance can be conferred by adrenal hormones, by preventing excessive inflammation and hypoglycemia.

30 October 2018 | doi: 10.1038/s41467-018-06986-5
Infection  Malaria  Parasite host response  Pathogens 

Structural reorganization of SHP2 by oncogenic mutations and implications for oncoprotein resistance to allosteric inhibition OPEN
Jonathan R. LaRochelle, Michelle Fodor, Vidyasiri Vemulapalli, Morvarid Mohseni, Ping Wang, Travis Stams, Matthew J. LaMarche, Rajiv Chopra, Michael G. Acker & Stephen C. Blacklow

Activating mutations of the non-receptor protein tyrosine phosphatase SHP2 can cause cancer. Here the authors present the crystal structure of SHP2E76K, the most frequent cancer-associated SHP2 mutation, which adopts an open-state structure and show that the allosteric inhibitor SHP099 can revert SHP2E76K to its closed, autoinhibited conformation.

30 October 2018 | doi: 10.1038/s41467-018-06823-9
Chemical biology  X-ray crystallography 

Integrated silicon qubit platform with single-spin addressability, exchange control and single-shot singlet-triplet readout OPEN
M. A. Fogarty, K. W. Chan, B. Hensen, W. Huang, T. Tanttu, C. H. Yang, A. Laucht, M. Veldhorst, F. E. Hudson, K. M. Itoh, D. Culcer, T. D. Ladd, A. Morello & A. S. Dzurak

Significant progress has been made developing the different methods needed for a spin-based quantum computer but the challenge of integrating them remains. Fogarty et al. present a system with single-spin addressability, spin-spin interactions and high-fidelity readout that provides a scalable foundation for error-corrected devices.

30 October 2018 | doi: 10.1038/s41467-018-06039-x
Electronic devices  Quantum dots  Quantum information  Qubits 

Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2 OPEN
Ricardo A. P. Pádua, Yizhi Sun, Ingrid Marko, Warintra Pitsawong, John B. Stiller, Renee Otten & Dorothee Kern

The protein tyrosine phosphatase SHP2 is a key regulator of cell cycle control. Here the authors combine NMR measurements and X-ray crystallography and show that wild-type SHP2 dynamically exchanges between a closed inactive conformation and an open activated form and that the oncogenic E76K mutation shifts the equilibrium to the open state, which is reversed by binding of the allosteric inhibitor SHP099.

30 October 2018 | doi: 10.1038/s41467-018-06814-w
Enzyme mechanisms  Solution-state NMR  X-ray crystallography 

The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family OPEN
Mary Galli, Arjun Khakhar, Zefu Lu, Zongliang Chen, Sidharth Sen, Trupti Joshi, Jennifer L. Nemhauser, Robert J. Schmitz & Andrea Gallavotti

AUXIN RESPONSE FACTORS (ARFs) are a family of plant-specific transcriptional factors involved in auxin signaling. Here, the authors adapt DAP-seq technology to show the binding landscape of 14 maize ARFs and reveal class-specific binding properties and transcriptional coordination by ARFs from different classes.

30 October 2018 | doi: 10.1038/s41467-018-06977-6
Auxin  Plant signalling  Transcriptional regulatory elements 

A perivascular niche for multipotent progenitors in the fetal testis OPEN
Deepti L. Kumar & Tony DeFalco

Leydig cells are steroidogenic cells in the testes and produce the androgens required for male development and spermatogenesis. Here the authors show that a multipotent progenitor population producing Leydig cells, pericytes and smooth muscle cells is maintained in a perivascular niche within the mouse fetal testis.

30 October 2018 | doi: 10.1038/s41467-018-06996-3
Differentiation  Organogenesis  Stem-cell niche 

An electrochemical thermal transistor OPEN
Aditya Sood, Feng Xiong, Shunda Chen, Haotian Wang, Daniele Selli, Jinsong Zhang, Connor J. McClellan, Jie Sun, Davide Donadio, Yi Cui, Eric Pop & Kenneth E. Goodson

Thermal transistors can enable game changing applications in energy harvesting and heat routing. Here, the authors demonstrate reversible thermal modulation of nearly 10 times by ion intercalation in MoS2 nanofilms. A new thermal microscopy technique allows operando imaging of Li ion segregation.

30 October 2018 | doi: 10.1038/s41467-018-06760-7
Condensed-matter physics  Electrochemistry  Imaging techniques  Nanoscale devices  Two-dimensional materials 

Implicit preference for human trustworthy faces in macaque monkeys OPEN
Manuela Costa, Alice Gomez, Elodie Barat, Guillaume Lio, Jean-René Duhamel & Angela Sirigu

Humans infer the trustworthiness of others based on subtle facial features such as the facial width-to-height ratio, but it is not known whether other primates are sensitive to these cues. Here, the authors show that macaque monkeys prefer to look at human faces which appear trustworthy to humans.

30 October 2018 | doi: 10.1038/s41467-018-06987-4
Animal behaviour  Evolution  Human behaviour  Social sciences 

Prefrontal projections to the thalamic nucleus reuniens mediate fear extinction OPEN
Karthik R. Ramanathan, Jingji Jin, Thomas F. Giustino, Martin R. Payne & Stephen Maren

Previous work has shown that the thalamic nucleus reuniens (RE) is involved in memory and emotion. Here the authors report that the RE and its inputs from the medial prefrontal cortex are indispensable for the top-down inhibition of fear memories after extinction.

30 October 2018 | doi: 10.1038/s41467-018-06970-z
Extinction  Neural circuits 

Synthesis and assembly of colloidal cuboids with tunable shape biaxiality OPEN
Yang Yang, Guangdong Chen, Srinivas Thanneeru, Jie He, Kun Liu & Zhihong Nie

Monodisperse biaxial colloidal particles are used as model systems to understand the phase behavior of biaxial molecules but high-quality biaxial colloids are limited. Here the authors describe gram-scale synthesis of uniform biaxial colloidal cuboids and their assembly into mesophasic structures.

30 October 2018 | doi: 10.1038/s41467-018-06975-8
Colloids  Self-assembly 

Manganese-catalyzed hydroboration of carbon dioxide and other challenging carbonyl groups OPEN
Christina Erken, Akash Kaithal, Suman Sen, Thomas Weyhermüller, Markus Hölscher, Christophe Werlé & Walter Leitner

Catalytic reduction of CO2 and biomass derivatives is of great current interest from a sustainable chemistry perspective. Here, the authors report a manganese pincer complex able to reduce under mild conditions carboxylic acids, carbonates and even carbon dioxide using pinacolborane as reducing agent.

30 October 2018 | doi: 10.1038/s41467-018-06831-9
Homogeneous catalysis  Sustainability 

Differential active site requirements for NDM-1 β-lactamase hydrolysis of carbapenem versus penicillin and cephalosporin antibiotics OPEN
Zhizeng Sun, Liya Hu, Banumathi Sankaran, B. V. Venkataram Prasad & Timothy Palzkill

The NDM-1 β-lactamase confers resistance to most β-lactam antibiotics. By functional analysis of residues required for hydrolysis, Sun et al. reveal stringent sequence constraints for carbapenems, suggesting that specific combinations of NDM-1 inhibitors might help reducing resistance development

30 October 2018 | doi: 10.1038/s41467-018-06839-1
Biochemistry  Enzyme mechanisms  Enzymes  Proteins  Structural biology 

3D virtual reconstruction of the Kebara 2 Neandertal thorax OPEN
Asier Gómez-Olivencia, Alon Barash, Daniel García-Martínez, Mikel Arlegi, Patricia Kramer, Markus Bastir & Ella Been

How different Neandertal morphology was from that of modern humans has been a subject of long debate. Here, the authors develop a 3D virtual reconstruction of the thorax of an adult male Neandertal, showing similar size to modern humans, yet with greater respiratory capacity due to its different shape.

30 October 2018 | doi: 10.1038/s41467-018-06803-z
Biological anthropology  Palaeontology 

Helminth-induced IL-4 expands bystander memory CD8+ T cells for early control of viral infection OPEN
Marion Rolot, Annette M. Dougall, Alisha Chetty, Justine Javaux, Ting Chen, Xue Xiao, Bénédicte Machiels, Murray E. Selkirk, Rick M. Maizels, Cornelis Hokke, Olivier Denis, Frank Brombacher, Alain Vanderplasschen, Laurent Gillet, William G. C. Horsnell & Benjamin G. Dewals

Parasitic helminth infection is known to impact upon the host response to other bystander inflammatory processes. Here the authors show that IL4 production induced by helminth infection results in expansion of bystander CD8+ memory T cells and enhanced control to viral infection.

