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Nature Communications -15 November 2017

Nature Communications

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  Latest Correspondence    
Correspondence: Challenges with dating weathering products to unravel ancient landscapes OPEN
Haakon Fossen, Anna K. Ksienzyk & Joachim Jacobs
15 November 2017 | doi: 10.1038/s41467-017-01457-9
Geochemistry  Geomorphology 

Correspondence: On the bonding in ligand-protected gold clusters OPEN
Henrik Grönbeck
15 November 2017 | doi: 10.1038/s41467-017-01292-y
Chemical physics  Nanoparticles 

Correspondence: Reply to ‘Challenges with dating weathering products to unravel ancient landscapes’ OPEN
Ola Fredin, Giulio Viola, Horst Zwingmann, Ronald Sørlie, Marco Brönner, Jan-Erik Lie, Else Margrethe Grandal, Axel Müller, Annina Margreth, Christoph Vogt & Jochen Knies
15 November 2017 | doi: 10.1038/s41467-017-01468-6
Geochemistry  Geodynamics  Geology  Geomorphology 

Correspondence: Reply to ‘Revisiting the theoretical cell membrane thermal capacitance response’ OPEN
Mikhail G. Shapiro, Kazuaki Homma, Sebastian Villarreal, Claus-Peter Richter & Francisco Bezanilla
10 November 2017 | doi: 10.1038/s41467-017-00436-4
Biophysics  Excitability  Membrane biophysics 

Correspondence: Revisiting the theoretical cell membrane thermal capacitance response OPEN
Michael Plaksin, Eitan Kimmel & Shy Shoham
10 November 2017 | doi: 10.1038/s41467-017-00435-5
Biomedical engineering  Cellular neuroscience  Computational biophysics 
  Latest Articles View all Articles  

Oscillators that sync and swarm OPEN
Kevin P. O’Keeffe, Hyunsuk Hong & Steven H. Strogatz

Collective self-organized behavior can be observed in a variety of systems such as colloids and microswimmers. Here O’Keeffe et al. propose a model of oscillators which move in space and tend to synchronize with neighboring oscillators and outline five types of collective self-organized states.

15 November 2017 | doi: 10.1038/s41467-017-01190-3
Applied mathematics  Nonlinear phenomena  Phase transitions and critical phenomena 

Assay interference and off-target liabilities of reported histone acetyltransferase inhibitors OPEN
Jayme L. Dahlin, Kathryn M. Nelson, Jessica M. Strasser, Dalia Barsyte-Lovejoy, Magdalena M. Szewczyk, Shawna Organ, Matthew Cuellar, Gurpreet Singh, Jonathan H. Shrimp, Nghi Nguyen, Jordan L. Meier, Cheryl H. Arrowsmith, Peter J. Brown, Jonathan B. Baell & Michael A. Walters

A substantial obstacle in basic research is the use of poorly validated tool compounds with purported useful biological functions. Here, the authors systematically profile widely used histone acetyltransferase inhibitors and find that the majority are nonselective interference compounds.

15 November 2017 | doi: 10.1038/s41467-017-01657-3
Chemical tools  Drug discovery and development  High-throughput screening  Screening 

Observation of replica symmetry breaking in disordered nonlinear wave propagation OPEN
Davide Pierangeli, Andrea Tavani, Fabrizio Di Mei, Aharon J. Agranat, Claudio Conti & Eugenio DelRe

Replica symmetry breaking describes identical copies of a randomly interacting system exhibiting different dynamics. Here, Pierangeli et al. observe this critical phenomenon in the optical wave propagation inside a disordered nonlinear waveguide.

15 November 2017 | doi: 10.1038/s41467-017-01612-2
Nonlinear optics  Nonlinear phenomena  Optical physics  Phase transitions and critical phenomena 

Active diffusion and advection in Drosophila oocytes result from the interplay of actin and microtubules OPEN
Maik Drechsler, Fabio Giavazzi, Roberto Cerbino & Isabel M. Palacios

Intracellular transport is facilitated by a combination of processes including directed transport, advection and diffusion. Here the authors microscopically characterise the dynamics of the Drosophila oocyte and find distinct contributions of cytoskeletal components to advection and active diffusion.

