Nature Communications - 06 September 2017

Advertisement nature.com webcasts Nature Research Custom presents a webcast on: The future of nourishing the world sustainably Thursday, September 14 2017 8AM PDT | 11AM EDT| 4PM BST |5PM CEST Register for FREE Sponsored by:  Nestlé Research     Weekly Content Alert Nature Communications is now fully open access. Read more. 06 September 2017  Latest content: Articles Corrigendum Advertisement   Nature Biotechnology webcast on CAR-T cells: Latest advances and outstanding challenges Duration: 60 minutes with an opportunity to ask questions during the live broadcast! Date: Wednesday, September 20th, 2017 Time: 9 AM PDT| 12 PM EDT | 5 PM BST | 6 PM CEST  Register for FREE Sponsored by:  Lonza Journal homepage Recommend to library Web feed     Latest Articles View all Articles     Tunneling anisotropic magnetoresistance driven by magnetic phase transition OPEN X. Z. Chen, J. F. Feng, Z. C. Wang, J. Zhang, X. Y. Zhong, C. Song, L. Jin, B. Zhang, F. Li, M. Jiang, Y. Z. Tan, X. J. Zhou, G. Y. Shi, X. F. Zhou, X. D. Han, S. C. Mao, Y. H. Chen, X. F. Han & F. Pan Tunneling anisotropic magnetoresistance is promising for next generation memory devices but limited by the low efficiency and functioning temperature. Here the authors achieved 20% tunneling anisotropic magnetoresistance at room temperature in magnetic tunnel junctions with one α′-FeRh magnetic electrode. 06 September 2017 | doi: 10.1038/s41467-017-00290-4 Magnetic properties and materials  Phase transitions and critical phenomena  Spintronics  Surfaces, interfaces and thin films  Multivariate discovery and replication of five novel loci associated with Immunoglobulin G N-glycosylation OPEN Xia Shen, Lucija Klarić, Sodbo Sharapov, Massimo Mangino, Zheng Ning, Di Wu, Irena Trbojević-Akmačić, Maja Pučić-Baković, Igor Rudan, Ozren Polašek, Caroline Hayward, Timothy D. Spector, James F. Wilson, Gordan Lauc & Yurii S. Aulchenko Multivariate analysis methods can uncover the relationship between phenotypic measures characterised by modern omic techniques. Here the authors conduct a multivariate GWAS on IgG N-glycosylation phenotypes and identify 5 novel loci enriched in immune system genes. 06 September 2017 | doi: 10.1038/s41467-017-00453-3 Genome-wide association studies  High-throughput screening  Above-threshold scattering about a Feshbach resonance for ultracold atoms in an optical collider OPEN Milena S. J. Horvath, Ryan Thomas, Eite Tiesinga, Amita B. Deb & Niels Kjærgaard Studies on energy-dependent scattering of ultracold atoms were previously carried out near zero collision energies. Here, the authors observe a magnetic Feshbach resonance in ultracold Rb collisions for above-threshold energies and their method can also be used to detect higher partial wave resonances. 06 September 2017 | doi: 10.1038/s41467-017-00458-y Atomic and molecular collision processes  Matter waves and particle beams  Optical manipulation and tweezers  Ultracold gases  Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum  OPEN Danny Ionescu, Mina Bizic-Ionescu, Nicola Maio, Heribert Cypionka & Hans-Peter Grossart The cells of Achromatium bacteria are remarkably large and contain multiple chromosome copies. Here, Ionescu et al. show that chromosome copies within individual cells display high diversity, similar to that of bacterial communities, and contain tens of transposable elements. 06 September 2017 | doi: 10.1038/s41467-017-00342-9 Bacterial evolution  Bacterial genomics  Cellular microbiology  Microbial ecology  Silicon quantum processor with robust long-distance qubit couplings OPEN Guilherme Tosi, Fahd A. Mohiyaddin, Vivien Schmitt, Stefanie Tenberg, Rajib Rahman, Gerhard Klimeck & Andrea Morello Quantum computers will require a large network of coherent qubits, connected in a noise-resilient way. Tosi et al. present a design for a quantum processor based on electron-nuclear spins in silicon, with electrical control and coupling schemes that simplify qubit fabrication and operation. 06 September 2017 | doi: 10.1038/s41467-017-00378-x Quantum information  Qubits  APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism OPEN Ting-Wen Chen, Chi-Ching Lee, Hsuan Liu, Chi-Sheng Wu, Curtis R. Pickering, Po-Jung Huang, Jing Wang, Ian Yi-Feng Chang, Yuan-Ming Yeh, Chih-De Chen, Hsin-Pai Li, Ji-Dung Luo, Bertrand Chin-Ming Tan, Timothy En Haw Chan, Chuen Hsueh, Lichieh Julie Chu, Yi-Ting Chen, Bing Zhang, Chia-Yu Yang, Chih-Ching Wu et al. Oral squamous cell carcinoma is a prevalent malignancy in Taiwan. Here, the authors show that OSCC in Taiwanese show a frequent deletion polymorphism in the cytidine deaminases gene cluster APOBEC3 resulting in increased expression of A3A, which is shown to be of clinical prognostic relevance. 06 September 2017 | doi: 10.1038/s41467-017-00493-9 Cancer genomics  Oral cancer  Personalized medicine  Prognostic markers  Enoyl-CoA hydratase-1 regulates mTOR signaling and apoptosis by sensing nutrients OPEN Ya-Kun Zhang, Yuan-Yuan Qu, Yan Lin, Xiao-Hui Wu, Hou-Zao Chen, Xu Wang, Kai-Qiang Zhou, Yun Wei, Fushen Guo, Cui-Fang Yao, Xia-Di He, Li-Xia Liu, Chen Yang, Zong-Yuan Guan, Shi-Dong Wang, Jianyuan Zhao, De-Pei Liu, Shi-Min Zhao & Wei Xu Overnutrition has been linked to increased risk of cancer. Here, the authors show that exceeding nutrients suppress Enoyl-CoA hydratase-1 (ECHS1) activity by inducing its acetylation resulting in accumulation of fatty acids and branched-chain amino acids and oncogenic mTOR activation. 