Nature Communications -08 February 2017

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08 February 2017 
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  Latest Correspondence  
Correspondence: Spontaneous secondary mutations confound analysis of the essential two-component system WalKR in Staphylococcus aureus OPEN
06 February 2017 | doi: 10.1038/ncomms14403
  Latest Articles View all Articles  
Clustering of 770,000 genomes reveals post-colonial population structure of North America OPEN
Eunjung Han, Peter Carbonetto, Ross E. Curtis, Yong Wang, Julie M. Granka, Jake Byrnes, Keith Noto, Amir R. Kermany, Natalie M. Myres, Mathew J. Barber, Kristin A. Rand, Shiya Song, Theodore Roman, Erin Battat, Eyal Elyashiv, Harendra Guturu, Eurie L. Hong, Kenneth G. Chahine and Catherine A. Ball
Genetic data has led to great advances in our understanding of human evolution and dispersal, but information on more recent events is limited. Here, the authors analyse genotypes from 770,000 US individuals to map the fine-scale population structure of North America after European settlement.
07 February 2017 | doi: 10.1038/ncomms14238

Erythrocytes retain hypoxic adenosine response for faster acclimatization upon re-ascent OPEN
Anren Song, Yujin Zhang, Leng Han, Gennady G. Yegutkin, Hong Liu, Kaiqi Sun, Angelo D’Alessandro, Jessica Li, Harry Karmouty-Quintana, Takayuki Iriyama, Tingting Weng, Shushan Zhao, Wei Wang, Hongyu Wu, Travis Nemkov, Andrew W. Subudhi, Sonja Jameson-Van Houten, Colleen G. Julian, Andrew T. Lovering, Kirk C. Hansen et al.
Humans that reach high altitude soon after the first ascent show faster adaptation to hypoxia. Song et al. show that this adaptive response relies on decreased red blood cell uptake of plasma adenosine due to reduced levels of nucleoside transporter ENT1 resulting from coordinated adenosine generation by ectonucleotidase CD73 and activation of A2B receptors.
07 February 2017 | doi: 10.1038/ncomms14108

A unique Pd-catalysed Heck arylation as a remote trigger for cyclopropane selective ring-opening OPEN
Sukhdev Singh, Jeffrey Bruffaerts, Alexandre Vasseur and Ilan Marek
Functionalizing multiple, distant sites across a molecule is a challenge. Here the authors report a remote functionalization strategy, whereby an initial Heck reaction leads to chain-walking of palladium across a molecule, ring-opening cyclopropanes while retaining the stereochemistry in the product.
07 February 2017 | doi: 10.1038/ncomms14200

Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome OPEN
Andrea J. Cohen, Alina Saiakhova, Olivia Corradin, Jennifer M. Luppino, Katreya Lovrenert, Cynthia F. Bartels, James J. Morrow, Stephen C. Mack, Gursimran Dhillon, Lydia Beard, Lois Myeroff, Matthew F. Kalady, Joseph Willis, James E. Bradner, Ruth A. Keri, Nathan A. Berger, Shondra M. Pruett-Miller, Sanford D. Markowitz and Peter C. Scacheri
Active enhancers are defined by the presence of post-translational modifications of histones. Here, the authors use these marks to identify enhancers recurrently activated in colorectal cancer and find that these enhancers turn on oncogenes and are associated with known risk loci for developing the disease.
07 February 2017 | doi: 10.1038/ncomms14400

Armc5 deletion causes developmental defects and compromises T-cell immune responses OPEN
Yan Hu, Linjiang Lao, Jianning Mao, Wei Jin, Hongyu Luo, Tania Charpentier, Shijie Qi, Junzheng Peng, Bing Hu, Mieczyslaw Martin Marcinkiewicz, Alain Lamarre and Jiangping Wu
Mutations in ARMC5 are associated with risk of primary macronodular adrenal gland hyperplasia. Here the authors show that mice lacking Armc5 have adrenal gland hyperplasia and defective T-cell proliferation, differentiation, survival and in vivo T-cell-mediated immune responses.
07 February 2017 | doi: 10.1038/ncomms13834

A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity OPEN
Haruna Takao, Kei Hirabayashi, Yuki Nishigaya, Haruna Kouriki, Tetsuko Nakaniwa, Yoshinori Hagiwara, Jiro Harada, Hideaki Sato, Toshimasa Yamazaki, Yoichi Sakakibara, Masahito Suiko, Yujiro Asada, Yasuhiro Takahashi, Ken Yamamoto, Keiichi Fukuyama, Masakazu Sugishima and Kei Wada
Biliverdin reductase (BVR) catalyses the last step in haem degradation. Here the authors present the crystal structure of cyanobacterial BVR bound to its substrate biliverdin and oxidised cofactor NADP+, which was used to propose the catalytic mechanism of this enzyme.
07 February 2017 | doi: 10.1038/ncomms14397

Theta and beta synchrony coordinate frontal eye fields and anterior cingulate cortex during sensorimotor mapping OPEN
Sahand Babapoor-Farrokhran, Martin Vinck, Thilo Womelsdorf and Stefan Everling
Frontal eye fields (FEF) and anterior cingulate cortex (ACC) are coactivated during cognitive tasks, but the precise format of their interaction is not known. Here the authors show that phase coupling between ACC -FEF in theta and beta frequency bands better predicts behavioural performance.
07 February 2017 | doi: 10.1038/ncomms13967