15 November 2017 | doi: 10.1038/s41467-017-01414-6
Actin  Intracellular movement  Microtubules 

Structural basis of adaptor-mediated protein degradation by the tail-specific PDZ-protease Prc OPEN
Ming-Yuan Su, Nilanjan Som, Chia-Yun Wu, Shih-Chieh Su, Yi-Ting Kuo, Lu-Chu Ke, Meng-Ru Ho, Shiou-Ru Tzeng, Ching-Hao Teng, Dominique Mengin-Lecreulx, Manjula Reddy & Chung-I Chang

MepS is a peptidoglycan (PG) cross-link specific hydrolase needed for cell wall expansion and its cellular levels must be tightly regulated. Here the authors present the structure of the MepS degrading protease Prc bound to its adaptor NlpI and propose a model how the NlpI-Prc complex mediates MepS degradation.

15 November 2017 | doi: 10.1038/s41467-017-01697-9
Bacteriology  Protein quality control  X-ray crystallography 

The microbiota protects against respiratory infection via GM-CSF signaling OPEN
Rebecca L. Brown, Richard P. Sequeira & Thomas B. Clarke

The microbiota promotes resistance to respiratory infection through unclear mechanisms. Here, the authors identify members of the gut and upper airway microbiota that protect against respiratory infection by Streptococcus pneumoniae and Klebsiella pneumoniae by activating GM-CSF signaling.

15 November 2017 | doi: 10.1038/s41467-017-01803-x
Microbial communities  Innate immunity  Pathogens 

Quantitative analysis of protein-protein interactions and post-translational modifications in rare immune populations OPEN
Ayelet Avin, Maayan Levy, Ziv Porat & Jakub Abramson

Rare immune or stem cell populations are difficult to quantitatively analyze for protein-protein interactions or post-translational modifications despite advances in proteomics. Here the authors develop proximity ligation imaging cytometry for high-resolution detection at a single cell level.

15 November 2017 | doi: 10.1038/s41467-017-01808-6
Fluorescence imaging  Immunological techniques  Post-translational modifications  Protein–protein interaction networks 

Protruding organic surfaces triggered by in-plane electric fields OPEN
Danqing Liu, Nicholas B. Tito & Dirk J. Broer

Effective haptic interfaces are advantageous for technology that involves human-computer interaction. Here Liu et al. fabricate thin liquid crystal polymer network coatings which can be modulated by applying an alternating electric field; such switchable topography could be applied to haptic interfaces.

15 November 2017 | doi: 10.1038/s41467-017-01448-w
Actuators  Liquid crystals 

Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus OPEN
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J. Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M. Nöthen, Albert J. Becker, Per Hoffmann, Thomas Sander et al.

Most SNPs are located in non-coding genomic regions and their function remains elusive. Here, the authors perform a genome-wide scan of expression and DNA methylation quantitative trait loci in human hippocampal tissue to provide a resource for the functional interpretation of SNPs in brain disorders.

15 November 2017 | doi: 10.1038/s41467-017-01818-4
Epigenetics in the nervous system  Epigenomics  Gene expression  Neurological disorders 

Activating cobalt(II) oxide nanorods for efficient electrocatalysis by strain engineering OPEN
Tao Ling, Dong-Yang Yan, Hui Wang, Yan Jiao, Zhenpeng Hu, Yao Zheng, Lirong Zheng, Jing Mao, Hui Liu, Xi-Wen Du, Mietek Jaroniec & Shi-Zhang Qiao

The efficiencies of materials-based catalysts are determined by the surface atomic and electronic structures, but harnessing this relationship can be challenging. Here, by engineering strain into cobalt oxide, the authors transform a once poor hydrogen evolution catalyst into one that is competitive with the state of the art.