06 September 2017 | doi: 10.1038/s41467-017-00489-5 Acetylation  Cancer metabolism  Nutrient signalling  Reconstructing cell cycle and disease progression using deep learning OPEN Philipp Eulenberg, Niklas Köhler, Thomas Blasi, Andrew Filby, Anne E. Carpenter, Paul Rees, Fabian J. Theis & F. Alexander Wolf The interpretation of information-rich, high-throughput single-cell data is a challenge requiring sophisticated computational tools. Here the authors demonstrate a deep convolutional neural network that can classify cell cycle status on-the-fly. 06 September 2017 | doi: 10.1038/s41467-017-00623-3 Cell division  Image processing  Machine learning  HSP90 inhibition enhances cancer immunotherapy by upregulating interferon response genes OPEN Rina M. Mbofung, Jodi A. McKenzie, Shruti Malu, Min Zhang, Weiyi Peng, Chengwen Liu, Isere Kuiatse, Trang Tieu, Leila Williams, Seram Devi, Emily Ashkin, Chunyu Xu, Lu Huang, Minying Zhang, Amjad H. Talukder, Satyendra C. Tripathi, Hiep Khong, Nikunj Satani, Florian L. Muller, Jason Roszik et al. Many patients fail to respond to T cell based immunotherapies. Here, the authors, through a high-throughput screening, identify HSP90 inhibitors as a class of preferred drugs for treatment combination with immunotherapy. 06 September 2017 | doi: 10.1038/s41467-017-00449-z Cancer immunotherapy  Targeted therapies  Assay to visualize specific protein oxidation reveals spatio-temporal regulation of SHP2 OPEN Ryouhei Tsutsumi, Jana Harizanova, Rabea Stockert, Katrin Schröder, Philippe I. H. Bastiaens & Benjamin G. Neel Protein-tyrosine phosphatases (PTPs) are thought to be major targets of receptor-activated reactive oxygen species (ROS). Here the authors describe a method that allows the localized visualization of oxidized intermediates of PTPs inside cells during signaling, and provide support for the “redoxosome” model. 06 September 2017 | doi: 10.1038/s41467-017-00503-w Endosomes  Fluorescence imaging  Growth factor signalling  Post-translational modifications  Non-parametric genetic prediction of complex traits with latent Dirichlet process regression models OPEN Ping Zeng & Xiang Zhou Genetic prediction of complex traits with polygenic architecture has wide application from animal breeding to disease prevention. Here, Zeng and Zhou develop a non-parametric genetic prediction method based on latent Dirichlet Process regression models. 06 September 2017 | doi: 10.1038/s41467-017-00470-2 Computational models  Genome-wide association studies  An in-silico approach to predict and exploit synthetic lethality in cancer metabolism OPEN Iñigo Apaolaza, Edurne San José-Eneriz, Luis Tobalina, Estíbaliz Miranda, Leire Garate, Xabier Agirre, Felipe Prósper & Francisco J. Planes Exploiting synthetic lethality is a promising approach for cancer therapy. Here, the authors present an approach to identifying such interactions by finding genetic minimal cut sets (gMCSs) that block cancer proliferation, and apply it to study the lethality of RRM1 inhibition in multiple myeloma. 06 September 2017 | doi: 10.1038/s41467-017-00555-y Biochemical reaction networks  Cancer metabolism  Towards designer organelles by subverting the peroxisomal import pathway OPEN Laura L. Cross, Rupesh Paudyal, Yasuko Kamisugi, Alan Berry, Andrew C. Cuming, Alison Baker & Stuart L. Warriner Designer organelles could allow the isolation of synthetic biological pathways from endogenous components of the host cell. Here the authors engineer a peroxisomal protein import pathway orthogonal to the naturally occurring system. 06 September 2017 | doi: 10.1038/s41467-017-00487-7 Molecular engineering in plants  Protein design  Protein trafficking in plants  Synthetic biology  The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan OPEN Nitish Mittal, Joao C. Guimaraes, Thomas Gross, Alexander Schmidt, Arnau Vina-Vilaseca, Danny D. Nedialkova, Florian Aeschimann, Sebastian A. Leidel, Anne Spang & Mihaela Zavolan The transcription factor Gcn4 is known to regulate yeast amino acid synthesis. Here, the authors show that Gcn4 also acts as a repressor of protein biosynthesis in a range of conditions that enhance yeast lifespan, such as ribosomal protein knockout, calorie restriction or mTOR inhibition. 06 September 2017 | doi: 10.1038/s41467-017-00539-y Ageing  Gene expression  Ribosome  Saccharomyces cerevisiae  Alkaline earth metal vanadates as sodium-ion battery anodes OPEN Xiaoming Xu, Chaojiang Niu, Manyi Duan, Xuanpeng Wang, Lei Huang, Junhui Wang, Liting Pu, Wenhao Ren, Changwei Shi, Jiasheng Meng, Bo Song & Liqiang Mai The development of suitable anode materials is essential to advance sodium-ion battery technologies. Here the authors report that alkaline earth metal vanadates are promising candidates due to the favorable electrochemical properties and interesting sodium-storage mechanism. 06 September 2017 | doi: 10.1038/s41467-017-00211-5 Batteries  Nanowires  Reactivation of dead sulfide species in lithium polysulfide flow battery for grid scale energy storage OPEN Yang Jin, Guangmin Zhou, Feifei Shi, Denys Zhuo, Jie Zhao, Kai Liu, Yayuan Liu, Chenxi Zu, Wei Chen, Rufan Zhang, Xuanyi Huang & Yi Cui Lithium polysulfide batteries suffer from the precipitation of insoluble and irreversible sulfide species on the surface of carbon and lithium. Here the authors show a reactivation strategy by a reaction with cheap sulfur powder under stirring and heating to recover the cell capacity. 06 September 2017 | doi: 10.1038/s41467-017-00537-0 Batteries  Chemical engineering  Electron paramagnetic resonance microscopy using spins in diamond under ambient conditions OPEN David A. Simpson, Robert G. Ryan, Liam T. Hall, Evgeniy Panchenko, Simon C. Drew, Steven Petrou, Paul S. Donnelly, Paul Mulvaney & Lloyd C. L. Hollenberg Electron paramagnetic resonance spectroscopy has important scientific and medical uses but improving the resolution of conventional methods requires cryogenic, vacuum environments. Simpson et al. show nitrogen vacancy centres can be used for sub-micronmetre imaging with improved sensitivity in ambient conditions. 