Comparative influenza protein interactomes identify the role of plakophilin 2 in virus restriction OPEN
Lingyan Wang, Bishi Fu, Wenjun Li, Girish Patil, Lin Liu, Martin E. Dorf and Shitao Li
Protein interaction networks can identify host proteins that affect virus replication. Here, the authors compare the protein interactomes of several influenza A virus strains and identify plakophilin 2 as a restriction factor that inhibits formation of the viral polymerase complex.
07 February 2017 | doi: 10.1038/ncomms13876

CRISPR–Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis OPEN
GiWon Shin, Susan M. Grimes, HoJoon Lee, Billy T. Lau, Li C. Xia and Hanlee P. Ji
Microsatellite genotyping is a common molecular method of for identification but current methods have restricted throughput. The authors demonstrate STR-Seq, which combines next generation sequencing with targeted in vitro CRISPR-Cas9 fragmentation to enable massively parallel analysis in the thousands.
07 February 2017 | doi: 10.1038/ncomms14291

Two factor-based reprogramming of rodent and human fibroblasts into Schwann cells OPEN
Pietro Giuseppe Mazzara, Luca Massimino, Marta Pellegatta, Giulia Ronchi, Alessandra Ricca, Angelo Iannielli, Serena Gea Giannelli, Marco Cursi, Cinzia Cancellieri, Alessandro Sessa, Ubaldo Del Carro, Angelo Quattrini, Stefano Geuna, Angela Gritti, Carla Taveggia and Vania Broccoli
Schwann cells (SCs) myelinate peripheral nerve axons and offer opportunities for the treatment of injuries and demyelinating diseases but reliable and renewable sources of these cells are hard to come by. Here the authors reprogram rat, mouse and human fibroblasts into Schwann cells using two transcription factors.
07 February 2017 | doi: 10.1038/ncomms14088

Molecular determinant of the effects of hydrostatic pressure on protein folding stability OPEN
Calvin R. Chen and George I. Makhatadze
Proteins can be both stabilized and destabilized by pressure. Here the authors analyse the factors contributing to both negative and positive protein volume change upon denaturation, and shed light on the molecular determinants allowing proteins to be stable at high pressures.
07 February 2017 | doi: 10.1038/ncomms14561

Small-molecule-biased formyl peptide receptor agonist compound 17b protects against myocardial ischaemia-reperfusion injury in mice OPEN
Cheng Xue Qin, Lauren T. May, Renming Li, Nga Cao, Sarah Rosli, Minh Deo, Amy E. Alexander, Duncan Horlock, Jane E. Bourke, Yuan H. Yang, Alastair G. Stewart, David M. Kaye, Xiao-Jun Du, Patrick M. Sexton, Arthur Christopoulos, Xiao-Ming Gao and Rebecca H. Ritchie
G Protein-Coupled Receptors (GPCRs) can adopt different conformations, each linked to distinct cellular outcomes. Here the authors show that compound 17b, a novel agonist of the GPCR family member FPR, robustly activates cardioprotective but not detrimental FPR signalling, showing beneficial therapeutic effect in a mouse model of cardiac infarction.
07 February 2017 | doi: 10.1038/ncomms14232

Nanoscale ππ stacked molecules are bound by collective charge fluctuations OPEN
Jan Hermann, Dario Alfè and Alexandre Tkatchenko
Attractive, non-covalent interactions between aromatic rings—termed ππ stacking—is common in chemistry but difficult to model. Here the authors report a quantum-mechanical model to show the importance of collective charge fluctuations for understanding pi-stacked supramolecular systems.
07 February 2017 | doi: 10.1038/ncomms14052

DEK-targeting DNA aptamers as therapeutics for inflammatory arthritis OPEN
Nirit Mor-Vaknin, Anjan Saha, Maureen Legendre, Carmelo Carmona-Rivera, M Asif Amin, Bradley J. Rabquer, Marta J. Gonzales-Hernandez, Julie Jorns, Smriti Mohan, Srilakshmi Yalavarthi, Dave A. Pai, Kristine Angevine, Shelley J. Almburg, Jason S. Knight, Barbara S. Adams, Alisa E. Koch, David A. Fox, David R. Engelke, Mariana J. Kaplan and David M. Markovitz et al.
DEK is a secreted protein abundant in the synovia of patients with juvenile idiopathic arthritis. Here the authors show DEK is important for neutrophil extracellular trap formation and joint inflammation, and demonstrate therapeutic efficacy of DEK-targeting aptamers in a mouse model of arthritis.
06 February 2017 | doi: 10.1038/ncomms14252

Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features OPEN
Ryohei Seki, Cai Li, Qi Fang, Shinichi Hayashi, Shiro Egawa, Jiang Hu, Luohao Xu, Hailin Pan, Mao Kondo, Tomohiko Sato, Haruka Matsubara, Namiko Kamiyama, Keiichi Kitajima, Daisuke Saito, Yang Liu, M. Thomas P. Gilbert, Qi Zhou, Xing Xu, Toshihiko Shiroishi, Naoki Irie et al.
The transition from non-avian dinosaurs to birds capable of powered flight represents a major evolutionary transition. Here the authors analyse 48 bird genomes and identify avian-specific highly conserved elements with roles in avian limb development.
06 February 2017 | doi: 10.1038/ncomms14229

Major sulfonate transporter Soa1 in Saccharomyces cerevisiae and considerable substrate diversity in its fungal family OPEN
Sylvester Holt, Harish Kankipati, Stijn De Graeve, Griet Van Zeebroeck, Maria R. Foulquié-Moreno, Stinus Lindgreen and Johan M. Thevelein
Sulfonates are a major source of sulphur for soil microbes but their cellular uptake is still not fully understood. Here the authors show that Saccharomyces cerevisiae YIL166C(SOA1) encodes for an inorganic sulphur transporter that can also function as a sulfonate and choline sulphate transporter.
06 February 2017 | doi: 10.1038/ncomms14247