30 October 2018 | doi: 10.1038/s41467-018-06978-5
CD8-positive T cells  Infection  Parasitic infection  Viral infection 

Weaker plant-enemy interactions decrease tree seedling diversity with edge-effects in a fragmented tropical forest OPEN
Meghna Krishnadas, Robert Bagchi, Sachin Sridhara & Liza S. Comita

Tree diversity decreases at the edges of fragmented forests. Here, Krishnadas et al. find that weaker top-down regulation by insects and fungal pathogens during seedling recruitment contributes to reduced tree seedling diversity near forest edges in a human-modified landscape.

30 October 2018 | doi: 10.1038/s41467-018-06997-2
Community ecology  Conservation biology  Tropical ecology 

The structure of a β2-microglobulin fibril suggests a molecular basis for its amyloid polymorphism OPEN
Matthew G. Iadanza, Robert Silvers, Joshua Boardman, Hugh I. Smith, Theodoros K. Karamanos, Galia T. Debelouchina, Yongchao Su, Robert G. Griffin, Neil A. Ranson & Sheena E. Radford

Impaired kidney function can lead to an increase of β2-microglobulin (β2m) serum levels, which can cause β2m aggregation and amyloid fibril formation. Here the authors combine cryo-EM and magic angle spinning NMR measurements to determine the structure of a β2m fibril and they also present the low resolution model of a β2m fibril with a different morphology.

30 October 2018 | doi: 10.1038/s41467-018-06761-6
Cryoelectron microscopy  Protein aggregation  Solid-state NMR 

Network integration of multi-tumour omics data suggests novel targeting strategies OPEN
Ítalo Faria do Valle, Giulia Menichetti, Giorgia Simonetti, Samantha Bruno, Isabella Zironi, Danielle Fernandes Durso, José C. M. Mombach, Giovanni Martinelli, Gastone Castellani & Daniel Remondini

Tumours of different tissues can show similarities in genomic alterations. Here, the authors combine tumour transcriptome and protein interaction data in a network-based analysis of 11 tumours types, and identify clusters of tumours with specific signatures for multi-tumour drug targeting and survival prognosis.

30 October 2018 | doi: 10.1038/s41467-018-06992-7
Cancer genomics  Data integration  Network topology  Systems analysis 

Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure OPEN

The mechanisms underlying the transition from cardiac hypertrophy to heart failure following pressure overload are incompletely understood. Here the authors identify the gene programs encoding the morphological and functional characteristics of cardiomyocytes during the transition from early hypertrophy to heart failure via single-cell transcriptomics, establishing a key role for p53 signalling.

30 October 2018 | doi: 10.1038/s41467-018-06639-7
Cardiac hypertrophy  Heart failure  RNA sequencing 

Predictive multiphase evolution in Al-containing high-entropy alloys OPEN
L. J. Santodonato, P. K. Liaw, R. R. Unocic, H. Bei & J. R. Morris

Exploration of high entropy alloy phases where little experimental data exists is still challenging. Here, the authors develop an approach where parameters from first principle simulations are incorporated into Monte Carlo simulations to reproduce phase evolution of aluminium-containing high entropy alloys.

30 October 2018 | doi: 10.1038/s41467-018-06757-2
Atomistic models  Metals and alloys 

Laser-induced vapour nanobubbles improve drug diffusion and efficiency in bacterial biofilms OPEN
Eline Teirlinck, Ranhua Xiong, Toon Brans, Katrien Forier, Juan Fraire, Heleen Van Acker, Nele Matthijs, Riet De Rycke, Stefaan C. De Smedt, Tom Coenye & Kevin Braeckmans

Eradication of bacterial infections can be hindered by poor penetration of antibiotics through biofilms. Here, Teirlinck et al. show that laser-induced vapour nanobubbles formed around plasmonic nanoparticles can be used to locally disturb biofilm integrity and improve antibiotic diffusion.

30 October 2018 | doi: 10.1038/s41467-018-06884-w
Antibiotics  Biofilms  Nanoparticles  Optics and photonics 

Dynamics of individual molecular shuttles under mechanical force OPEN
Teresa Naranjo, Kateryna M. Lemishko, Sara de Lorenzo, Álvaro Somoza, Felix Ritort, Emilio M. Pérez & Borja Ibarra

Molecular shuttles are bi-stable and stimuli-responsive systems that are considered potential elements for molecular machinery. Here, the authors use optical tweezers to measure the force dependent real-time kinetics of individual molecular shuttles under aqueous conditions.

30 October 2018 | doi: 10.1038/s41467-018-06905-8
Physical chemistry  Supramolecular chemistry 

SUMOylation of ROR-γt inhibits IL-17 expression and inflammation via HDAC2 OPEN
Amir Kumar Singh, Prashant Khare, Abeer Obaid, Kevin P. Conlon, Venkatesha Basrur, Ronald A. DePinho & K. Venuprasad

Interleukin-17 (IL-17)-secreting CD4 T cells (Th17) are induced by the master transcription factor RORγt, and are important for anti-fungal immunity and inflammatory responses. Here the authors show that Ubc9-mediated SUMOylation of RORγt induces HDAC2 binding to IL-17 promoter for suppressing IL-17 production in Th17 cells.

30 October 2018 | doi: 10.1038/s41467-018-06924-5
Epigenetics in immune cells  Mucosal immunology  Sumoylation  T-helper 17 cells 

A high-energy sulfur cathode in carbonate electrolyte by eliminating polysulfides via solid-phase lithium-sulfur transformation OPEN
Xia Li, Mohammad Banis, Andrew Lushington, Xiaofei Yang, Qian Sun, Yang Zhao, Changqi Liu, Qizheng Li, Biqiong Wang, Wei Xiao, Changhong Wang, Minsi Li, Jianwen Liang, Ruying Li, Yongfeng Hu, Lyudmila Goncharova, Huamin Zhang, Tsun-Kong Sham & Xueliang Sun

Carbonate-based electrolytes can impart advantages in lithium sulfur batteries, but performance is often limited by incompatibility with sulfur-based cathodes. Here the authors elucidate a mechanism for conversion of sulfur to lithium sulfide and demonstrate improved performance in a Li-S cell.

30 October 2018 | doi: 10.1038/s41467-018-06877-9
Batteries  Characterization and analytical techniques 

Sources, propagation and consequences of stochasticity in cellular growth OPEN
Philipp Thomas, Guillaume Terradot, Vincent Danos & Andrea Y. Weiße

The drivers of growth rate variability in bacteria are yet unknown. Here, the authors present a theory to predict the growth dynamics of individual cells and use a stochastic cell model integrating metabolism, gene expression and replication to identify the processes that underlie growth variation.

30 October 2018 | doi: 10.1038/s41467-018-06912-9
Cell growth  Cellular noise  Stochastic modelling 

Locking loop movement in the ubiquinone pocket of complex I disengages the proton pumps OPEN
Alfredo Cabrera-Orefice, Etienne Galemou Yoga, Christophe Wirth, Karin Siegmund, Klaus Zwicker, Sergio Guerrero-Castillo, Volker Zickermann, Carola Hunte & Ulrich Brandt

Proton pumping of mitochondrial complex I depends on the reduction of ubiquinone but the molecular mechanism of energy conversion is unclear. Here, the authors provide structural and biochemical evidence showing that movement of loop TMH1-2 in complex I subunit ND3 is required to drive proton pumping.

29 October 2018 | doi: 10.1038/s41467-018-06955-y
Enzyme mechanisms  Mitochondrial proteins  X-ray crystallography 

Seeded X-ray free-electron laser generating radiation with laser statistical properties OPEN
Oleg Yu. Gorobtsov, Giuseppe Mercurio, Flavio Capotondi, Petr Skopintsev, Sergey Lazarev, Ivan A. Zaluzhnyy, Miltcho B. Danailov, Martina Dell'Angela, Michele Manfredda, Emanuele Pedersoli, Luca Giannessi, Maya Kiskinova, Kevin C. Prince, Wilfried Wurth & Ivan A. Vartanyants

Free electron lasers are emerging as important tools for nonlinear spectroscopy in the X-ray regime. Here the authors demonstrate the second order coherence of a seeded FEL source that may be useful for measurements in quantum optics.