06 September 2017 | doi: 10.1038/s41467-017-00466-y Optical properties of diamond  Imaging  Promoting Drp1-mediated mitochondrial fission in midlife prolongs healthy lifespan of Drosophila melanogaster  OPEN Anil Rana, Matheus P. Oliveira, Andy V. Khamoui, Ricardo Aparicio, Michael Rera, Harry B. Rossiter & David W. Walker Mitochondrial fission and fusion are important mechanisms to maintain mitochondrial function. Here, the authors report that middle-aged flies have more elongated, or ‘hyper-fused’ mitochondria, and show that induction of mitochondrial fission in midlife, but not in early life, extends the health and life of flies. 06 September 2017 | doi: 10.1038/s41467-017-00525-4 Ageing  Drosophila  Mitochondria  Ultrafast isomerization in acetylene dication after carbon K-shell ionization OPEN Zheng Li, Ludger Inhester, Chelsea Liekhus-Schmaltz, Basile F. E. Curchod, James W. Snyder, Nikita Medvedev, James Cryan, Timur Osipov, Stefan Pabst, Oriol Vendrell, Phil Bucksbaum & Todd J. Martinez The timescale of isomerization in molecules involving ultrafast migration of constituent atoms is difficult to measure. Here the authors report that sub-100 fs isomerization time on acetylene dication in lower electronic states is not possible and point to misinterpretation of recent experimental results. 06 September 2017 | doi: 10.1038/s41467-017-00426-6 Atomic and molecular interactions with photons  Chemical physics  Molecular dynamics  Hydrogen bond based smart polymer for highly selective and tunable capture of multiply phosphorylated peptides OPEN Guangyan Qing, Qi Lu, Xiuling Li, Jing Liu, Mingliang Ye, Xinmiao Liang & Taolei Sun Capture of low-abundance multiply phosphorylated peptides (MPPs) is difficult due to limitation of enrichment materials and their interactions with phosphates. Here the authors show, a smart polymer driven by specific but tunable hydrogen bonding interactions can differentially complex with MPPs, singly phosphorylated and non-modified peptides. 06 September 2017 | doi: 10.1038/s41467-017-00464-0 Biosurfaces  Polymer chemistry  Polymers  Protein enrichment  Ratiometric Matryoshka biosensors from a nested cassette of green- and orange-emitting fluorescent proteins OPEN Cindy Ast, Jessica Foret, Luke M. Oltrogge, Roberto De Michele, Thomas J. Kleist, Cheng-Hsun Ho & Wolf B. Frommer Single fluorescent protein biosensors are susceptible to expression and instrumental artifacts. Here Ast et al. describe a dual fluorescent protein design whereby a reference fluorescent protein is nested within a reporter fluorescent protein to control for such artifacts while preserving sensitivity and dynamic range. 05 September 2017 | doi: 10.1038/s41467-017-00400-2 Ca2+ imaging  Cell biology  Fluorescent proteins  Plant cell biology  Observing the oxidation of platinum OPEN Matthijs A. Spronsen, Joost W. M. Frenken & Irene M. N. Groot Improving platinum as an oxidation catalyst requires understanding its structure under catalytic conditions. Here, the authors discover that catalytically important surface oxides form only when Pt is exposed to high pressure and temperature, highlighting the need to study catalysts in realistic environments. 05 September 2017 | doi: 10.1038/s41467-017-00643-z Chemical physics  Heterogeneous catalysis  Scanning probe microscopy  Surfaces, interfaces and thin films  pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification OPEN Ming-Qi Liu, Wen-Feng Zeng, Pan Fang, Wei-Qian Cao, Chao Liu, Guo-Quan Yan, Yang Zhang, Chao Peng, Jian-Qiang Wu, Xiao-Jin Zhang, Hui-Jun Tu, Hao Chi, Rui-Xiang Sun, Yong Cao, Meng-Qiu Dong, Bi-Yun Jiang, Jiang-Ming Huang, Hua-Li Shen, Catherine C. L. Wong, Si-Min He et al. Protein glycosylation is a heterogeneous post-translational modification that generates greater proteomic diversity that is difficult to analyze. Here the authors describe pGlyco 2.0, a workflow for the precise one step identification of intact N-glycopeptides at the proteome scale. 05 September 2017 | doi: 10.1038/s41467-017-00535-2 Bioinformatics  Glycomics  Mass spectrometry  Proteomic analysis  Land-locked mammalian Golgi reveals cargo transport between stable cisternae OPEN Myun Hwa Dunlop, Andreas M. Ernst, Lena K. Schroeder, Derek K. Toomre, Grégory Lavieu & James E. Rothman The different composition of Golgi cisternae gave rise to two different models for intra-Golgi traffic: one where stable cisternae communicate via vesicles and another one where cisternae biochemically mature to ensure anterograde transport. Here, the authors provide evidence in support of the stable compartments model. 05 September 2017 | doi: 10.1038/s41467-017-00570-z Golgi  Secretion  Biosynthesis of the nosiheptide indole side ring centers on a cryptic carrier protein NosJ OPEN Wei Ding, Wenjuan Ji, Yujie Wu, Runze Wu, Wan-Qiu Liu, Tianlu Mo, Junfeng Zhao, Xiaoyan Ma, Wei Zhang, Ping Xu, Zixin Deng, Boping Tang, Yi Yu & Qi Zhang Thiopeptides such as nosiheptide are clinically-interesting antimicrobial natural products. Here the authors show the functional dissection of a series of enzymes involved in nosiheptide biosynthesis, revealing a unique biosynthetic pathway that centers on a previously-unknown carrier protein. 