15 November 2017 | doi: 10.1038/s41467-017-01872-y
Electrocatalysis  Structural properties 

Unique transcriptome signatures and GM-CSF expression in lymphocytes from patients with spondyloarthritis OPEN
M. H. Al-Mossawi, L. Chen, H. Fang, A. Ridley, J. de Wit, N. Yager, A. Hammitzsch, I. Pulyakhina, B. P. Fairfax, D. Simone, Yao Yi, S. Bandyopadhyay, K. Doig, R Gundle, B. Kendrick, F. Powrie, J. C. Knight & P. Bowness

Spondyloarthritis is an inflammatory disease with Th17 cells implicated in the pathogenesis. Here the authors show that patients with spondyloarthritis have increased numbers of GM-CSF-secreting blood and synovial lymphocytes, Th17 or not, that carry a unique transcriptional profile including enhanced GPR65 expression.

15 November 2017 | doi: 10.1038/s41467-017-01771-2
Innate lymphoid cells  Monokines  T-helper 17 cells  Translational immunology 

The industrial anaerobe Clostridium acetobutylicum uses polyketides to regulate cellular differentiation OPEN
Nicolaus A. Herman, Seong Jong Kim, Jeffrey S. Li, Wenlong Cai, Hiroyuki Koshino & Wenjun Zhang

Polyketides are secondary metabolites mainly found in aerobic organisms with wide applications in medicine and agriculture. Here, the authors uncover new polyketides native to the anaerobic bacterium Clostridium acetobutylicum and show their role in triggering sporulation and granulose accumulation.

15 November 2017 | doi: 10.1038/s41467-017-01809-5
Applied microbiology  Metabolic engineering  Natural product synthesis 

FBXO32 promotes microenvironment underlying epithelial-mesenchymal transition via CtBP1 during tumour metastasis and brain development OPEN
Sanjeeb Kumar Sahu, Neha Tiwari, Abhijeet Pataskar, Yuan Zhuang, Marina Borisova, Mustafa Diken, Susanne Strand, Petra Beli & Vijay K. Tiwari

Epithelial-to-mesenchymal transition (EMT) regulates both processes of organism development and changes in cell state causing disease. Here, the authors show that an E3 ubiquitin ligase, FBXO32, regulates EMT via CtBP1 and the transcriptional program, and also mediates cancer metastatic burden and neurogenesis.

15 November 2017 | doi: 10.1038/s41467-017-01366-x
Breast cancer  Cancer microenvironment  Epigenetics  Neurogenesis 

Imaging spectroscopy of solar radio burst fine structures OPEN
E. P. Kontar, S. Yu, A. A. Kuznetsov, A. G. Emslie, B. Alcock, N. L. S. Jeffrey, V. N. Melnik, N. H. Bian & P. Subramanian

Radio observations of the solar atmosphere provide a unique view on the non-thermal processes in the outer atmosphere. Here the authors use LOFAR observations to demonstrate that the observed radio burst characteristics are dominated by propagation effects rather than underlying emission variations.

15 November 2017 | doi: 10.1038/s41467-017-01307-8
Astrophysical plasmas  Solar physics  Stars 

Suppression of SRCAP chromatin remodelling complex and restriction of lymphoid lineage commitment by Pcid2 OPEN
Buqing Ye, Benyu Liu, Liuliu Yang, Guanling Huang, Lu Hao, Pengyan Xia, Shuo Wang, Ying Du, Xiwen Qin, Pingping Zhu, Jiayi Wu, Nobuo Sakaguchi, Junyan Zhang & Zusen Fan

Haematopoiesis and the generation of lymphoid cell subsets are controlled by delicate genetic programs enforced via epigenetic regulation. Here the authors show that Pcid2 interacts with ZNHIT1, a component of the SRCAP chromatin remodelling complex, to critically modulate the differentiation of multipotent progenitors.

15 November 2017 | doi: 10.1038/s41467-017-01788-7
Chromatin remodelling  Epigenetics in immune cells  Lymphopoiesis  Myelopoiesis 

Phage display and selection of lanthipeptides on the carboxy-terminus of the gene-3 minor coat protein OPEN
Johannes H. Urban, Markus A. Moosmeier, Tobias Aumüller, Marcus Thein, Tjibbe Bosma, Rick Rink, Katharina Groth, Moritz Zulley, Katja Siegers, Kathrin Tissot, Gert N. Moll & Josef Prassler

Lanthipeptides are a class of cyclic post-translationally modified peptides with potential drug-like properties. Here the authors develop a phage display system by expressing lanthipeptide precursors as C-terminal fusions to the phage M13 coat protein pIII in E. coli along with the heterologous modifying enzymes.