29 October 2018 | doi: 10.1038/s41467-018-06743-8
Free-electron lasers  Optical spectroscopy 

Reduction spheroids preserve a uranium isotope record of the ancient deep continental biosphere OPEN
Sean McMahon, Ashleigh v. S. Hood, John Parnell & Stephen Bowden

Red beds contain reduction spheroids that formed underground millions of years ago and whose origin remains poorly constrained. Here the authors use uranium isotopes to identify ancient fingerprints of bacteria in these features, confirming that they were produced by subsurface life in the geological past.

29 October 2018 | doi: 10.1038/s41467-018-06974-9
Astrobiology  Element cycles  Environmental microbiology  Palaeontology 

Reference-point centering and range-adaptation enhance human reinforcement learning at the cost of irrational preferences OPEN
Sophie Bavard, Maël Lebreton, Mehdi Khamassi, Giorgio Coricelli & Stefano Palminteri

Humans often make sub-optimal decisions, choosing options that are less advantageous than available alternatives. Using computational modeling of behavior, the authors demonstrate that such irrational choices can arise from context dependence in reinforcement learning.

29 October 2018 | doi: 10.1038/s41467-018-06781-2
Neuroscience  Psychology 

Molecular definition of group 1 innate lymphoid cells in the mouse uterus OPEN
Iva Filipovic, Laura Chiossone, Paola Vacca, Russell S. Hamilton, Tiziano Ingegnere, Jean-Marc Doisne, Delia A. Hawkes, Maria Cristina Mingari, Andrew M. Sharkey, Lorenzo Moretta & Francesco Colucci

Studying the uterine lymphocyte pool is difficult due to its dynamic nature induced by various pregnancy-related factors. Here the authors provide, using transcriptome data from sorted mouse group 1 innate lymphoid cells (ILC), a molecular atlas of these cells, which implicates tissue-resident natural killer cells as a hub for uterine immune crosstalk.

29 October 2018 | doi: 10.1038/s41467-018-06918-3
Applied immunology  Gene regulation in immune cells  Innate lymphoid cells  Transforming growth factor beta 

Direct observation of selective autophagy induction in cells and tissues by self-assembled chiral nanodevice OPEN
Maozhong Sun, Tiantian Hao, Xiaoyun Li, Aihua Qu, Liguang Xu, Changlong Hao, Chuanlai Xu & Hua Kuang

Chiral assemblies have gained great interest for probing intracellular effects. Here, the authors report on the development of an upconversion nanoparticle-centred yolk-shell nanoparticle tetrahedron for the induction of autophagy and the monitoring of ATP levels both in living cells and in vivo.

29 October 2018 | doi: 10.1038/s41467-018-06946-z
Biomaterials  Materials chemistry  Materials science  Nanoscale materials 

Candida albicans gains azole resistance by altering sphingolipid composition OPEN
Jiaxin Gao, Haitao Wang, Zeyao Li, Ada Hang-Heng Wong, Yi-Zheng Wang, Yahui Guo, Xin Lin, Guisheng Zeng, Yue Wang & Jianbin Wang

The fungal pathogen Candida albicans is diploid, which hinders genome-wide studies. Here, Gao et al. present a piggyBac transposon-mediated mutagenesis system using stable haploid C. albicans strains, and use it to identify genes and mechanisms underlying azole resistance.

29 October 2018 | doi: 10.1038/s41467-018-06944-1
Fungi  Microbiology 

Chemical shifts in molecular solids by machine learning OPEN
Federico M. Paruzzo, Albert Hofstetter, Félix Musil, Sandip De, Michele Ceriotti & Lyndon Emsley

Solid-state nuclear magnetic resonance combined with quantum chemical shift predictions is limited by high computational cost. Here, the authors use machine learning based on local atomic environments to predict experimental chemical shifts in molecular solids with accuracy similar to density functional theory.

29 October 2018 | doi: 10.1038/s41467-018-06972-x
Computational science  Structural properties  Structure prediction 

Pressure-induced emission of cesium lead halide perovskite nanocrystals OPEN
Zhiwei Ma, Zhun Liu, Siyu Lu, Lingrui Wang, Xiaolei Feng, Dongwen Yang, Kai Wang, Guanjun Xiao, Lijun Zhang, Simon A. T. Redfern & Bo Zou

The potential optoelectronic applications of metal halide perovskites make exploration and tuning of their optical properties of great interest. Here the authors show that non-emitting zero-dimensional cesium lead halide perovskites become strongly fluorescent under high pressure, due to distortion-induced effects.

29 October 2018 | doi: 10.1038/s41467-018-06840-8
Materials science  Physical chemistry 

Line excitation array detection fluorescence microscopy at 0.8 million frames per second OPEN
Chris Martin, Tianqi Li, Evan Hegarty, Peisen Zhao, Sudip Mondal & Adela Ben-Yakar

Demanding biological imaging applications require extremely fast detection methods. Here, the authors demonstrate Line Excitation Array Detection, their developed technique for performing fluorescence microscopy in 3D with 0.8 million frames per second, by applying it to flow cytometry and neuron detection.

29 October 2018 | doi: 10.1038/s41467-018-06775-0
Fluorescence imaging  High-throughput screening 

Ultrafast carbon monoxide photolysis and heme spin-crossover in myoglobin via nonadiabatic quantum dynamics OPEN
Konstantin Falahati, Hiroyuki Tamura, Irene Burghardt & Miquel Huix-Rotllant

Myoglobin bound to carbon monoxide undergoes an ultrafast light-induced reaction, which ends up in a photolyzed carbon monoxide and a spin transition of the iron center. Here, the authors employ quantum wavepacket dynamics to show that photolysis precedes the spin transition, a mechanism dominated by strong electron-nuclear couplings.

29 October 2018 | doi: 10.1038/s41467-018-06615-1
Computational chemistry  Metalloproteins  Photobiology  Quantum chemistry 

Homeostasis of protein and mRNA concentrations in growing cells OPEN
Jie Lin & Ariel Amir

For various organisms, mRNA and protein copy numbers scale with cell volume. Here, the authors show that this result emerges naturally when ribosomes and RNAPs limit expression. Furthermore, the authors show that within their model this result breaks down for a sufficiently high volume/DNA ratio.

29 October 2018 | doi: 10.1038/s41467-018-06714-z
Biological physics  Gene expression  Statistical physics, thermodynamics and nonlinear dynamics  Stochastic modelling 

Cell specific delivery of modified mRNA expressing therapeutic proteins to leukocytes OPEN
Nuphar Veiga, Meir Goldsmith, Yasmin Granot, Daniel Rosenblum, Niels Dammes, Ranit Kedmi, Srinivas Ramishetti & Dan Peer

Therapeutic alteration of protein expression using modified mRNA is limited by immunogenicity and instability in vivo. Here the authors use antibody-coated lipid nanoparticles to deliver mRNA to leukocytes and drive expression of anti-inflammatory cytokines in an inflammatory bowel disease mouse model.

29 October 2018 | doi: 10.1038/s41467-018-06936-1
Drug delivery  Nanobiotechnology  Nanomedicine  Nucleic-acid therapeutics  Pharmaceutics 

6mer seed toxicity in tumor suppressive microRNAs OPEN
Quan Q. Gao, William E. Putzbach, Andrea E. Murmann, Siquan Chen, Aishe A. Sarshad, Johannes M. Peter, Elizabeth T. Bartom, Markus Hafner & Marcus E. Peter

Small interfering (siRNAs) can be toxic to cancer cells. Here the authors investigate the toxicity of microRNA in cancer cells by performing a siRNA screen that tests the miRNA activities of an extensive list of miRNAs with different 6mer seed sequences.

29 October 2018 | doi: 10.1038/s41467-018-06526-1

Activity enhancement of cobalt catalysts by tuning metal-support interactions OPEN
Carlos Hernández Mejía, Tom W. van Deelen & Krijn P. de Jong

Tuning metal-support interaction can strongly influence the performance of a catalyst, and is thus essential for catalyst design. Here, the authors investigate reduction-oxidation-reduction treatments as a method to affect metal-support interactions of cobalt-based catalysts in Fischer-Tropsch synthesis.

26 October 2018 | doi: 10.1038/s41467-018-06903-w
Catalyst synthesis  Heterogeneous catalysis  Nanoparticles  Solid-state chemistry 

IL-7 receptor blockade blunts antigen-specific memory T cell responses and chronic inflammation in primates OPEN
Lyssia Belarif, Caroline Mary, Lola Jacquemont, Hoa Le Mai, Richard Danger, Jeremy Hervouet, David Minault, Virginie Thepenier, Veronique Nerrière-Daguin, Elisabeth Nguyen, Sabrina Pengam, Eric Largy, Arnaud Delobel, Bernard Martinet, Stéphanie Le Bas-Bernardet, Sophie Brouard, Jean-Paul Soulillou, Nicolas Degauque, Gilles Blancho, Bernard Vanhove et al.