05 September 2017 | doi: 10.1038/s41467-017-00439-1 Biochemistry  Microbiology  Integrative genomics of microglia implicates DLG4 (PSD95) in the white matter development of preterm infants OPEN Michelle L. Krishnan, Juliette Steenwinckel, Anne-Laure Schang, Jun Yan, Johanna Arnadottir, Tifenn Charpentier, Zsolt Csaba, Pascal Dournaud, Sara Cipriani, Constance Auvynet, Luigi Titomanlio, Julien Pansiot, Gareth Ball, James P. Boardman, Andrew J. Walley, Alka Saxena, Ghazala Mirza, Bobbi Fleiss, A. David Edwards, Enrico Petretto et al. Inflammation mediated by microglia plays a key role in brain injury associated with preterm birth, but little is known about the microglial response in preterm infants. Here, the authors integrate molecular and imaging data from animal models and preterm infants, and find that microglial expression of DLG4 plays a role. 05 September 2017 | doi: 10.1038/s41467-017-00422-w Experimental models of disease  Gene regulatory networks  Glial development  Paediatric research  Signalling strength determines proapoptotic functions of STING OPEN Muhammet F. Gulen, Ute Koch, Simone M. Haag, Fabian Schuler, Lionel Apetoh, Andreas Villunger, Freddy Radtke & Andrea Ablasser The cGAS/STING signalling pathway is responsible for sensing intracellular DNA and activating downstream inflammatory genes. Here the authors show mouse primary T cells and T leukaemia are hyperresponsive to STING agonist, and this strong STING signalling is associated with apoptosis induction. 05 September 2017 | doi: 10.1038/s41467-017-00573-w Cell death and immune response  Immune cell death  Innate immunity  Signal transduction  Endocytic sorting motif interactions involved in Nef-mediated downmodulation of CD4 and CD3 OPEN Santiago Manrique, Daniel Sauter, Florian A. Horenkamp, Sebastian Lülf, Hangxing Yu, Dominik Hotter, Kanchan Anand, Frank Kirchhoff & Matthias Geyer HIV and simian immunodeficiency virus (SIV) Nef proteins both stimulate the clathrin-mediated endocytosis of CD4 but differ in downmodulation of the immune receptor CD3. Here, the authors present the structure of SIV Nef bound to the ExxxLM motif of another Nef molecule, which allows them to propose a model how Nef recognizes these motifs in CD3 and CD4. 05 September 2017 | doi: 10.1038/s41467-017-00481-z Infectious diseases  X-ray crystallography  Unpredictability of escape trajectory explains predator evasion ability and microhabitat preference of desert rodents OPEN Talia Y. Moore, Kimberly L. Cooper, Andrew A. Biewener & Ramanarayan Vasudevan Biomechanical understanding of animal gait and maneuverability has primarily been limited to species with more predictable, steady-state movement patterns. Here, the authors develop a method to quantify movement predictability, and apply the method to study escape-related movement in several species of desert rodents. 05 September 2017 | doi: 10.1038/s41467-017-00373-2 Applied mathematics  Behavioural ecology  Biomechanics  Exact broadband excitation of two-level systems by mapping spins to springs OPEN Jr-Shin Li, Justin Ruths & Steffen J. Glaser Coherent control of two-level systems is crucial for achieving fidelity in spectroscopy and quantum computing, but inherent nonlinearities and parameter variation have, to date, required an approximate, numerical approach. Here, Li et al. show how to map a spin ensemble to a spring model so analytic pulses can be designed using linear methods. 05 September 2017 | doi: 10.1038/s41467-017-00441-7 NMR spectroscopy  Theoretical physics  Internalized TSH receptors en route to the TGN induce local Gs-protein signaling and gene transcription OPEN Amod Godbole, Sandra Lyga, Martin J. Lohse & Davide Calebiro Recent investigations suggest that G-protein-coupled receptors (GPCRs) can signal during intracellular trafficking. Here the authors use fluorescence microscopy approaches to directly visualize and investigate functional consequences of GPCR-mediated signaling at the Golgi/trans-Golgi network. 05 September 2017 | doi: 10.1038/s41467-017-00357-2 Fluorescence imaging  G protein-coupled receptors  Hormone receptors  Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation OPEN Nathan Harmston, Elizabeth Ing-Simmons, Ge Tan, Malcolm Perry, Matthias Merkenschlager & Boris Lenhard Metazoan genomes contain many clusters of conserved noncoding elements. Here, the authors provide evidence that these clusters coincide with distinct topologically associating domains in humans and Drosophila, revealing a conserved regulatory genomic architecture. 05 September 2017 | doi: 10.1038/s41467-017-00524-5 Data integration  Evolutionary developmental biology  Gene regulation  Emergence of native peptide sequences in prebiotic replication networks OPEN Jayanta Nanda, Boris Rubinov, Denis Ivnitski, Rakesh Mukherjee, Elina Shtelman, Yair Motro, Yifat Miller, Nathaniel Wagner, Rivka Cohen-Luria & Gonen Ashkenasy The synthesis of biopolymers in living cells is perfected by complex machinery, however this was not the case on early Earth. Here the authors show the role of non-enzymatic replication in the enrichment of certain products within prebiotically relevant mixtures. 05 September 2017 | doi: 10.1038/s41467-017-00463-1 Chemical origin of life  Supramolecular chemistry  Phenotype-driven precision oncology as a guide for clinical decisions one patient at a time OPEN Shumei Chia, Joo-Leng Low, Xiaoqian Zhang, Xue-Lin Kwang, Fui-Teen Chong, Ankur Sharma, Denis Bertrand, Shen Yon Toh, Hui-Sun Leong, Matan T. Thangavelu, Jacqueline S. G. Hwang, Kok-Hing Lim, Thakshayeni Skanthakumar, Hiang-Khoon Tan, Yan Su, Siang Hui Choo, Hannes Hentze, Iain B. H. Tan, Alexander Lezhava, Patrick Tan et al. Treatment response in patient-derived models may serve as a biomarker for response in the clinic. Here, the authors use paired patient-derived mouse xenografts and patient-derived primary culture models from head and neck squamous cell carcinomas, including metastasis, as models for high-throughput screening of anti-cancer drugs. 