Structure of the homodimeric androgen receptor ligand-binding domain OPEN
Marta Nadal, Stefan Prekovic, Nerea Gallastegui, Christine Helsen, Montserrat Abella, Karolina Zielinska, Marina Gay, Marta Vilaseca, Marta Taulès, Adriaan B. Houtsmuller, Martin E. van Royen, Frank Claessens, Pablo Fuentes-Prior and Eva Estébanez-Perpiñá
The androgen receptor is crucial for the development and physiology of reproductive organs. Here the authors present the structure of the androgen receptor ligand-binding domain bound to dihydrotestosterone, identifying a homodimerization interface that is crucial for receptor activity in vivo.
06 February 2017 | doi: 10.1038/ncomms14388

A CAF40-binding motif facilitates recruitment of the CCR4-NOT complex to mRNAs targeted by Drosophila Roquin OPEN
Annamaria Sgromo, Tobias Raisch, Praveen Bawankar, Dipankar Bhandari, Ying Chen, Duygu Kuzuoğlu-Öztürk, Oliver Weichenrieder and Elisa Izaurralde
Roquin proteins downregulate target mRNA expression by recruiting effectors such as the CCR4-NOT deadenylase complex. Here the authors provide molecular details of how Roquin proteins recruit the CCR4-NOT complex to repress the expression of its targets.
06 February 2017 | doi: 10.1038/ncomms14307

Angle resolved photoemission spectroscopy reveals spin charge separation in metallic MoSe2 grain boundary OPEN
Yujing Ma, Horacio Coy Diaz, José Avila, Chaoyu Chen, Vijaysankar Kalappattil, Raja Das, Manh-Huong Phan, Tilen Čadež, José M. P. Carmelo, Maria C. Asensio and Matthias Batzill
Line defects are 1D structures often embedded within 2D materials. Here, the authors use angle resolved photoemission spectroscopy to unveil the 1D nature of electron behaviour in such defects in atomically thin MoS2, providing evidence for spin- and charge-separation.
06 February 2017 | doi: 10.1038/ncomms14231

Dissection of goadsporin biosynthesis by in vitro reconstitution leading to designer analogues expressed in vivo OPEN
Taro Ozaki, Kona Yamashita, Yuki Goto, Morito Shimomura, Shohei Hayashi, Shumpei Asamizu, Yoshinori Sugai, Haruo Ikeda, Hiroaki Suga and Hiroyasu Onaka
Goadsporin is an antibacterial peptide highly customized by multiple post-translational modifying enzymes. Here, the authors dissect its biosynthetic pathway by in vitro reconstitution and use their insights to produce goadsporin analogues in vitro and in vivo.
06 February 2017 | doi: 10.1038/ncomms14207

Cryptic bioactivity capacitated by synthetic hybrid plant peptides OPEN
Yuki Hirakawa, Hidefumi Shinohara, Kai Welke, Stephan Irle, Yoshikatsu Matsubayashi, Keiko U. Torii and Naoyuki Uchida
Peptide hormones play versatile roles in plant development and environmental responses. Here the authors report the engineering of a synthetic plant peptide that acts on meristems through interaction with both the CLV1 and TDR/PXY receptors of Arabidopsis thaliana.
06 February 2017 | doi: 10.1038/ncomms14318

Photo-driven redox-neutral decarboxylative carbon-hydrogen trifluoromethylation of (hetero)arenes with trifluoroacetic acid OPEN
Jin Lin, Zhi Li, Jian Kan, Shijun Huang, Weiping Su and Yadong Li
C–H bond functionalization has become an important tool for many organic transformations, however such reactions typically require stoichiometric amounts of external oxidants. Here the authors report the photo-driven decarboxylative C–H trifluoromethylation of arenes using only low amounts of oxidant.
06 February 2017 | doi: 10.1038/ncomms14353

Genome-wide association analysis implicates dysregulation of immunity genes in chronic lymphocytic leukaemia OPEN
Philip J. Law, Sonja I. Berndt, Helen E. Speedy, Nicola J. Camp, Georgina P. Sava, Christine F. Skibola, Amy Holroyd, Vijai Joseph, Nicola J. Sunter, Alexandra Nieters, Silvia Bea, Alain Monnereau, David Martin-Garcia, Lynn R. Goldin, Guillem Clot, Lauren R. Teras, Inés Quintela, Brenda M. Birmann, Sandrine Jayne, Wendy Cozen et al.
Chronic lymphocytic leukaemia has a hereditary component, much of which remains to be identified. Here, the authors perform a genome-wide association study and find new risk loci for the disease, which are associated with genes involved in immune function.
06 February 2017 | doi: 10.1038/ncomms14175

Cooling a mechanical resonator with nitrogen-vacancy centres using a room temperature excited state spin–strain interaction OPEN
E. R. MacQuarrie, M. Otten, S. K. Gray and G. D. Fuchs
An efficient cooling mechanism for nanoscale mechanical resonators would help improve their properties for use in sensing applications. Here, the authors demonstrate a strong interaction between NV centres and a resonator and show how it could be harnessed to achieve a large cooling rate.
06 February 2017 | doi: 10.1038/ncomms14358