Chronic inflammation often involves reactivation of memory adaptive immune. Here the authors show, using non-human primate models, that a single dose of anti-IL-7 receptor monoclonal antibody that exhibits antagonist but not agonist properties can reduce the frequency of antigen-specific T cell to help repress chronic skin inflammation.

26 October 2018 | doi: 10.1038/s41467-018-06804-y
Immunological memory  Immunotherapy  Interleukins  T cells 

Distinct patterns of brain activity mediate perceptual and motor and autonomic responses to noxious stimuli OPEN
Laura Tiemann, Vanessa D. Hohn, Son Ta Dinh, Elisabeth S. May, Moritz M. Nickel, Joachim Gross & Markus Ploner

Pain is a complex phenomenon involving not just the perception of pain, but also autonomic and motor responses. Here, the authors show that these different dimensions of pain are associated with distinct patterns of neural responses to noxious stimuli as measured using EEG.

26 October 2018 | doi: 10.1038/s41467-018-06875-x
Human behaviour  Neural circuits  Pain  Sensory processing 

Determinants of promoter and enhancer transcription directionality in metazoans OPEN
Mahmoud M. Ibrahim, Aslihan Karabacak, Alexander Glahs, Ena Kolundzic, Antje Hirsekorn, Alexa Carda, Baris Tursun, Robert P. Zinzen, Scott A. Lacadie & Uwe Ohler

Divergent transcription from promoters and enhancers occurs in many species, but it is unclear if it is a general feature of all eukaryotic cis regulatory elements. Here the authors define cis regulatory elements in worms, flies, and human; and identify several differences in regulatory architecture among metazoans.

26 October 2018 | doi: 10.1038/s41467-018-06962-z
Epigenomics  Gene regulation  Genome informatics  Transcription 

Breaking the scaling relationship via thermally stable Pt/Cu single atom alloys for catalytic dehydrogenation OPEN
Guodong Sun, Zhi-Jian Zhao, Rentao Mu, Shenjun Zha, Lulu Li, Sai Chen, Ketao Zang, Jun Luo, Zhenglong Li, Stephen C. Purdy, A. Jeremy Kropf, Jeffrey T. Miller, Liang Zeng & Jinlong Gong

Enhancing the catalytic activity of noble-metal alloys is frequently accompanied by side reactions. Here, the authors describe an approach to break the scaling relationship for propane dehydrogenation, by assembling single atom alloys, to achieve simultaneous enhancement of propylene selectivity and propane conversion.

26 October 2018 | doi: 10.1038/s41467-018-06967-8
Atomistic models  Chemical engineering  Heterogeneous catalysis 

Mass spectrometry and Monte Carlo method mapping of nanoparticle ligand shell morphology OPEN
Zhi Luo, Yanfei Zhao, Tamim Darwish, Yue Wang, Jing Hou & Francesco Stellacci

Determining the arrangement of ligands on a nanoparticle is challenging, given the limitations of existing characterization tools. Here, the authors describe an accessible method for resolving ligand shell morphology that uses simple MALDI-TOF mass spectrometry measurements in conjunction with an open-access Monte Carlo fitting program.

26 October 2018 | doi: 10.1038/s41467-018-06939-y
Characterization and analytical techniques  Mass spectrometry  Nanoparticles  Surface chemistry 

Engineering bacterial vortex lattice via direct laser lithography OPEN
Daiki Nishiguchi, Igor S Aranson, Alexey Snezhko & Andrey Sokolov

Geometrically confined suspensions of swimming bacteria can self-organize into an ordered state. Here, the authors use tiny pillars to trigger organization of bacterial motion into a stable lattice of vortices with a long-range antiferromagnetic order and control vortex direction through pillar chirality.

26 October 2018 | doi: 10.1038/s41467-018-06842-6
Bioinspired materials  Cellular motility  Self-assembly 

Optimization of carbon and energy utilization through differential translational efficiency OPEN
Mahmoud M. Al-Bassam, Ji-Nu Kim, Livia S. Zaramela, Benjamin P. Kellman, Cristal Zuniga, Jacob M. Wozniak, David J. Gonzalez & Karsten Zengler

Microorganisms must regulate allocation of resources in nutrient-limited conditions. Here, the authors combine Ribo-seq, RNA-seq and TSS-seq to study resource allocation in the acetogen C. ljungdahlii, and show that dynamic regulation of translational efficiency of metabolic pathways is critical.

26 October 2018 | doi: 10.1038/s41467-018-06993-6
Computational biology and bioinformatics  Microbiology  Ribosome  Systems biology 

Sexual rejection via a vomeronasal receptor-triggered limbic circuit OPEN
Takuya Osakada, Kentaro K. Ishii, Hiromi Mori, Ryo Eguchi, David M. Ferrero, Yoshihiro Yoshihara, Stephen D. Liberles, Kazunari Miyamichi & Kazushige Touhara

Sex pheromones that increase mating have been reported across a number of different species, yet there is little known about pheromones that suppress female mating drive. This study reports that juvenile female mice release a pheromone, ESP22, which suppresses sexual receptivity of adult female mice by evoking a robust rejection behavior upon male mounting.

26 October 2018 | doi: 10.1038/s41467-018-07003-5
Neural circuits  Pheromone 

Non-catalytic signaling by pseudokinase ILK for regulating cell adhesion OPEN
Julia Vaynberg, Koichi Fukuda, Fan Lu, Katarzyna Bialkowska, Yinghua Chen, Edward F. Plow & Jun Qin

Pseudokinase ILK is essential for dynamic communication between focal adhesion complexes and F-actin filaments. Here, the authors show that ILK regulates such communication by complexing with PINCH and Parvin to trigger F-actin filament bundling through previously unrecognized actin binding motifs in PINCH and Parvin

26 October 2018 | doi: 10.1038/s41467-018-06906-7
Focal adhesion  Solution-state NMR 

Spatiotemporal regulation of the GPCR activity of BAI3 by C1qL4 and Stabilin-2 controls myoblast fusion OPEN
Noumeira Hamoud, Viviane Tran, Takahiro Aimi, Wataru Kakegawa, Sylvie Lahaie, Marie-Pier Thibault, Ariane Pelletier, G. William Wong, In-San Kim, Artur Kania, Michisuke Yuzaki, Michel Bouvier & Jean-François Côté

Myoblast fusion is an essential step in muscle growth and regeneration, and is regulated by the G-protein coupled receptor (GPCR) BAI3. Here Hamoud et al. show that the GPCR activity of BAI3 is spatiotemporally regulated during myoblast fusion, and identify C1qL4 and Stabilin-2 as, respectively, negative and positive regulators of its activity.

26 October 2018 | doi: 10.1038/s41467-018-06897-5
Developmental biology  Extracellular signalling molecules  Muscle stem cells 

Designing soft materials with interfacial instabilities in liquid films OPEN
J. Marthelot, E. F. Strong, P. M. Reis & P.-T. Brun

Interfacial instabilities can be damaging as they may lead to fabrication defects. Here the authors harness a fluid instability to their advantage to produce thin polymeric films with drop-shaped structures which have tailored geometrical properties.

26 October 2018 | doi: 10.1038/s41467-018-06984-7
Fluid dynamics  Mechanical engineering  Self-assembly 

Cooperative mechanisms of oxygen vacancy stabilization and migration in the isolated tetrahedral anion Scheelite structure OPEN
Xiaoyan Yang, Alberto J. Fernández-Carrión, Jiehua Wang, Florence Porcher, Franck Fayon, Mathieu Allix & Xiaojun Kuang

Fast oxide ion conductors are the key materials for some technological devices. Here the authors report the creation and stabilization of oxygen vacancies in BiVO4 Scheelite with isolated tetrahedral anion structures for improved ionic conducting performance and understanding of the conduction mechanism.

26 October 2018 | doi: 10.1038/s41467-018-06911-w
Chemical physics  Computational methods  Electronic materials  Solid-state chemistry  Solid-state NMR 

Deacetylation of serine hydroxymethyl-transferase 2 by SIRT3 promotes colorectal carcinogenesis OPEN
Zhen Wei, Jinglue Song, Guanghui Wang, Ximao Cui, Jun Zheng, Yunlan Tang, Xinyuan Chen, Jixi Li, Long Cui, Chen-Ying Liu & Wei Yu

Serine hydroxymethyltransferase 2 (SHMT2) converts serine to glycine in mitochondria and is upregulated in a variety of cancers. Here the authors show that acetylation of the lysine-95 (K95) residue negatively regulates SHMT2 expression and activity and is deacetylated by SIRT3 in colorectal cancer.