05 September 2017 | doi: 10.1038/s41467-017-00451-5 Cancer models  Cancer therapy  Liver X receptors constrain tumor development and metastasis dissemination in PTEN-deficient prostate cancer OPEN Anthony Alioui, Julie Dufour, Valerio Leoni, Anke Loregger, Martina Moeton, Luigi Iuliano, Chiara Zerbinati, Amandine Septier, Pierre Val, Allan Fouache, Vincenzo Russo, David H. Volle, Jean-Marc A. Lobaccaro, Noam Zelcer & Silvère Baron Treatment of prostate cancer, especially in its advanced stage, is still challenging; therefore, strategies to prevent metastatic dissemination are of great interest. Here the authors reveal a crucial role for liver X receptors in suppressing prostate carcinogenesis and metastatic progression in PTEN-null tumors. 05 September 2017 | doi: 10.1038/s41467-017-00508-5 Cancer metabolism  Prostate  Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant OPEN Jennifer L. Bowen, Patrick J. Kearns, Jarrett E. K. Byrnes, Sara Wigginton, Warwick J. Allen, Michael Greenwood, Khang Tran, Jennifer Yu, James T. Cronin & Laura A. Meyerson Environmental factors often outweigh host heritable factors in structuring host-associated microbiomes. Here, Bowen et al. show that host lineage is crucial for determination of rhizosphere bacterial communities in Phragmites australis, a globally distributed invasive plant. 05 September 2017 | doi: 10.1038/s41467-017-00626-0 Invasive species  Microbial ecology  Microbiome  Symbiosis  Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer OPEN Matteo D′Antonio, Donate Weghorn, Agnieszka D′Antonio-Chronowska, Florence Coulet, Katrina M. Olson, Christopher DeBoever, Frauke Drees, Angelo Arias, Hakan Alakus, Andrea L. Richardson, Richard B. Schwab, Emma K. Farley, Shamil R. Sunyaev & Kelly A Frazer Cancer driver mutations can occur within noncoding genomic sequences. Here, the authors develop a statistical approach to identify candidate noncoding driver mutations in DNase I hypersensitive sites in breast cancer and experimentally demonstrate they are regulatory elements of known cancer genes. 05 September 2017 | doi: 10.1038/s41467-017-00100-x Breast cancer  Cancer genomics  Next-generation sequencing  Transcriptional regulatory elements  Cre/lox-assisted non-invasive in vivo tracking of specific cell populations by positron emission tomography OPEN Non-invasive cell tracking is a powerful method to visualize cells in vivo under physiological and pathophysiological conditions. Here Thunemann et al. generate a mouse model for in vivo tracking and quantification of specific cell types by combining a PET reporter gene with Cre-dependent activation that can be exploited for any cell population for which a Cre mouse line is available. 05 September 2017 | doi: 10.1038/s41467-017-00482-y Allergy  Experimental models of disease  Myocardial infarction  Positron-emission tomography  Transgenic organisms  Decidualisation and placentation defects are a major cause of age-related reproductive decline OPEN Laura Woods, Vicente Perez-Garcia, Jens Kieckbusch, Xiaoqiu Wang, Francesco DeMayo, Francesco Colucci & Myriam Hemberger Advanced maternal age has been associated with lower reproductive success and higher risk of pregnancy complications. Here the authors show that maternal ageing-related embryonic abnormalities in mouse are caused by decidualisation and placentation defects that can be rescued by transferring the embryo from an old to a young uterus. 05 September 2017 | doi: 10.1038/s41467-017-00308-x Ageing  Embryogenesis  Reproductive biology  A potent series targeting the malarial cGMP-dependent protein kinase clears infection and blocks transmission OPEN David A. Baker, Lindsay B. Stewart, Jonathan M. Large, Paul W. Bowyer, Keith H. Ansell, María B. Jiménez-Díaz, Majida El Bakkouri, Kristian Birchall, Koen J. Dechering, Nathalie S. Bouloc, Peter J. Coombs, David Whalley, Denise J. Harding, Ela Smiljanic-Hurley, Mary C. Wheldon, Eloise M. Walker, Johannes T. Dessens, María José Lafuente, Laura M. Sanz, Francisco-Javier Gamo et al. Protein kinases are promising drug targets for treatment of malaria. Here, starting with a medicinal chemistry approach, Baker et al. generate an imidazopyridine that selectively targets Plasmodium falciparum PKG, inhibits blood stage parasite growth in vitro and in mice and blocks transmission to mosquitoes. 05 September 2017 | doi: 10.1038/s41467-017-00572-x Drug development  Drug discovery and development  Kinases  Malaria  Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities OPEN Elena Butaitė, Michael Baumgartner, Stefan Wyder & Rolf Kümmerli Lab strains of Pseudomonas are model systems for the evolution of cooperation over public goods (iron-scavenging siderophores). Here, Butaitė et al. add ecological and evolutionary insight into this system by showing that cheating and resistance to cheating both shape competition for iron in natural Pseudomonas communities. 04 September 2017 | doi: 10.1038/s41467-017-00509-4 Evolutionary ecology  Microbial ecology  Social evolution  Genetically engineered red cells expressing single domain camelid antibodies confer long-term protection against botulinum neurotoxin OPEN Nai-Jia Huang, Novalia Pishesha, Jean Mukherjee, Sicai Zhang, Rhogerry Deshycka, Valentino Sudaryo, Min Dong, Charles B. Shoemaker & Harvey F. Lodish The therapeutic use of single-chain antibodies (VHHs) is limited by their short half-life in the circulation. Here the authors engineer mouse and human red blood cells to express VHHs against botulinum neurotoxin A (BoNT/A) on their surface and show that an infusion of these cells into mice confers long lasting protection against a high dose of BoNT/A. 04 September 2017 | doi: 10.1038/s41467-017-00448-0 Antibody fragment therapy  Cell therapies  Genetic engineering  Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes OPEN Hoang Long Pham, Adison Wong, Niying Chua, Wei Suong Teo, Wen Shan Yew & Matthew Wook Chang Cells are exposed to shifts in environmental pH, which direct their metabolism and behavior. Here the authors design pH-sensing riboswitches to create a gene expression program, digitalize the system to respond to a narrow pH range and apply it to evolve host cells with improved tolerance to a variety of organic acids. 