Identification of BPIFA1/SPLUNC1 as an epithelium-derived smooth muscle relaxing factor OPEN
Tongde Wu, Julianne Huang, Patrick J. Moore, Michael S. Little, William G. Walton, Robert C. Fellner, Neil E. Alexis, Y. Peter Di, Matthew R. Redinbo, Stephen L. Tilley and Robert Tarran
Asthma is characterized by abnormal airway hyperresponsiveness. Here the authors identify BPIFA1 as a factor secreted by airway epithelial cells, and show that it regulates contractility of airway smooth muscle cells by binding to and regulating the Orai1 Ca2+ channel.
06 February 2017 | doi: 10.1038/ncomms14118

Ufd2p synthesizes branched ubiquitin chains to promote the degradation of substrates modified with atypical chains OPEN
Chao Liu, Weixiao Liu, Yihong Ye and Wei Li
How ubiquitination affects the proteins it modifies varies according to the type of linkage between ubiquitin moieties. Here, Liu et al. show how yeast Udf2p promotes K48 linkage formation onto K29-linked chains to generate branched K29-K48 ubiquitin chains that target its substrate to the proteasome.
06 February 2017 | doi: 10.1038/ncomms14274

Cell fate decisions emerge as phages cooperate or compete inside their host OPEN
Jimmy T. Trinh, Tamás Székely, Qiuyan Shao, Gábor Balázsi and Lanying Zeng
The bacteriophage lambda and its host Escherichia coli provide a model system to study cell-fate decisions. Here, Trinh et al. develop a four-colour fluorescence system at the single-cell/single-virus/single-viral-DNA level and find phages cooperate during lysogenization and compete during lysis.
06 February 2017 | doi: 10.1038/ncomms14341

FAK signalling controls insulin sensitivity through regulation of adipocyte survival OPEN
Cynthia T. Luk, Sally Yu Shi, Erica P. Cai, Tharini Sivasubramaniyam, Mansa Krishnamurthy, Jara J. Brunt, Stephanie A. Schroer, Daniel A. Winer and Minna Woo
The kinase FAK is important for integrin signalling and promotes cell survival. Here, the authors demonstrate FAK regulates adipocyte survival, and is particularly important for maintaining insulin sensitivity during adipose tissue expansion in the context of a calorie-rich diet.
06 February 2017 | doi: 10.1038/ncomms14360

Killing by Type VI secretion drives genetic phase separation and correlates with increased cooperation OPEN
Luke McNally, Eryn Bernardy, Jacob Thomas, Arben Kalziqi, Jennifer Pentz, Sam P. Brown, Brian K. Hammer, Peter J. Yunker and William C. Ratcliff
The Type VI Secretory System (T6SS) is used by some bacteria to kill non-kin competitors. Here, McNally and colleagues combine mathematical modelling, experiments with Vibrio cholera and phylogenetic analysis to show that by eliminating nearby non-kin the T6SS may also favour cooperation among kin.
06 February 2017 | doi: 10.1038/ncomms14371

Proton enhanced dynamic battery chemistry for aprotic lithium–oxygen batteries OPEN
Yun Guang Zhu, Qi Liu, Yangchun Rong, Haomin Chen, Jing Yang, Chuankun Jia, Li-Juan Yu, Amir Karton, Yang Ren, Xiaoxiong Xu, Stefan Adams and Qing Wang
Water is believed to undermine the performance of aprotic lithium–air batteries. However, the authors here disclose different battery chemistry, showing that both lithium ions and protons are involved in the battery reactions in the presence of water, leading to an unprecedented dynamic product.
06 February 2017 | doi: 10.1038/ncomms14308

An unexpected N-terminal loop in PD-1 dominates binding by nivolumab OPEN
Shuguang Tan, Hao Zhang, Yan Chai, Hao Song, Zhou Tong, Qihui Wang, Jianxun Qi, Gary Wong, Xiaodong Zhu, William J. Liu, Shan Gao, Zhongfu Wang, Yi Shi, Fuquan Yang, George F. Gao and Jinghua Yan
Programmed cell death 1 (PD-1) is a key target for cancer immunotherapy. Here the authors present the crystal structure of the extracellular PD-1 domain with the clinically approved monoclonal antibody nivolumab, which shows that the N-terminal PD-1 loop is crucial for antibody binding.
06 February 2017 | doi: 10.1038/ncomms14369

Axon degeneration induces glial responses through Draper-TRAF4-JNK signalling OPEN
Tsai-Yi Lu, Jennifer M. MacDonald, Lukas J. Neukomm, Amy E. Sheehan, Rachel Bradshaw, Mary A. Logan and Marc R. Freeman
The engulfment receptor Draper is known to promote glial activation and phagocytosis of debris upon axonal injury. Lu et al. identify TNF receptor associated factor 4 (TRAF4) as a binding partner of Draper, and map out the signalling cascade leading to reactive gliosis in Drosophila.
06 February 2017 | doi: 10.1038/ncomms14355

mTORC1-independent TFEB activation via Akt inhibition promotes cellular clearance in neurodegenerative storage diseases OPEN
Michela Palmieri, Rituraj Pal, Hemanth R. Nelvagal, Parisa Lotfi, Gary R. Stinnett, Michelle L. Seymour, Arindam Chaudhury, Lakshya Bajaj, Vitaliy V. Bondar, Laura Bremner, Usama Saleem, Dennis Y. Tse, Deepthi Sanagasetti, Samuel M. Wu, Joel R. Neilson, Fred A. Pereira, Robia G. Pautler, George G. Rodney, Jonathan D. Cooper and Marco Sardiello et al.
The transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis. Here authors show that trehalose, an mTOR-independent autophagy inducer, alleviates the pathological phenotypes in a mouse model of neurodegenerative disease. Trehalose acts by inhibiting Akt, which normally suppresses TFEB via an mTORC1-independent mechanism.
06 February 2017 | doi: 10.1038/ncomms14338