26 October 2018 | doi: 10.1038/s41467-018-06812-y
Cancer metabolism  Post-translational modifications 

All-optical nonequilibrium pathway to stabilising magnetic Weyl semimetals in pyrochlore iridates OPEN
Gabriel E. Topp, Nicolas Tancogne-Dejean, Alexander F. Kemper, Angel Rubio & Michael A. Sentef

Topological states may emerge in nonequilibrium but the mechanisms are much less understood. Here Topp et al. propose a nonequilibrium route to obtain the magnetic Weyl semimetallic phase in pyrochlore iridates by ultrafast modification of the effective electron-electron interactions with short laser pulses.

26 October 2018 | doi: 10.1038/s41467-018-06991-8
Electronic properties and materials  Topological insulators 

The transcription factor Foxp1 preserves integrity of an active Foxp3 locus in extrathymic Treg cells OPEN
Sayantani Ghosh, Sinchita Roy-Chowdhuri, Keunsoo Kang, Sin-Hyeog Im & Dipayan Rudra

Regulatory T (Treg) cells suppress immune cell activation to maintain immune homeostasis, and have their lineage enforced by the master transcription factor Foxp3. Here the authors show that Foxp3 expression is promoted and maintained by a related family member, Foxp1, specifically in peripherally induced Treg but not in Treg cells of thymic origin.

26 October 2018 | doi: 10.1038/s41467-018-07018-y
Adaptive immunity  Gene regulation in immune cells  Mucosal immunology  Regulatory T cells 

Long time-scales in primate amygdala neurons support aversive learning OPEN
Aryeh H. Taub, Yosef Shohat & Rony Paz

During learning of an association between a neutral cue and an aversive stimulus, there is a time lag between trials. Here, the authors examine how long inter-trial intervals are represented by the basolateral amygdala and anterior cingulate cortex to support learning rate and memory strength.

26 October 2018 | doi: 10.1038/s41467-018-07020-4
Amygdala  Learning and memory 

Mycoplasma genitalium adhesin P110 binds sialic-acid human receptors OPEN
David Aparicio, Sergi Torres-Puig, Mercè Ratera, Enrique Querol, Jaume Piñol, Oscar Q. Pich & Ignacio Fita

How the Mycoplasma genitalium cytadhesins P140 and P110 promote host cell invasion remains poorly understood. Here, combining structural analysis with functional assays, Aparicio et al. identify the P110 domain that binds to sialylated receptors essential for mycoplasma cytadherence.

26 October 2018 | doi: 10.1038/s41467-018-06963-y
Immunology  Microbiology  X-ray crystallography 

Multifunctional molecular modulators for perovskite solar cells with over 20% efficiency and high operational stability OPEN
Dongqin Bi, Xiong Li, Jovana V. Milić, Dominik J. Kubicki, Norman Pellet, Jingshan Luo, Thomas LaGrange, Pierre Mettraux, Lyndon Emsley, Shaik M. Zakeeruddin & Michael Grätzel

Engineering hybrid perovskites at the molecular level to solve the stability problem remains a challenge. Here Grätzel et al. design a multifunctional molecular modulator that interacts with the perovskite via modes elucidated by solid state NMR spectroscopy and show high efficiency and operational stability.

26 October 2018 | doi: 10.1038/s41467-018-06709-w
Energy harvesting  Materials chemistry 

Extremely rapid isotropic irradiation of nanoparticles with ions generated in situ by a nuclear reaction OPEN
Jan Havlik, Vladimira Petrakova, Jan Kucka, Helena Raabova, Dalibor Panek, Vaclav Stepan, Zuzana Zlamalova Cilova, Philipp Reineck, Jan Stursa, Jan Kucera, Martin Hruby & Petr Cigler

Mass production of nanoparticles containing well-controlled structural defects is a challenge. Here the authors demonstrate the feasibility of homogeneous ion irradiation generated in a nuclear reactor, for the preparation of fluorescent nanodiamonds and silicon carbide nanoparticles.

26 October 2018 | doi: 10.1038/s41467-018-06789-8
Design, synthesis and processing  Experimental nuclear physics  Synthesis and processing 

High-energy-density dual-ion battery for stationary storage of electricity using concentrated potassium fluorosulfonylimide OPEN
Kostiantyn V. Kravchyk, Preeti Bhauriyal, Laura Piveteau, Christoph P. Guntlin, Biswarup Pathak & Maksym V. Kovalenko

Lithium-free graphite dual-ion battery offers a new means of energy storage. Here the authors show such device utilizing a highly concentrated electrolyte solution of KFSI in alkyl carbonates that exhibits a high energy density and high energy efficiency as well as an average discharge voltage of 4.7 V.

26 October 2018 | doi: 10.1038/s41467-018-06923-6

A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma OPEN
Maolei Zhang, Kun Zhao, Xiaoping Xu, Yibing Yang, Sheng Yan, Ping Wei, Hui Liu, Jianbo Xu, Feizhe Xiao, Huangkai Zhou, Xuesong Yang, Nunu Huang, Jinglei Liu, Kejun He, Keping Xie, Gong Zhang, Suyun Huang & Nu Zhang

Functional peptides can be encoded by short open reading frames in non-coding RNA. Here, the authors identify a 87aa peptide encoded by the circular form of the long intergenic non-protein-coding RNA p53-induced transcript (LINC-PINT) that can reduce glioblastoma proliferation via interaction with PAF1 which sequentially inhibits the transcriptional elongation of some oncogenes.

26 October 2018 | doi: 10.1038/s41467-018-06862-2
CNS cancer  Non-coding RNAs 

High-power hybrid biofuel cells using layer-by-layer assembled glucose oxidase-coated metallic cotton fibers OPEN
Cheong Hoon Kwon, Yongmin Ko, Dongyeeb Shin, Minseong Kwon, Jinho Park, Wan Ki Bae, Seung Woo Lee & Jinhan Cho

Biofuel cells offer biocompatibility and operation at mild conditions, but application is limited by relatively low output power. Here the authors use layer-by-layer assembly for glucose oxidase-coated metallic cotton fibers for use as electrodes in a hybrid biofuel cell to achieve high output power.

26 October 2018 | doi: 10.1038/s41467-018-06994-5
Electrocatalysis  Electrochemistry  Fuel cells 

An optical reaction micro-turbine OPEN
Silvio Bianchi, Gaszton Vizsnyiczai, Stefano Ferretti, Claudio Maggi & Roberto Di Leonardo

Light can be used to rotate micrometric turbines that usually rely on scattering to redistribute optical momentum and generate a mechanical torque. Here, 3D microfabricated light guiding structures can reroute an incoming flow of optical energy to generate a strong, uniform and controllable torque.

26 October 2018 | doi: 10.1038/s41467-018-06947-y
Fluidics  Micro-optics  Photonic devices 

Multifunctional sequence-defined macromolecules for chemical data storage OPEN
Steven Martens, Annelies Landuyt, Pieter Espeel, Bart Devreese, Peter Dawyndt & Filip Du Prez

Sequence-defined macromolecules consist of a defined chain length and topology and can be used in applications such as antibiotics and data storage. Here the authors developed two algorithms to encode text fragments and QR codes as a collection of oligomers and to reconstruct the original data.

26 October 2018 | doi: 10.1038/s41467-018-06926-3
Cheminformatics  Organic chemistry  Polymer chemistry 

Flexible and stable high-energy lithium-sulfur full batteries with only 100% oversized lithium OPEN
Jian Chang, Jian Shang, Yongming Sun, Luis K. Ono, Dongrui Wang, Zhijun Ma, Qiyao Huang, Dongdong Chen, Guoqiang Liu, Yi Cui, Yabing Qi & Zijian Zheng

Lightweight and flexible energy storage devices are needed to persistently power wearable devices. Here the authors employ metallized carbon fabrics as hosts for sulfur and lithium to achieve flexibility, electrochemical stability and high energy density in a lithium-sulfur battery.

26 October 2018 | doi: 10.1038/s41467-018-06879-7
Energy science and technology  Materials science 

Genome-wide analyses identify a role for SLC17A4 and AADAT in thyroid hormone regulation OPEN
Alexander Teumer, Layal Chaker, Stefan Groeneweg, Yong Li, Celia Di Munno, Caterina Barbieri, Ulla T. Schultheiss, Michela Traglia, Tarunveer S. Ahluwalia, Masato Akiyama, Emil Vincent R. Appel, Dan E. Arking, Alice Arnold, Arne Astrup, Marian Beekman, John P. Beilby, Sofie Bekaert, Eric Boerwinkle, Suzanne J. Brown, Marc De Buyzere et al.