04 September 2017 | doi: 10.1038/s41467-017-00511-w Biotechnology  Synthetic biology  Demonstration of sub-luminal propagation of single-cycle terahertz pulses for particle acceleration OPEN D. A. Walsh, D. S. Lake, E. W. Snedden, M. J. Cliffe, D. M. Graham & S. P. Jamison Controlled generation of terahertz radiation with subluminal phase velocities is a key issue in laser-driven particle acceleration. Here, the authors demonstrate a travelling-source approach utilizing the group-to-phase front conversion to overcome the sub-luminal propagation limit. 04 September 2017 | doi: 10.1038/s41467-017-00490-y Terahertz optics  Ultrafast photonics  Convergent Akt activation drives acquired EGFR inhibitor resistance in lung cancer OPEN Kirstine Jacobsen, Jordi Bertran-Alamillo, Miguel Angel Molina, Cristina Teixidó, Niki Karachaliou, Martin Haar Pedersen, Josep Castellví, Mónica Garzón, Carles Codony-Servat, Jordi Codony-Servat, Ana Giménez-Capitán, Ana Drozdowskyj, Santiago Viteri, Martin R. Larsen, Ulrik Lassen, Enriqueta Felip, Trever G. Bivona, Henrik J. Ditzel & Rafael Rosell EGFR-mutant non-small cell lung cancer are often resistant to EGFR tyrosine kinase inhibitor treatment. In this study, the authors show that resistant tumors display high Akt activation and that a combined treatment with AKT inhibitors causes synergistic tumour growth inhibition in vitro and in vivo. 04 September 2017 | doi: 10.1038/s41467-017-00450-6 Cancer therapeutic resistance  Non-small-cell lung cancer  Durable and self-hydrating tungsten carbide-based composite polymer electrolyte membrane fuel cells OPEN Weiqing Zheng, Liang Wang, Fei Deng, Stephen A. Giles, Ajay K. Prasad, Suresh G. Advani, Yushan Yan & Dionisios G. Vlachos The proton conductivity of polymer electrolyte membranes in fuel cells dictates their performance, but requires sufficient water management. Here, the authors report a simple method to produce well-dispersed transition metal carbide nanoparticles as additives to enhance the performance of Nafion membranes in fuel cells. 04 September 2017 | doi: 10.1038/s41467-017-00507-6 Electrocatalysis  Fuel cells  Herbivores rescue diversity in warming tundra by modulating trait-dependent species losses and gains OPEN Elina Kaarlejärvi, Anu Eskelinen & Johan Olofsson Warming can reduce plant diversity but it is unclear which species will be lost or gained under interacting global changes. Kaarlejärvi et al. manipulate temperature, herbivory and nutrients in a tundra system and find that herbivory maintains diversity under warming by reducing species losses and promoting gains. 04 September 2017 | doi: 10.1038/s41467-017-00554-z Biodiversity  Climate-change ecology  Community ecology  Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia OPEN Sachith Mettananda, Chris A. Fisher, Deborah Hay, Mohsin Badat, Lynn Quek, Kevin Clark, Philip Hublitz, Damien Downes, Jon Kerry, Matthew Gosden, Jelena Telenius, Jackie A. Sloane-Stanley, Paula Faustino, Andreia Coelho, Jessica Doondeea, Batchimeg Usukhbayar, Paul Sopp, Jacqueline A. Sharpe, Jim R. Hughes, Paresh Vyas et al. β-thalassemia is characterised by the presence of an excess of α-globin chains, which contribute to erythrocyte pathology. Here the authors use CRISP/Cas9 to reduce α-globin expression in hematopoietic precursors, and show effectiveness in xenograft assays in mice. 04 September 2017 | doi: 10.1038/s41467-017-00479-7 Anaemia  CRISPR-Cas9 genome editing  Haematopoietic stem cells  Sirt6 deficiency exacerbates podocyte injury and proteinuria through targeting Notch signaling OPEN Min Liu, Kaili Liang, Junhui Zhen, Meng Zhou, Xiaojie Wang, Ziying Wang, Xinbing Wei, Yan Zhang, Yu Sun, Zhuanli Zhou, Hua Su, Chun Zhang, Ningjun Li, Chengjiang Gao, Jun Peng & Fan Yi Podocytes are essential components of the renal glomerular filtration barrier and podocyte dysfunction leads to proteinuric kidney disease. Here Liu et al. show that Sirt6 protects podocytes from apoptosis and inflammation by increasing autophagic flux through inhibition of the Notch pathway. 04 September 2017 | doi: 10.1038/s41467-017-00498-4 Glomerular diseases  Podocytes  Stromal and epithelial transcriptional map of initiation progression and metastatic potential of human prostate cancer OPEN Svitlana Tyekucheva, Michaela Bowden, Clyde Bango, Francesca Giunchi, Ying Huang, Chensheng Zhou, Arrigo Bondi, Rosina Lis, Mieke Van Hemelrijck, Ove Andrén, Sven-Olof Andersson, R. William Watson, Stephen Pennington, Stephen P. Finn, Neil E. Martin, Meir J. Stampfer, Giovanni Parmigiani, Kathryn L. Penney, Michelangelo Fiorentino, Lorelei A. Mucci et al. Stromal cells contribute to tumor development but the mechanisms regulating this process are still unclear. Here the authors analyze gene expression profiles in the prostate and show that stromal gene signature changes ahead of the epithelial gene signature as prostate cancer initiates and progresses. 