The ancient CYP716 family is a major contributor to the diversification of eudicot triterpenoid biosynthesis OPEN
Karel Miettinen, Jacob Pollier, Dieter Buyst, Philipp Arendt, René Csuk, Sven Sommerwerk, Tessa Moses, Jan Mertens, Prashant D Sonawane, Laurens Pauwels, Asaph Aharoni, José Martins, David R. Nelson and Alain Goossens
Cytochrome P450 family enzymes have an essential role in the creation of triterpenoid diversity in plants. Here, the authors describe triterpenoid synthesis as mediated by CYP716 enzymes in medicinal plant species, and perform phylogenetic analysis to describe CYP716 molecular evolution in plants.
06 February 2017 | doi: 10.1038/ncomms14153

Ultrahigh-resolution imaging of water networks by atomic force microscopy OPEN
Akitoshi Shiotari and Yoshiaki Sugimoto
The structure of water in the first layer on surfaces is essential to our understanding of various phenomena, such as surface wettability and heterogeneous catalysis. Here, the authors use atomic force microscopy with a CO-functionalized tip to image water defects on copper surface at atomic resolution.
03 February 2017 | doi: 10.1038/ncomms14313

Prenatal thalamic waves regulate cortical area size prior to sensory processing OPEN
Verónica Moreno-Juan, Anton Filipchuk, Noelia Antón-Bolaños, Cecilia Mezzera, Henrik Gezelius, Belen Andrés, Luis Rodríguez-Malmierca, Rafael Susín, Olivier Schaad, Takuji Iwasato, Roland Schüle, Michael Rutlin, Sacha Nelson, Sebastien Ducret, Miguel Valdeolmillos, Filippo M. Rijli and Guillermina López-Bendito
How sensory maps are formed in the brain is only partially understood. Here the authors describe spontaneous calcium waves that propagate across different sensory nuclei in the embryonic thalamus; disrupting the wave pattern triggers thalamic gene expression changes and eventually alters the size of cortical areas.
03 February 2017 | doi: 10.1038/ncomms14172

The inverse-trans-influence in tetravalent lanthanide and actinide bis(carbene) complexes OPEN
Matthew Gregson, Erli Lu, David P. Mills, Floriana Tuna, Eric J. L. McInnes, Christoph Hennig, Andreas C. Scheinost, Jonathan McMaster, William Lewis, Alexander J. Blake, Andrew Kerridge and Stephen T. Liddle
The inverse-trans-influence has been shown to operate in high oxidation state actinide complexes. Here, the authors report tetravalent cerium, uranium and thorium bis(carbene) complexes with trans C=M=C cores where experimental and theoretical data also suggest the presence of an inverse-trans-effect.
03 February 2017 | doi: 10.1038/ncomms14137

Host-inherent variability influences the transcriptional response of Staphylococcus aureus during in vivo infection OPEN
Robert Thänert, Oliver Goldmann, Andreas Beineke and Eva Medina
Drugs inhibiting virulence factors of bacterial pathogens are under development. Here, Thänert et al. analyse the transcriptomes of host and pathogen during Staphylococcus aureus infection of two mouse strains, and show that virulence determinants are differentially expressed in different mouse strains.
03 February 2017 | doi: 10.1038/ncomms14268

Disorder enabled band structure engineering of a topological insulator surface OPEN
Yishuai Xu, Janet Chiu, Lin Miao, Haowei He, Zhanybek Alpichshev, A. Kapitulnik, Rudro R. Biswas and L. Andrew Wray
The surface electrons in a topological insulator are resistant to localization by nonmagnetic disorder, but are affected by lattice disorder. Here, the authors show that resonance states near lattice defects on the surface have significance beyond the localized regime usually associated with impurity bands.
03 February 2017 | doi: 10.1038/ncomms14081

Evolution of Shh endoderm enhancers during morphological transition from ventral lungs to dorsal gas bladder OPEN
Tomoko Sagai, Takanori Amano, Akiteru Maeno, Tetsuaki Kimura, Masatoshi Nakamoto, Yusuke Takehana, Kiyoshi Naruse, Norihiro Okada, Hiroshi Kiyonari and Toshihiko Shiroishi
Endoderm enhancer MACS1 of Sonic Hedgehog is conserved in animals with lungs. Here, the authors show that mouse without MACS1 has defective laryngeal development, and use phylogenetic analyses to show association of evolutionary lung-gas bladder transition with change of the enhancer.
03 February 2017 | doi: 10.1038/ncomms14300

Bloch surface waves confined in one dimension with a single polymeric nanofibre OPEN
Ruxue Wang, Hongyan Xia, Douguo Zhang, Junxue Chen, Liangfu Zhu, Yong Wang, Erchan Yang, Tianyang Zang, Xiaolei Wen, Gang Zou, Pei Wang, Hai Ming, Ramachandram Badugu and Joseph R. Lakowicz
Typically nanofibres need to be placed on solid substrates for the next generation of devices, but this prevents light guiding. Here Wang et al. numerically and experimentally demonstrate that when a nanofibre is placed on a dielectric multilayer, it supports a Bloch surface wave confined in one dimension.
03 February 2017 | doi: 10.1038/ncomms14330

Molecular basis for protection of ribosomal protein L4 from cellular degradation OPEN
Ferdinand M. Huber and André Hoelz
Acl4 is a dedicated assembly chaperone for ribosomal protein RpL4 that recognizes RpL4 in the cytoplasm to facilitate its nuclear import. Here the authors reveal the mechanism whereby Acl4 recognizes RpL4 and functions to protect it from Tom1-mediated degradation until RpL4 incorporation into the maturing 60S pre-ribosomal subunit.
02 February 2017 | doi: 10.1038/ncomms14354