Thyroid dysfunction is a common public health problem and associated with cardiovascular co-morbidities. Here, the authors carry out genome-wide meta-analysis for thyroid hormone (TH) levels, hyper- and hypothyroidism and identify SLC17A4 as a TH transporter and AADAT as a TH metabolizing enzyme.

26 October 2018 | doi: 10.1038/s41467-018-06356-1
Endocrine system and metabolic diseases  Genome-wide association studies  Thyroid diseases  Thyroid gland 

Common helical V1V2 conformations of HIV-1 Envelope expose the α4β7 binding site on intact virions OPEN
Constantinos Kurt Wibmer, Simone I. Richardson, Jason Yolitz, Claudia Cicala, James Arthos, Penny L. Moore & Lynn Morris

Antibodies blocking the V1V2 domain of HIV Envelope from binding integrin are associated with positive disease outcomes. Here, Wibmer et al. determine the structure of full length V1V2 bound to these antibodies, revealing an alternative fold of V1V2 with exposed integrin-binding sites that functions on non-native Envelope.

26 October 2018 | doi: 10.1038/s41467-018-06794-x
Antibodies  HIV infections  Vaccines  X-ray crystallography 

A FRET biosensor for necroptosis uncovers two different modes of the release of DAMPs OPEN
Shin Murai, Yoshifumi Yamaguchi, Yoshitaka Shirasaki, Mai Yamagishi, Ryodai Shindo, Joanne M. Hildebrand, Ryosuke Miura, Osamu Nakabayashi, Mamoru Totsuka, Taichiro Tomida, Satomi Adachi-Akahane, Sotaro Uemura, John Silke, Hideo Yagita, Masayuki Miura & Hiroyasu Nakano

Necroptotic cells activate MLKL and release inflammatory DAMPs, although the underlying regulatory mechanisms of this process are poorly understood. Here, Murai et al. develop a necroptosis-specific FRET sensor (SMART) that monitors MLKL membrane translocation to identify two modes of DAMP release.

26 October 2018 | doi: 10.1038/s41467-018-06985-6
Cell death and immune response  Necroptosis  Protein–protein interaction networks 

Oriented electron transmission in polyoxometalate-metalloporphyrin organic framework for highly selective electroreduction of CO2 OPEN
Yi-Rong Wang, Qing Huang, Chun-Ting He, Yifa Chen, Jiang Liu, Feng-Cui Shen & Ya-Qian Lan

While CO2 reduction provides a way to remove carbon from the atmosphere, it is challenging to design effective, selective materials for this process. Here, authors construct metal-organic frameworks from polyoxometalates and porphryins to direct electron flow and improve CO2 reduction efficiencies.

26 October 2018 | doi: 10.1038/s41467-018-06938-z
Electrocatalysis  Heterogeneous catalysis  Metal–organic frameworks  Organic–inorganic nanostructures 

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival OPEN
Daniele Ramazzotti, Avantika Lal, Bo Wang, Serafim Batzoglou & Arend Sidow

Identifying molecular subtypes of cancer can improve personalized treatment. Here the authors present CIMLR, an algorithm that integrates multi-omic data to reveal cancer subtypes; subtypes discovered by CIMLR differ in activity of cancer-associated pathways and are significantly predictive of patient outcomes.

26 October 2018 | doi: 10.1038/s41467-018-06921-8

The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD OPEN
Taylor K. Soderborg, Sarah E. Clark, Christopher E. Mulligan, Rachel C. Janssen, Lyndsey Babcock, Diana Ir, Dominick J. Lemas, Linda K. Johnson, Tiffany Weir, Laurel L. Lenz, Daniel N. Frank, Teri L. Hernandez, Kristine A. Kuhn, Angelo D'Alessandro, Linda A. Barbour, Karim C. El Kasmi & Jacob E. Friedman

Infants born to obese mothers have altered microbiome and increased risk of obesity and NAFLD. Here the authors establish causality by showing that maternal obesity-shaped infant gut microbiome induces macrophage dysfunction, inflammation, and diet-induced metabolic disease in germ-free mice.

26 October 2018 | doi: 10.1038/s41467-018-06929-0
Microbiome  Non-alcoholic fatty liver disease  Obesity  Risk factors 

Generation of axenic Aedes aegypti demonstrate live bacteria are not required for mosquito development OPEN
Maria A. Correa, Brian Matusovsky, Doug E. Brackney & Blaire Steven

The mosquito gut microbiota is important for the insect's development and fitness. Here Correa et al. present a method for rearing microbial-free Aedes aegypti mosquitoes, showing that the microbiota is not essential for mosquito development, and providing a method for manipulation of the mosquito microbiome.

26 October 2018 | doi: 10.1038/s41467-018-07014-2
Biological techniques  Microbial communities  Microbiology 

Structural delineation of potent transmission-blocking epitope I on malaria antigen Pfs48/45 OPEN
Prasun Kundu, Anthony Semesi, Matthijs M. Jore, Merribeth J. Morin, Virginia L. Price, Alice Liang, Jingxing Li, Kazutoyo Miura, Robert W. Sauerwein, C. Richter King & Jean-Philippe Julien

Malaria protein Pfs48/45 is a promising transmission-blocking antigen targeted by antibodies. Here, the authors determine the structure of its transmission-blocking epitope I, and generate a humanized monoclonal antibody that binds Pfs48/45 with high affinity.

26 October 2018 | doi: 10.1038/s41467-018-06742-9
Malaria  X-ray crystallography 

Collagen prolyl 4-hydroxylase 1 is essential for HIF-1α stabilization and TNBC chemoresistance OPEN
Gaofeng Xiong, Rachel L. Stewart, Jie Chen, Tianyan Gao, Timothy L. Scott, Luis M. Samayoa, Kathleen O'Connor, Andrew N. Lane & Ren Xu

Hyperactivation of HIF-1α is crucial in progression of triple-negative breast cancer, but how HIF-1α stability is maintained in a hypoxia-independent manner is unclear. Here, the authors show collagen prolyl-4-hydroylase 1 stabilises HIF-1α and is involved in chemoresistance in TNBC.

26 October 2018 | doi: 10.1038/s41467-018-06893-9
Biochemistry  Cancer  Cell biology 

Identifying long-term stable refugia for relict plant species in East Asia OPEN
Cindy Q. Tang, Tetsuya Matsui, Haruka Ohashi, Yi-Fei Dong, Arata Momohara, Sonia Herrando-Moraira, Shenhua Qian, Yongchuan Yang, Masahiko Ohsawa, Hong Truong Luu, Paul J. Grote, Pavel V. Krestov, Ben LePage, Marinus Werger, Kevin Robertson, Carsten Hobohm, Chong-Yun Wang, Ming-Chun Peng, Xi Chen, Huan-Chong Wang et al.

East Asia contains "relict" plant species that persist under narrow climatic conditions after once having wider distributions. Here, using distribution records coupled with ecological niche models, the authors identify long-term stable refugia possessing past, current and future climatic suitability favoring ancient plant lineages.

26 October 2018 | doi: 10.1038/s41467-018-06837-3
Biogeography  Climate-change ecology  Plant ecology 

Mutual inhibition between PTEN and PIP3 generates bistability for polarity in motile cells OPEN
Satomi Matsuoka & Masahiro Ueda

PIP3 and its phosphatase (PTEN) are enriched mutually exclusively on the anterior and posterior membranes of eukaryotic motile cells. Here authors manipulate PIP3 level and use single-molecule imaging to show that PIP3 suppresses the membrane localization of PTEN.

26 October 2018 | doi: 10.1038/s41467-018-06856-0
Chemotaxis  Phosphoinositol signalling  Single-molecule biophysics 

Deconvolution of octahedral Pt3Ni nanoparticle growth pathway from in situ characterizations OPEN
Xiaochen Shen, Changlin Zhang, Shuyi Zhang, Sheng Dai, Guanghui Zhang, Mingyuan Ge, Yanbo Pan, Stephen M. Sharkey, George W. Graham, Adrian Hunt, Iradwikanari Waluyo, Jeffrey T. Miller, Xiaoqing Pan & Zhenmeng Peng

Understanding the growth pathway of faceted alloy nanoparticles at the atomic level is crucial to morphology control and property tuning, but remains a challenge. Here, the authors reveal the particle growth and facet formation mechanisms of octahedral Pt3Ni nanoparticles using multiple cutting-edge in situ techniques.