15 November 2017 | doi: 10.1038/s41467-017-01413-7
High-throughput screening  Peptides  Protein design 

Ca2+ signals initiate at immobile IP3 receptors adjacent to ER-plasma membrane junctions OPEN
Nagendra Babu Thillaiappan, Alap P. Chavda, Stephen C. Tovey, David L. Prole & Colin W. Taylor

IP3 receptors mediate Ca2+ release from the endoplasmic reticulum. Here the authors show that only a small fraction of IP3 receptors initiate Ca2+ signals; these immobile IP3 receptors adjacent to the plasma membrane are optimally placed to control STIM1-dependent Ca2+ entry.

15 November 2017 | doi: 10.1038/s41467-017-01644-8
Calcium channels  Calcium signalling 

HIV-1 counteracts an innate restriction by amyloid precursor protein resulting in neurodegeneration OPEN
Qingqing Chai, Vladimir Jovasevic, Viacheslav Malikov, Yosef Sabo, Scott Morham, Derek Walsh & Mojgan H. Naghavi

HIV infection results in elevated beta-amyloid (Aβ) levels in the brain, but the underlying mechanisms are unclear. Here, the authors show that amyloid precursor protein inhibits virion production and that HIV Gag, counteracting this antiviral function, results in secretase-dependent Aβ production and neuron degeneration.

15 November 2017 | doi: 10.1038/s41467-017-01795-8
HIV infections  Mechanisms of disease  Neurodegenerative diseases  Virus–host interactions 

Structural basis for tRNA-dependent cysteine biosynthesis OPEN
Meirong Chen, Koji Kato, Yume Kubo, Yoshikazu Tanaka, Yuchen Liu, Feng Long, William B. Whitman, Pascal Lill, Christos Gatsogiannis, Stefan Raunser, Nobutaka Shimizu, Akira Shinoda, Akiyoshi Nakamura, Isao Tanaka & Min Yao

tRNA-dependent cysteine biosynthesis is catalyzed by the transsulfursome protein complex. Here, the authors use a multidisciplinary approach to structurally characterize the archaeal transsulfursome and propose a model for tRNA channeling in the complex.

15 November 2017 | doi: 10.1038/s41467-017-01543-y
Electron microscopy  SAXS  tRNAs  X-ray crystallography 

Polo-like kinase 1 coordinates biosynthesis during cell cycle progression by directly activating pentose phosphate pathway OPEN
Xiaoyu Ma, Lin Wang, De Huang, Yunyan Li, Dongdong Yang, Tingting Li, Fudong Li, Linchong Sun, Haoran Wei, Kun He, Fazhi Yu, Debiao Zhao, Lan Hu, Songge Xing, Zhaoji Liu, Kui Li, Jing Guo, Zhenye Yang, Xin Pan, Ailing Li et al.

Polo-like kinase 1 (Plk1) is a key regulator of mitosis. Here, the authors show that Plk1 activates the pentose phosphate pathway in cancer cells by directly phosphorylating glucose-6-phosphate dehydrogenase (G6PD) and that such activation is critical for cell cycle progression and cancer cell growth.

15 November 2017 | doi: 10.1038/s41467-017-01647-5
Cancer metabolism  Cell division  Cell growth  Phosphorylation 

Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features OPEN
Martin Pannek, Zeljko Simic, Matthew Fuszard, Marat Meleshin, Dante Rotili, Antonello Mai, Mike Schutkowski & Clemens Steegborn

Sirtuins are NAD+-dependent protein lysine deacylases that act as metabolic regulators and are linked to aging-related diseases. Here the authors present the Sirt4 crystal structure and show that the enzyme has dehydroxymethylglutarylation activity and is regulated by NADH.

15 November 2017 | doi: 10.1038/s41467-017-01701-2
Enzymes  X-ray crystallography 

Transient cardiomyocyte fusion regulates cardiac development in zebrafish OPEN
Suphansa Sawamiphak, Zacharias Kontarakis, Alessandro Filosa, Sven Reischauer & Didier Y. R. Stainier

Cell fusion regulates several physiological events, for example, fusion of myoblasts in skeletal muscle formation, but it is unclear if this process occurs in the heart. Here, the authors use transgenic reporters in zebrafish to show transient cardiomyocyte fusion, modulating cardiac development and function.