Cooperative expression of atomic chirality in inorganic nanostructures OPEN
Peng-peng Wang, Shang-Jie Yu, Alexander O Govorov and Min Ouyang
Cooperative chirality is common in organic and biomolecular systems but is rarely explored in inorganic materials. Here, the authors combine synthesis and theory to uncover cooperative chirality in inorganic nanocrystals, arising from the interplay of independently-controlled crystallographic and morphological chirality.
02 February 2017 | doi: 10.1038/ncomms14312

Atmospheric oxygen regulation at low Proterozoic levels by incomplete oxidative weathering of sedimentary organic carbon OPEN
Stuart J. Daines, Benjamin J. W. Mills and Timothy M. Lenton
It is unclear why atmospheric O2 remained at low levels for >1.5 billion years following the Great Oxidation Event. Here, the authors show that tectonic recycling of previously accumulated sedimentary organic carbon, and oxygen sensitivity of its oxidative weathering stabilized O2 at ∼1–10% of present levels.
02 February 2017 | doi: 10.1038/ncomms14379

Waveguide-coupled nanopillar metal-cavity light-emitting diodes on silicon OPEN
V. Dolores-Calzadilla, B. Romeira, F. Pagliano, S. Birindelli, A. Higuera-Rodriguez, P. J. van Veldhoven, M. K. Smit, A. Fiore and D. Heiss
Despite much progress, nanoscale light sources suitable for photonic integration are lacking. Here, the authors present a metal-cavity nanopillar LED on a silicon substrate working at telecommunications wavelengths, which demonstrates compatibility with membrane-on-Si photonic integration platforms.
02 February 2017 | doi: 10.1038/ncomms14323

Petit-spot as definitive evidence for partial melting in the asthenosphere caused by CO2 OPEN
Shiki Machida, Tetsu Kogiso and Naoto Hirano
The genesis of primitive CO2-rich alkali magma at petit-spot volcanoes is still poorly understood. Here, the authors perform high pressure and temperature experiments to show that the CO2-rich melt is derived from the asthenosphere.
02 February 2017 | doi: 10.1038/ncomms14302

Targeting the latent cytomegalovirus reservoir with an antiviral fusion toxin protein OPEN
B. A. Krishna, K. Spiess, E. L. Poole, B. Lau, S. Voigt, T. N. Kledal, M. M. Rosenkilde and J. H. Sinclair
Reactivation of human cytomegalovirus in immunosuppressed transplant patients can cause severe complications. Here, Krishna et al. show that a fusion toxin protein that specifically binds the viral surface protein US28 can be used to kill latently infected monocytes and their progenitor cells in vitro.
02 February 2017 | doi: 10.1038/ncomms14321

Ellipsoidal analysis of coordination polyhedra OPEN
James Cumby and J. Paul Attfield
Simple polyhedra in crystalline compounds are often deformed, so methods for analysing their distortions are useful. Here, the authors demonstrate that analysis of the minimum bounding ellipsoid of a coordination polyhedron provides a general method for studying distortion.
01 February 2017 | doi: 10.1038/ncomms14235

Neutrophils dominate the immune cell composition in non-small cell lung cancer OPEN
Julia Kargl, Stephanie E. Busch, Grace H. Y. Yang, Kyoung-Hee Kim, Mark L. Hanke, Heather E. Metz, Jesse J. Hubbard, Sylvia M. Lee, David K. Madtes, Martin W. McIntosh and A. McGarry Houghton
Tumour immune evasion can involve multiple strategies. Here, the authors characterize the immune populations from clinical specimens of lung cancer in conjunction with TCR-β sequencing and show abundant neutrophils affecting cytotoxic T-cell content and the frequent presence of tumour-specific T-cell clones.
01 February 2017 | doi: 10.1038/ncomms14381

Self-surface charge exfoliation and electrostatically coordinated 2D hetero-layered hybrids OPEN
Min-Quan Yang, Yi-Jun Xu, Wanheng Lu, Kaiyang Zeng, Hai Zhu, Qing-Hua Xu and Ghim Wei Ho
Synthesis of atomically thin 2D hetero-layered structures remains a challenge. Here, the authors report a scalable approach to fabricating 2D hetero-layered metal chalcogenides of various compositions: self-surface charge exfoliation, followed by electrostatic coupling.
01 February 2017 | doi: 10.1038/ncomms14224

HOPX hypermethylation promotes metastasis via activating SNAIL transcription in nasopharyngeal carcinoma OPEN
Xianyue Ren, Xiaojing Yang, Bin Cheng, Xiaozhong Chen, Tianpeng Zhang, Qingmei He, Bin Li, Yingqin Li, Xinran Tang, Xin Wen, Qian Zhong, Tiebang Kang, Musheng Zeng, Na Liu and Jun Ma
HOPX is a transcription factor epigenetically silenced in several cancers. Here the authors, by analysing methylation profiles, identify HOPX as a suppressor of metastasis in nasopharyngeal carcinoma: mechanistically HOPX inhibits SNAIL transcription through deacetylation-mediated silencing.
01 February 2017 | doi: 10.1038/ncomms14053

A cocktail of three virulent bacteriophages prevents Vibrio cholerae infection in animal models OPEN
Minmin Yen, Lynne S. Cairns and Andrew Camilli
There has been a renewed interest in the potential use of bacterial viruses (phages) for treatment or prevention of bacterial infections. Here the authors show that a cocktail of three phages can prevent cholera-like diarrhoea in animals infected with Vibrio cholerae.
01 February 2017 | doi: 10.1038/ncomms14187