26 October 2018 | doi: 10.1038/s41467-018-06900-z
Nanoparticle synthesis  Natural gas 

Enhanced mRNA FISH with compact quantum dots OPEN
Yang Liu, Phuong Le, Sung Jun Lim, Liang Ma, Suresh Sarkar, Zhiyuan Han, Stephen J. Murphy, Farhad Kosari, George Vasmatzis, John C. Cheville & Andrew M. Smith

FISH-based techniques to image and count mRNA in single cells can be limited by the photophysical properties of organic dyes. Here the authors develop photostable quantum dot FISH probes for multiplexed imaging.

26 October 2018 | doi: 10.1038/s41467-018-06740-x
Diagnostic markers  Fluorescence in situ hybridization  Microscopy  Permeation and transport  Quantum dots 

Dietary cholesterol promotes steatohepatitis related hepatocellular carcinoma through dysregulated metabolism and calcium signaling OPEN
Jessie Qiaoyi Liang, Narcissus Teoh, Lixia Xu, Sharon Pok, Xiangchun Li, Eagle S. H. Chu, Jonathan Chiu, Ling Dong, Evi Arfianti, W. Geoffrey Haigh, Matthew M. Yeh, George N. Ioannou, Joseph J. Y. Sung, Geoffrey Farrell & Jun Yu

Nonalcoholic steatohepatitis (NASH) and dietary cholesterol are risk factors for hepatocellular carcinoma (HCC). Here, the authors utilise mouse models to show that dietary cholesterol induces NASH by deregulating genes involved in metabolism, inflammation and calcium signaling to induce NASH-HCC.

26 October 2018 | doi: 10.1038/s41467-018-06931-6
Cancer genomics  Genomics 

Mesopontine cholinergic inputs to midbrain dopamine neurons drive stress-induced depressive-like behaviors OPEN
Sebastian P. Fernandez, Loïc Broussot, Fabio Marti, Thomas Contesse, Xavier Mouska, Mariano Soiza-Reilly, Hélène Marie, Philippe Faure & Jacques Barik

Dopamine neurons in the ventral tegmental area (VTA) are implicated in depressive-like behaviors. Here, the authors show that cholinergic inputs to the VTA from the laterodorsal tegmentum regulate intrinsic plasticity of VTA DA neurons to mediate stress-induced depressive-like behaviors.

25 October 2018 | doi: 10.1038/s41467-018-06809-7
Neural circuits  Neuroscience 

Long-term positioning and polar preference of chemoreceptor clusters in E. coli OPEN
Moriah Koler, Eliran Peretz, Chetan Aditya, Thomas S. Shimizu & Ady Vaknin

Bacterial chemoreceptors form clusters, preferably at  the cell poles. Here, Koler et al. show that polar and lateral clusters exhibit distinct long-term positional dynamics   and that polar bias may be due to differences in mobility of receptor complexes between the polar and lateral cell regions.

25 October 2018 | doi: 10.1038/s41467-018-06835-5
Biophysics  Microbiology  Molecular biology 

Evidence for persistence of the SHIV reservoir early after MHC haploidentical hematopoietic stem cell transplantation OPEN
Lucrezia Colonna, Christopher W. Peterson, John B. Schell, Judith M. Carlson, Victor Tkachev, Melanie Brown, Alison Yu, Sowmya Reddy, Willi M. Obenza, Veronica Nelson, Patricia S. Polacino, Heather Mack, Shiu-Lok Hu, Katie Zeleski, Michelle Hoffman, Joe Olvera, Scott N. Furlan, Hengqi Zheng, Agne Taraseviciute, Daniel J. Hunt et al.

Allogeneic hematopoietic cell transplantation (allo-HCT) has led to the cure of HIV in one individual, but the underlying mechanisms are unclear. Here, the authors present a model of allo-HCT in SHIV-infected nonhuman primates and show that the SHIV reservoir persists in multiple tissues early after transplantation.

25 October 2018 | doi: 10.1038/s41467-018-06736-7
Allotransplantation  Animal disease models  Bone marrow transplantation  HIV infections 

Structural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex OPEN
Carolin Sailer, Fabian Offensperger, Alexandra Julier, Kai-Michael Kammer, Ryan Walker-Gray, Matthew G. Gold, Martin Scheffner & Florian Stengel

Oncoprotein E6 facilitates the E6AP-catalyzed ubiquitination of p53. Here, the authors study the structural basis of this process by qualitative and quantitative cross-linking mass spectrometry, providing insights into E6AP-E6-p53 complex assembly and the conformational dynamics that enable p53 ubiquitination.

25 October 2018 | doi: 10.1038/s41467-018-06953-0
Mass spectrometry  Structural biology  Ubiquitylated proteins 

Host suppression of quorum sensing during catheter-associated urinary tract infections OPEN
Stephanie J. Cole, Cherisse L. Hall, Maren Schniederberend, John M. Farrow III, Jonathan R. Goodson, Everett C. Pesci, Barbara I. Kazmierczak & Vincent T. Lee

Pseudomonas aeruginosa can cause chronic infections on medical devices by forming biofilms, a process regulated by quorum sensing (QS). Here, the authors show that P. aeruginosa is unable to perceive QS signals in the presence of either host urine or urea, and clinical isolates are often defective in QS.

25 October 2018 | doi: 10.1038/s41467-018-06882-y
Bacteriology  Microbial communities  Pathogens 

Contribution of epigenetic variation to adaptation in Arabidopsis OPEN
Marc W. Schmid, Christian Heichinger, Diana Coman Schmid, Daniela Guthörl, Valeria Gagliardini, Rémy Bruggmann, Sirisha Aluri, Catharine Aquino, Bernhard Schmid, Lindsay A. Turnbull & Ueli Grossniklaus

Whether plant epigenetic variation is subject to selection and contributes to adaptation is under debate. Here, the authors compare DNA methylation and phenotypes of Arabidopsis lines subject to simulated selection and their nearly isogenic ancestors and provide evidence that epigenetic variation contributes to adaptive responses.

25 October 2018 | doi: 10.1038/s41467-018-06932-5
Epigenomics  Plant genetics 

Phase-controlled Fourier-transform spectroscopy OPEN
Kazuki Hashimoto & Takuro Ideguchi

Fourier transform spectrometers are generally limited to slow scanning rates at high resolution. Here the authors demonstrate highly efficient Fourier transform spectroscopy using a dynamic phase-control technique that enables fast acquisition without compromising bandwidth or resolution.

25 October 2018 | doi: 10.1038/s41467-018-06956-x
Characterization and analytical techniques  Optical spectroscopy 

Medial temporal lobe functional connectivity predicts stimulation-induced theta power OPEN
E. A. Solomon, J. E. Kragel, R. Gross, B. Lega, M. R. Sperling, G. Worrell, S. A. Sheth, K. A. Zaghloul, B. C. Jobst, J. M. Stein, S. Das, R. Gorniak, C. S. Inman, S. Seger, D. S. Rizzuto & M. J. Kahana

Direct electrical brain stimulation can induce widespread changes in neural activity, offering a means to modulate network-wide activity and treat disease. Here, the authors show that the low-frequency functional connectivity profile of a stimulation target predicts where induced theta activity occurs.

25 October 2018 | doi: 10.1038/s41467-018-06876-w
Electroencephalography – EEG  Neural circuits  Neurophysiology  Neuroscience 

Improved methods for marking active neuron populations OPEN

Methods to directly label active neurons are still lacking. Here the authors develop CaMPARI2, a photoconvertible fluorescent protein sensor for neuronal activity with improved brightness and calcium binding kinetics, as well as an antibody to amplify the activated sensor signal in fixed samples.

25 October 2018 | doi: 10.1038/s41467-018-06935-2
Ca2+ imaging  Cellular neuroscience  Protein design 

RhoGAP domain-containing fusions and PPAPDC1A fusions are recurrent and prognostic in diffuse gastric cancer OPEN
Hanna Yang, Dongwan Hong, Soo Young Cho, Young Soo Park, Woo Ri Ko, Ju Hee Kim, Hoon Hur, Jongkeun Lee, Su-Jin Kim, Sun Young Kwon, Jae-Hyuk Lee, Do Youn Park, Kyu Sang Song, Heekyung Chang, Min-Hee Ryu, Kye Soo Cho, Jeong Won Kang, Myeong-Cherl Kook, Nina Thiessen, An He et al.