15 November 2017 | doi: 10.1038/s41467-017-01555-8
Cell biology  Heart development  Organogenesis 

PTEN is a protein phosphatase that targets active PTK6 and inhibits PTK6 oncogenic signaling in prostate cancer OPEN
Darren J. Wozniak, Andre Kajdacsy-Balla, Virgilia Macias, Susan Ball-Kell, Morgan L. Zenner, Wenjun Bie & Angela L. Tyner

PTEN is often lost in prostate cancer. In this study, the authors show that PTEN can act as a protein phosphatase that targets active PTK6, thereby regulating its oncogenic signaling in prostate cancer progression.

15 November 2017 | doi: 10.1038/s41467-017-01574-5
Mechanisms of disease  Tumour-suppressor proteins 

Emergent patterns of collective cell migration under tubular confinement OPEN
Wang Xi, Surabhi Sonam, Thuan Beng Saw, Benoit Ladoux & Chwee Teck Lim

Collective epithelial behaviours are studied in vitro in the context of flat sheets but a system to mimic tubular systems is lacking. Here, the authors develop a method to study collective behaviour in lumenal structures and show that several features depend on the extent of tubular confinement and/or curvature.

15 November 2017 | doi: 10.1038/s41467-017-01390-x
Cellular motility  Collective cell migration 

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients OPEN
Alyse K. Hawley, Masaru K. Nobu, Jody J. Wright, W. Evan Durno, Connor Morgan-Lang, Brent Sage, Patrick Schwientek, Brandon K. Swan, Christian Rinke, Monica Torres-Beltrán, Keith Mewis, Wen-Tso Liu, Ramunas Stepanauskas, Tanja Woyke & Steven J. Hallam

Little is known about Marinimicrobia, a group of bacteria that are prevalent in the oceans. Here, the authors study global populations of Marinimicrobia using single-cell genomics, metagenomics and metatranscriptomics, showing potential co-metabolic interactions and participation in the sulfur and nitrogen cycles.

15 November 2017 | doi: 10.1038/s41467-017-01376-9
Biogeochemistry  Metagenomics  Microbial ecology  Water microbiology 

DJ-1 controls bone homeostasis through the regulation of osteoclast differentiation OPEN
Hyuk Soon Kim, Seung Taek Nam, Se Hwan Mun, Sun-Kyeong Lee, Hyun Woo Kim, Young Hwan Park, Bokyung Kim, Kyung-Jong Won, Hae-Rim Kim, Yeong-Min Park, Hyung Sik Kim, Michael A. Beaven, Young Mi Kim & Wahn Soo Choi

Osteoclasts are involved in arthritis, and their differentiation depends on RANKL signaling. The author show that the ROS-scavenging protein DJ-1 negatively regulates RANKL signaling and that its ablation increases osteoclast numbers and exacerbates bone damage in mouse models of arthritis.

15 November 2017 | doi: 10.1038/s41467-017-01527-y
Bone  Osteoclasts  Osteoimmunology  Rheumatoid arthritis 

Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway OPEN
Elisa Benedetti, Maja Pučić-Baković, Toma Keser, Annika Wahl, Antti Hassinen, Jeong-Yeh Yang, Lin Liu, Irena Trbojević-Akmačić, Genadij Razdorov, Jerko Štambuk, Lucija Klarić, Ivo Ugrina, Maurice H. J. Selman, Manfred Wuhrer, Igor Rudan, Ozren Polasek, Caroline Hayward, Harald Grallert, Konstantin Strauch, Annette Peters et al.

IgG glycosylation is an important factor in immune function, yet the molecular details of protein glycosylation remain poorly understood. The data-driven approach presented here uses large-scale plasma IgG mass spectrometry measurements to infer new biochemical reactions in the glycosylation pathway.