Anisotropically organized three-dimensional culture platform for reconstruction of a hippocampal neural network OPEN
So Hyun Kim, Sun-Kyoung Im, Soo-Jin Oh, Sohyeon Jeong, Eui-Sung Yoon, C. Justin Lee, Nakwon Choi and Eun-Mi Hur
Alignment or anisotropic organisation within and between cells enables biological function but is challenging to engineer. Here, the authors align collagen fibres in a pre-strained polydimethylsiloxane mould to generate a 3D scaffold that guides hippocampal neuron axon growth to form CA3–CA1 neural circuits.
01 February 2017 | doi: 10.1038/ncomms14346

Dendritic cell MST1 inhibits Th17 differentiation OPEN
Chunxiao Li, Yujing Bi, Yan Li, Hui Yang, Qing Yu, Jian Wang, Yu Wang, Huilin Su, Anna Jia, Ying Hu, Linian Han, Jiangyuan Zhang, Simin Li, Wufan Tao and Guangwei Liu
The differentiation of Th17 cells is central to infection and autoimmunity. Here, the authors show that expression of MST1 by dendritic cells limits IL-6 production and thereby controls Th17 differentiation in immunity to fungal infection and experimental autoimmune encephalomyelitis.
01 February 2017 | doi: 10.1038/ncomms14275

Photo-induced oxidant-free oxidative C–H/N–H cross-coupling between arenes and azoles OPEN
Linbin Niu, Hong Yi, Shengchun Wang, Tianyi Liu, Jiamei Liu and Aiwen Lei
Functionalization of unactivated C–H bonds is an attractive strategy to introduce functionality without the need for pre-functionalized starting materials. Here the authors combine cobalt catalysis with photoredox catalysis, allowing arene-azole cross-coupling under oxidant-free conditions.
01 February 2017 | doi: 10.1038/ncomms14226

Ethological principles predict the neuropeptides co-opted to influence parenting OPEN
Christopher B. Cunningham, Majors J. Badgett, Richard B. Meagher, Ron Orlando and Allen J. Moore
Parental care involves shifts in numerous behaviours related to mating, feeding, aggression and social interaction. Here, the authors show that, in burying beetles, parenting is associated with increased levels of neuropeptides known to mediate these precursor behaviours, suggesting co-option of existing genetic pathways.
01 February 2017 | doi: 10.1038/ncomms14225

Dysfunction of ventrolateral striatal dopamine receptor type 2-expressing medium spiny neurons impairs instrumental motivation OPEN
Iku Tsutsui-Kimura, Hiroyuki Takiue, Keitaro Yoshida, Ming Xu, Ryutaro Yano, Hiroyuki Ohta, Hiroshi Nishida, Youcef Bouchekioua, Hideyuki Okano, Motokazu Uchigashima, Masahiko Watanabe, Norio Takata, Michael R. Drew, Hiromi Sano, Masaru Mimura and Kenji F. Tanaka
D2 receptor-expressing medium spiny neurons (D2-MSNs) are thought to suppress goal-directed behaviours. Here authors ablate D2-MSNs specifically in the ventrolateral striatum, and find that surprisingly, it leads to a reduction in goal-directed motivation in mice.
01 February 2017 | doi: 10.1038/ncomms14304

Hydraulic hydrogel actuators and robots optically and sonically camouflaged in water OPEN
Hyunwoo Yuk, Shaoting Lin, Chu Ma, Mahdi Takaffoli, Nicolas X. Fang and Xuanhe Zhao
Hydrogel actuators have been widely developed to be osmotic-driven but many are in fact only capable of producing low forces. Here, the authors developed high speed and high force hydrogel actuators capable of camouflage optically and sonically with low fatigue over multiple cycles.
01 February 2017 | doi: 10.1038/ncomms14230

β-arrestin-2 is an essential regulator of pancreatic β-cell function under physiological and pathophysiological conditions OPEN
Lu Zhu, Joana Almaça, Prasanna K. Dadi, Hao Hong, Wataru Sakamoto, Mario Rossi, Regina J. Lee, Nicholas C. Vierra, Huiyan Lu, Yinghong Cui, Sara M. McMillin, Nicole A. Perry, Vsevolod V. Gurevich, Amy Lee, Bryan Kuo, Richard D. Leapman, Franz M. Matschinsky, Nicolai M. Doliba, Nikhil M. Urs, Marc G. Caron et al.
Beta-arrestins have key roles in development and metabolic functions as euglycaemic control and insulin sentitivity. Here Zhu et al. show that beta-arrestin-2 regulates insulin secretion and glucose tolerance in mice by promoting CAMKII functions in beta cells.
01 February 2017 | doi: 10.1038/ncomms14295

A defined syphilis vaccine candidate inhibits dissemination of Treponema pallidum subspecies pallidum OPEN
Karen V. Lithgow, Rebecca Hof, Charmaine Wetherell, Drew Phillips, Simon Houston and Caroline E. Cameron
There are no vaccines for the prevention of syphilis, a disease caused by the bacterium Treponema pallidum subsp. pallidum. Here, the authors use an animal model of infection to show that immunization with the Tp0751 bacterial protein inhibits the pathogen’s spread within the body.
01 February 2017 | doi: 10.1038/ncomms14273