Diffuse Gastric Cancer (DGC) is increasingly being considered separate to intestinal type gastric cancer; several fusions events have been reported as drivers of the disease but few of those have been subsequently validated. Here the authors perform RNA-seq on early-onset DGC patients who had not been treated with chemotherapy or radiation and identify a previously unknown fusion.

25 October 2018 | doi: 10.1038/s41467-018-06747-4
Cancer genomics  Gastric cancer 

Enabling nanoscale flexoelectricity at extreme temperature by tuning cation diffusion OPEN
Leopoldo Molina-Luna, Shuai Wang, Yevheniy Pivak, Alexander Zintler, Héctor H. Pérez-Garza, Ronald G. Spruit, Qiang Xu, Min Yi, Bai-Xiang Xu & Matias Acosta

The limited number of materials with a switchable electrical polarization available for applications can be increased by exploiting the flexoelectric effect. Here, switchable polarization in nanoparticles induced by an elemental distribution dependent strain gradient up to 800 °C is demonstrated.

25 October 2018 | doi: 10.1038/s41467-018-06959-8
Actuators  Computational methods  Ferroelectrics and multiferroics  Nanoparticles  Transmission electron microscopy 

A biomaterial with a channel-like pore architecture induces endochondral healing of bone defects OPEN
A. Petersen, A. Princ, G. Korus, A. Ellinghaus, H. Leemhuis, A. Herrera, A. Klaumünzer, S. Schreivogel, A. Woloszyk, K. Schmidt-Bleek, S. Geissler, I. Heschel & G. N. Duda

A bioengineering approach to enhance the regeneration of large bone defects is lacking. Here, the authors show that a biomaterial scaffold with a channel-like pore architecture enables organized endochondral ossification through directional cell recruitment and extracellular matrix alignment.

25 October 2018 | doi: 10.1038/s41467-018-06504-7
Biomedical materials  Regeneration  Tissue engineering 

Nanocardboard as a nanoscale analog of hollow sandwich plates OPEN
Chen Lin, Samuel M. Nicaise, Drew E. Lilley, Joan Cortes, Pengcheng Jiao, Jaspreet Singh, Mohsen Azadi, Gerald G. Lopez, Meredith Metzler, Prashant K. Purohit & Igor Bargatin

Sandwich structures such as corrugated cardboard offer low weight and high bending stiffness, but they are difficult to produce at the nanoscale. Here, the authors combine webbing and perforation to produce alumina 'nanocardboard' with ultralow areal density that recovers without damage from extreme deformation.

25 October 2018 | doi: 10.1038/s41467-018-06818-6
Ceramics  Mechanical engineering  Metamaterials 

A homozygous loss-of-function mutation leading to CYBC1 deficiency causes chronic granulomatous disease OPEN
Gudny A. Arnadottir, Gudmundur L. Norddahl, Steinunn Gudmundsdottir, Arna B. Agustsdottir, Snaevar Sigurdsson, Brynjar O. Jensson, Kristbjorg Bjarnadottir, Fannar Theodors, Stefania Benonisdottir, Erna V. Ivarsdottir, Asmundur Oddsson, Ragnar P. Kristjansson, Gerald Sulem, Kristjan F. Alexandersson, Thorhildur Juliusdottir, Kjartan R. Gudmundsson, Jona Saemundsdottir, Adalbjorg Jonasdottir, Aslaug Jonasdottir, Asgeir Sigurdsson et al.

Mutations in genes encoding NAPDH oxidase subunits are known to be causative for the primary immunodeficiency chronic granulomatous disease (CGD). Here, the authors identify CYBC1 mutations in patients with CGD and show that CYBC1 is important for formation of the NADPH complex and respiratory burst.

25 October 2018 | doi: 10.1038/s41467-018-06964-x
Antimicrobial responses  Disease genetics  Immunological deficiency syndromes  Rare variants 

Rewriting the phase diagram of a diamagnetic liquid crystal by a magnetic field OPEN
Fatin Hajjaj, Takashi Kajitani, Hiroyuki Ohsumi, Yoshikazu Tanaka, Kenichi Kato, Masaki Takata, Hideaki Kitazawa, Taka-hisa Arima, Takuzo Aida & Takanori Fukushima

Magnetically induced phase behaviour in a soft matter system is of potential interest for magneto-responsive compounds. Here the authors fabricate a discotic ionic liquid crystalline hybrid material which can be switched from orthorhombic to cubic phase in the absence or presence of a strong magnetic field.

25 October 2018 | doi: 10.1038/s41467-018-06976-7
Liquid crystals  Self-assembly 

Adhesion to nanofibers drives cell membrane remodeling through one-dimensional wetting OPEN
Arthur Charles-Orszag, Feng-Ching Tsai, Daria Bonazzi, Valeria Manriquez, Martin Sachse, Adeline Mallet, Audrey Salles, Keira Melican, Ralitza Staneva, Aurélie Bertin, Corinne Millien, Sylvie Goussard, Pierre Lafaye, Spencer Shorte, Matthieu Piel, Jacomine Krijnse-Locker, Françoise Brochard-Wyart, Patricia Bassereau & Guillaume Duménil

Meningococci remodel the plasma membrane of host cells during infection. Here, Charles-Orszag et al. show that plasma membrane remodeling occurs independently of F-actin, along meningococcal type IV pili fibers, by a physical mechanism that they term 'one-dimensional' membrane wetting.

25 October 2018 | doi: 10.1038/s41467-018-06948-x
Cell biology  Cellular microbiology  Membrane biophysics  Pathogens 
Nature Communications
Frontiers in Cancer Science (FCS) 2018
More science events from
  Latest Author Corrections  
Author Correction: Biologically driven DOC release from peatlands during recovery from acidification OPEN
Hojeong Kang, Min Jung Kwon, Sunghyun Kim, Seunghoon Lee, Timothy G. Jones, Anna C. Johncock, Akira Haraguchi & Chris Freeman
31 October 2018 | doi: 10.1038/s41467-018-07157-2
Carbon cycle  Environmental chemistry  Microbial ecology  Wetlands ecology 

Author Correction: Jungle Express is a versatile repressor system for tight transcriptional control OPEN
Thomas L. Ruegg, Jose H. Pereira, Joseph C. Chen, Andy DeGiovanni, Pavel Novichkov, Vivek K. Mutalik, Giovani P. Tomaleri, Steven W. Singer, Nathan J. Hillson, Blake A. Simmons, Paul D. Adams & Michael P. Thelen
30 October 2018 | doi: 10.1038/s41467-018-07111-2
Applied microbiology  Synthetic biology  Transcriptional regulatory elements 
  Latest Publisher Corrections  
Publisher Correction: Female mice lacking Ftx lncRNA exhibit impaired X-chromosome inactivation and a microphthalmia-like phenotype OPEN
Yusuke Hosoi, Miki Soma, Hirosuke Shiura, Takashi Sado, Hidetoshi Hasuwa, Kuniya Abe, Takashi Kohda, Fumitoshi Ishino & Shin Kobayashi
31 October 2018 | doi: 10.1038/s41467-018-07100-5
Dosage compensation  Embryology  Epigenetic memory  Epigenetics 

Publisher Correction: Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer's disease OPEN
Rached Alkallas, Lisa Fish, Hani Goodarzi & Hamed S. Najafabadi
31 October 2018 | doi: 10.1038/s41467-018-07153-6
Dementia  Gene regulation  Gene regulatory networks  RNA decay 

Publisher Correction: Carrier density and disorder tuned superconductor-metal transition in a two-dimensional electron system OPEN
Zhuoyu Chen, Adrian G. Swartz, Hyeok Yoon, Hisashi Inoue, Tyler A. Merz, Di Lu, Yanwu Xie, Hongtao Yuan, Yasuyuki Hikita, Srinivas Raghu & Harold Y. Hwang
29 October 2018 | doi: 10.1038/s41467-018-06960-1
Superconducting devices  Superconducting properties and materials  Surfaces, interfaces and thin films 

Publisher Correction: Engineered bidirectional promoters enable rapid multi-gene co-expression optimization OPEN
Thomas Vogl, Thomas Kickenweiz, Julia Pitzer, Lukas Sturmberger, Astrid Weninger, Bradley W. Biggs, Eva-Maria Köhler, Armin Baumschlager, Jasmin Elgin Fischer, Patrick Hyden, Marlies Wagner, Martina Baumann, Nicole Borth, Martina Geier, Parayil Kumaran Ajikumar & Anton Glieder
29 October 2018 | doi: 10.1038/s41467-018-07112-1
Expression systems  Genetic vectors  High-throughput screening  Non-model organisms  Synthetic biology 

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