04 September 2017 | doi: 10.1038/s41467-017-00460-4 Cancer microenvironment  Microarrays  Prostate cancer  Identification of HSP90 inhibitors as a novel class of senolytics OPEN The accumulation of senescent cells is thought to contribute to the age-associated decline in tissue function. Here, the authors identify HSP90 inhibitors as a new class of senolytic compounds in an in vitro screening and show that administration of a HSP90 inhibitor reduces age-related symptoms in progeroid mice. 04 September 2017 | doi: 10.1038/s41467-017-00314-z Ageing  High-throughput screening  Non-alcoholic fatty liver disease  Senescence  Higher-order assembly of crystalline cylindrical micelles into membrane-extendable colloidosomes OPEN Hongjing Dou, Mei Li, Yan Qiao, Robert Harniman, Xiaoyu Li, Charlotte E. Boott, Stephen Mann & Ian Manners Functional nanoscale objects can be prepared via crystallization-driven self-assembly of diblock copolymers. Here the authors show the self-assembly of crystalline block copolymers into size-specific cylindrical micelles for the hierarchical construction of mechanically robust colloidosomes with a range of membrane textures. 04 September 2017 | doi: 10.1038/s41467-017-00465-z Colloids  Molecular capsules  Molecular self-assembly  Self-assembly  The cytoplasmic nuclear receptor RARγ controls RIP1 initiated cell death when cIAP activity is inhibited OPEN Qing Xu, Siriporn Jitkaew, Swati Choksi, Chamila Kadigamuwa, Jianhui Qu, Moran Choe, Jonathan Jang, Chengyu Liu & Zheng-gang Liu The molecular switch between how tumour necrosis factor (TNF) controls inflammation versus cell death is less well defined. Here, the authors show that the nuclear receptor retinoic acid receptor gamma is released from the nucleus to disrupt TNF initiated cell death complexes in the cytoplasm. 04 September 2017 | doi: 10.1038/s41467-017-00496-6 Apoptosis  Necroptosis  Dynamic plasticity in phototransduction regulates seasonal changes in color perception OPEN Tsuyoshi Shimmura, Tomoya Nakayama, Ai Shinomiya, Shoji Fukamachi, Masaki Yasugi, Eiji Watanabe, Takayuki Shimo, Takumi Senga, Toshiya Nishimura, Minoru Tanaka, Yasuhiro Kamei, Kiyoshi Naruse & Takashi Yoshimura Animal coloration and behavior can change seasonally, but it is unclear if visual sensitivity to color shifts as well. Here, Shimmura et al. show that medaka undergo seasonal behavioral change accompanied by altered expression of opsin genes, resulting in reduced visual sensitivity to mates during winter-like conditions. 04 September 2017 | doi: 10.1038/s41467-017-00432-8 Animal behaviour  Behavioural ecology  Circadian rhythms and sleep  Sensory processing  White light emission from a single organic molecule with dual phosphorescence at room temperature OPEN Zikai He, Weijun Zhao, Jacky W. Y. Lam, Qian Peng, Huili Ma, Guodong Liang, Zhigang Shuai & Ben Zhong Tang The development of single molecule white light-emitters is extremely challenging for pure phosphorescent metal-free systems at room temperature. Here the authors show a single pure organic room temperature phosphor, 4-chlorobenzoyldibenzothiophene, utilizing the emission from both T1 and T2 states. 04 September 2017 | doi: 10.1038/s41467-017-00362-5 Materials for optics  Optical materials  Optical spectroscopy  Thermal conductivity and air-mediated losses in periodic porous silicon membranes at high temperatures OPEN B. Graczykowski, A. El Sachat, J. S. Reparaz, M. Sledzinska, M. R. Wagner, E. Chavez-Angel, Y. Wu, S. Volz, Y. Wu, F. Alzina & C. M. Sotomayor Torres Nanostructuring of silicon allows acoustic phonon engineering, but the mechanism of related thermal transport in these structures is not fully understood. Here, the authors study the heat dissipation in silicon membranes with periodic nanoholes and show the importance of incoherent scattering. 04 September 2017 | doi: 10.1038/s41467-017-00115-4 Nanoscale materials  Thermodynamics  Rechargeable aqueous zinc-manganese dioxide batteries with high energy and power densities OPEN Ning Zhang, Fangyi Cheng, Junxiang Liu, Liubin Wang, Xinghui Long, Xiaosong Liu, Fujun Li & Jun Chen The development of rechargeable aqueous zinc batteries are challenging but promising for energy storage applications. With a mild-acidic triflate electrolyte, here the authors show a high-performance Zn-MnO2 battery in which the MnO2 cathode undergoes Zn2+ (de)intercalation. 01 September 2017 | doi: 10.1038/s41467-017-00467-x Batteries  Energy  A prophage tail-like protein is deployed by Burkholderia bacteria to feed on fungi OPEN Durga Madhab Swain, Sunil Kumar Yadav, Isha Tyagi, Rahul Kumar, Rajeev Kumar, Srayan Ghosh, Joyati Das & Gopaljee Jha Some bacteria can feed on live fungi through unclear mechanisms. Here, the authors show that a T3SS-secreted protein, which is homologous to phage tail proteins, allows a Burkholderia gladioli strain to kill and feed on various fungal species. 01 September 2017 | doi: 10.1038/s41467-017-00529-0 Antifungal agents  Bacterial secretion  Fungi  Microbial ecology  IgSF21 promotes differentiation of inhibitory synapses via binding to neurexin2α OPEN Yuko Tanabe, Yusuke Naito, Cristina Vasuta, Alfred Kihoon Lee, Youssouf Soumounou, Michael W. Linhoff & Hideto Takahashi Molecular mechanisms regulating the development of inhibitory synapses are poorly understood. Here the authors show that IgSF21 interacts with neurexin2α to induce presynaptic differentiation of inhibitory synapses, and that mice lacking IgSF21 exhibit deficits in inhibitory synaptic transmission. 