Processable high internal phase Pickering emulsions using depletion attraction OPEN
KyuHan Kim, Subeen Kim, Jiheun Ryu, Jiyoon Jeon, Se Gyu Jang, Hyunjun Kim, Dae-Gab Gweon, Won Bin Im, Yosep Han, Hyunjung Kim and Siyoung Q. Choi
The fabrication of emulsion droplets stabilized by solid particles adsorbed on the interface is restricted to delicate interfacial conditions. Here, Kim et al. show a general approach to prepare them using the depletion interaction, modified by soluble polymers, between particles and emulsions.
01 February 2017 | doi: 10.1038/ncomms14305

Serotonin-dependent kinetics of feeding bursts underlie a graded response to food availability in C. elegans OPEN
Kyung Suk Lee, Shachar Iwanir, Ronen B. Kopito, Monika Scholz, John A. Calarco, David Biron and Erel Levine
Regulating food intake is an important physiological mechanism. Here, the authors use a custom microfluidic device to investigate feeding dynamics in C. elegans, and identify roles of serotonergic neurons in regulating bursts of feeding in response to food availability.
01 February 2017 | doi: 10.1038/ncomms14221

Complexion-mediated martensitic phase transformation in Titanium OPEN
J. Zhang, C. C. Tasan, M. J. Lai, A. -C. Dippel and D. Raabe
One way of tuning mechanical properties of alloys lies in utilizing athermal phase transitions. Here authors report a complexion-mediated martensitic transformation in Ti alloys yielding a nanolaminate structure of martensite bounded by planar complexions, promising new strategies for the design of high strength Ti alloys.
01 February 2017 | doi: 10.1038/ncomms14210

Regulation of FT splicing by an endogenous cue in temperate grasses OPEN
Zhengrui Qin, Jiajie Wu, Shuaifeng Geng, Nan Feng, Fengjuan Chen, Xingchen Kong, Gaoyuan Song, Kai Chen, Aili Li, Long Mao and Liang Wu
The correct timing of transition from the vegetative to reproductive stage is critical during the plant life cycle. Here the authors show that age dependent alternative splicing of FLOWERING LOCUS T mRNA regulates phase transitions in Brachypodium distachyon.
01 February 2017 | doi: 10.1038/ncomms14320

Phase transformation mechanism in lithium manganese nickel oxide revealed by single-crystal hard X-ray microscopy OPEN
Saravanan Kuppan, Yahong Xu, Yijin Liu and Guoying Chen
As an intercalation electrode material for lithium ion batteries, spinel Li x Mn1.5Ni0.5O4 possesses a metastable nature during the electrochemical operation. Here the authors reveal the phase transformation mechanism by using single-crystal hard X-ray microscopy to detect the local phase distribution.
01 February 2017 | doi: 10.1038/ncomms14309
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  Latest Corrigenda  
Corrigendum: Greenland subglacial drainage evolution regulated by weakly connected regions of the bed OPEN
Matthew J. Hoffman, Lauren C. Andrews, Stephen F. Price, Ginny A. Catania, Thomas A. Neumann, Martin P. Lüthi, Jason Gulley, Claudia Ryser, Robert L. Hawley and Blaine Morriss
07 February 2017 | doi: 10.1038/ncomms14501

Corrigendum: A magneto-electro-optical effect in a plasmonic nanowire material OPEN
João Valente, Jun-Yu Ou, Eric Plum, Ian J. Youngs and Nikolay I. Zheludev
07 February 2017 | doi: 10.1038/ncomms14497
Physical Sciences  Materials science  Nanotechnology  Optical physics 

Corrigendum: Daxx inhibits hypoxia-induced lung cancer cell metastasis by suppressing the HIF-1α/HDAC1/Slug axis OPEN
Ching-Wen Lin, Lu-Kai Wang, Shu-Ping Wang, Yih-Leong Chang, Yi-Ying Wu, Hsuan-Yu Chen, Tzu-Hung Hsiao, Wei-Yun Lai, Hsuan-Hsuan Lu, Ya-Hsuan Chang, Shuenn-Chen Yang, Ming-Wei Lin, Chi-Yuan Chen, Tse-Ming Hong and Pan-Chyr Yang
07 February 2017 | doi: 10.1038/ncomms14502
  Latest Errata  
Erratum: Plasticity and ductility in graphene oxide through a mechanochemically induced damage tolerance mechanism OPEN
Xiaoding Wei, Lily Mao, Rafael A. Soler-Crespo, Jeffrey T. Paci, Jiaxing Huang, SonBinh T. Nguyen and Horacio D. Espinosa
07 February 2017 | doi: 10.1038/ncomms14488
Chemical Sciences  Materials science  Nanotechnology 

Erratum: Quantum enhanced feedback cooling of a mechanical oscillator using nonclassical light OPEN
Clemens Schäfermeier, Hugo Kerdoncuff, Ulrich B. Hoff, Hao Fu, Alexander Huck, Jan Bilek, Glen I. Harris, Warwick P. Bowen, Tobias Gehring and Ulrik L. Andersen
03 February 2017 | doi: 10.1038/ncomms14489
  Latest Retraction  
Retraction: Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus OPEN
Quanjiang Ji, Peter J. Chen, Guangrong Qin, Xin Deng, Ziyang Hao, Zdzislaw Wawrzak, Won-sik Yeo, Jenny Winjing Quang, Hoonsik Cho, Guan-Zheng Luo, Xiaocheng Weng, Qiancheng You, Chi-Hao Luan, Xiaojing Yang, Taeok Bae, Kunqian Yu, Hualiang Jiang and Chuan He
06 February 2017 | doi: 10.1038/ncomms14331
Biological Sciences  Biochemistry  Microbiology 
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