01 September 2017 | doi: 10.1038/s41467-017-00333-w Cellular neuroscience  Molecular neuroscience  Direct imaging of delayed magneto-dynamic modes induced by surface acoustic waves OPEN Michael Foerster, Ferran Macià, Nahuel Statuto, Simone Finizio, Alberto Hernández-Mínguez, Sergi Lendínez, Paulo V. Santos, Josep Fontcuberta, Joan Manel Hernàndez, Mathias Kläui & Lucia Aballe Understanding the effects of local dynamic strain on magnetization may help the development of magnetic devices. Foerster et al. demonstrate stroboscopic imaging that allows the observation of both strain and magnetization dynamics in nickel when surface acoustic waves are driven in the substrate. 01 September 2017 | doi: 10.1038/s41467-017-00456-0 Magnetic properties and materials  Surfaces, interfaces and thin films  Hepcidin is regulated by promoter-associated histone acetylation and HDAC3 OPEN Sant-Rayn Pasricha, Pei Jin Lim, Tiago L. Duarte, Carla Casu, Dorenda Oosterhuis, Katarzyna Mleczko-Sanecka, Maria Suciu, Ana Rita Da Silva, Kinda Al-Hourani, João Arezes, Kirsty McHugh, Sarah Gooding, Joe N. Frost, Katherine Wray, Ana Santos, Graça Porto, Emmanouela Repapi, Nicki Gray, Simon J. Draper, Neil Ashley et al. Hepcidin controls systemic iron levels by inhibiting intestinal iron absorption and iron recycling. Here, Pasricha et al. demonstrate that the hepcidin-chromatin locus displays HDAC3-mediated reversible epigenetic modifications during both erythropoiesis and iron deficiency. 01 September 2017 | doi: 10.1038/s41467-017-00500-z Epigenetics  Iron  Liver  Multiple periodicity in a nanoparticle-based single-electron transistor OPEN O. Bitton, D. B. Gutman, R. Berkovits & A. Frydman Single-electron transistors are elements for nanoscale electronics. Employing single-electron transistors based on gold nanoparticles, Bitton et al., report a fabrication technique that allows precise control over the coupling between a nanodot and leads, resulting in new transport characteristics. 01 September 2017 | doi: 10.1038/s41467-017-00442-6 Electronic devices  Electronic properties and materials  Timely regulated sorting from early to late endosomes is required to maintain cerebellar long-term depression OPEN Taegon Kim, Yukio Yamamoto & Keiko Tanaka-Yamamoto Long term depression (LTD) of the cerebellum is known to be mediated by postsynaptic trafficking of glutamate receptor AMPAR. Here, Kim and colleagues show that early- to late-endosomal sorting of AMPAR represents the switch from expression to maintenance phase of cerebellar LTD. 01 September 2017 | doi: 10.1038/s41467-017-00518-3 Biophysical models  Cellular neuroscience  Long-term depression  Optogenetics  Ultrathin metal–organic framework membrane production by gel–vapour deposition OPEN Wanbin Li, Pengcheng Su, Zhanjun Li, Zehai Xu, Fei Wang, Huase Ou, Jiaheng Zhang, Guoliang Zhang & Eddy Zeng MOF-based membranes have shown great promise in separation applications, but producing thin membranes that allow for high fluxes remains challenging. Here, the authors use a gel–vapour deposition strategy to fabricate composite membranes with less than 20 nm thicknesses and high gas permeances and selectivities. 01 September 2017 | doi: 10.1038/s41467-017-00544-1 Chemical engineering  Metal–organic frameworks  Synthesis and processing    Nature Communications JOBS of the week Postdoctoral Research Associate / Research Fellow University of Exeter Brain Science Researcher KIST (Korea Institute of Sience and Technology) Staff Scientist Positions Smithsonian Tropical Research Institute (STRI) Institute Director Medical Research Council - Laboratory of Molecular Biology Multiple Clinical Professor Positions University of California - Davis Research Fellow University of Edinburgh Exciting PhD Positions in Modern Biology VBC PhD Programme Postdoctoral Research Fellow University of British Columbia, Stewart Blusson Quantum Matter Institute Postdoctoral Fellow in Cardiovascular Basic Research CUNY School of Medicine Principal Investigator Ontario Institute for Cancer Research (OICR) More Science jobs from Nature Communications EVENT Gene Therapy to Address Unmet Needs in Neurology 10.11.17 Washington, DC, USA More science events from     Latest Corrigendum       Corrigendum: p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis OPEN Robert A. H. van de Ven, Jolien S. de Groot, Danielle Park, Robert van Domselaar, Danielle de Jong, Karoly Szuhai, Elsken van der Wall, Oscar M. Rueda, H. Raza Ali, Carlos Caldas, Paul J. van Diest, Martin W. Hetzer, Erik Sahai & Patrick W. B. Derksen 06 September 2017 | doi: 10.1038/ncomms16030 Adherens junctions  Breast cancer  Cytokinesis  Mechanisms of disease      Advertisement npj Climate and Atmospheric Science: open for submissions An open access, online-only journal providing researchers, policy makers and the public with the latest research on weather and climate, publishing high-quality papers that focus on topics including climate dynamics, climate variability, weather and climate prediction, climate change, weather extremes, atmospheric composition including aerosols, the hydrological cycle and atmosphere-ocean interactions. Find out more>>   Advertisement Focus on actinide chemistry  Nature Chemistry presents a Focus which explores recent developments in actinide chemistry. The collection of articles feature uranium(VI) dianions bearing four U—N multiple bonds, berkelium(IV) stabilized in aqueous solution and a plutonium material showing evidence for the delocalization of 5ƒ electrons.  Read the Focus    Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com  More Nature Events You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at:www.nature.com/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For other enquiries, please contact our customer feedback department Springer Nature | One New York Plaza, Suite 4500 | New York | NY 10004-1562 | USA Springer Nature's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.