14 November 2017 | doi: 10.1038/s41467-017-01525-0
Biochemical networks  Glycobiology  Statistical methods 

Chromosome segregation occurs by microtubule pushing in oocytes OPEN
Kimberley Laband, Rémi Le Borgne, Frances Edwards, Marine Stefanutti, Julie C. Canman, Jean-Marc Verbavatz & Julien Dumont

In oocytes of most species atypical spindles assembled in the absence of centrosomes drive chromosome segregation, however the forces driving this process are unclear. Here the authors found that spindle poles are largely dispensable and that inter-chromosomal microtubules of the central spindle control chromosomal segregation.

14 November 2017 | doi: 10.1038/s41467-017-01539-8
Chromosome segregation  Meiosis  Microtubules 

Time-resolved diffraction of shock-released SiO2 and diaplectic glass formation OPEN
A. E. Gleason, C. A. Bolme, H. J. Lee, B. Nagler, E. Galtier, R. G. Kraus, R. Sandberg, W. Yang, F. Langenhorst & W. L. Mao

Our understanding of shock metamorphism and thus the collision of planetary bodies is limited by a dependence on ex situ analyses. Here, the authors perform in situ analysis on shocked-produced densified glass and show that estimates of impactor size based on traditional techniques are likely inflated.

14 November 2017 | doi: 10.1038/s41467-017-01791-y
Meteoritics  Phase transitions and critical phenomena 

NOG1 increases grain production in rice OPEN
Xing Huo, Shuang Wu, Zuofeng Zhu, Fengxia Liu, Yongcai Fu, Hongwei Cai, Xianyou Sun, Ping Gu, Daoxin Xie, Lubin Tan & Chuanqing Sun

Rice grain yield is a quantitative trait determined by multiple genes. Here, the authors find NOG1, which encodes an enoyl-CoA hydratase/isomerase in fatty acid β-oxidation pathway, can increase grain yield by enhancing grain number per panicle without affecting the other yield component traits.

14 November 2017 | doi: 10.1038/s41467-017-01501-8
Agricultural genetics  Natural variation in plants  Plant breeding 

Intertwining DNA-RNA nanocapsules loaded with tumor neoantigens as synergistic nanovaccines for cancer immunotherapy OPEN
Guizhi Zhu, Lei Mei, Harshad D. Vishwasrao, Orit Jacobson, Zhantong Wang, Yijing Liu, Bryant C. Yung, Xiao Fu, Albert Jin, Gang Niu, Qin Wang, Fuwu Zhang, Hari Shroff & Xiaoyuan Chen

Nucleic acid nanomedicines are promising for cancer drug delivery. Here, the authors show using a mouse model the tumor immunotherapeutic efficacy of nanovaccines based on intertwining DNA-RNA nanocapsules loaded with DNA CpG, Stat3-silencing short hairpin RNA and tumor-specific peptide neoantigens.

14 November 2017 | doi: 10.1038/s41467-017-01386-7
Immunosuppression  Molecular medicine  Nanotechnology in cancer 

A conformational switch in initiation factor 2 controls the fidelity of translation initiation in bacteria OPEN
Kelvin Caban, Michael Pavlov, Måns Ehrenberg & Ruben L. Gonzalez Jr

The GTP-bound form of initiation factor 2 (IF2) promotes translation initiation by accelerating 50S ribosomal subunit joining the 30S ribosomal initiation complex (30S IC). Here the authors use single-molecule FRET and ensemble rapid kinetic methods to uncover the mechanism behind IF2-mediated subunit joining.

14 November 2017 | doi: 10.1038/s41467-017-01492-6
GTP-binding protein regulators  Ribosome  Single-molecule biophysics 

Significance estimation for large scale metabolomics annotations by spectral matching OPEN
Kerstin Scheubert, Franziska Hufsky, Daniel Petras, Mingxun Wang, Louis-Félix Nothias, Kai Dührkop, Nuno Bandeira, Pieter C. Dorrestein & Sebastian Böcker

Matching fragment spectra to reference library spectra is an important procedure for annotating small molecules in untargeted mass spectrometry based metabolomics studies. Here, the authors develop strategies to estimate false discovery rates (FDR) by empirical Bayes and target-decoy based methods which enable a user to define the scoring criteria for spectral matching.

14 November 2017 | doi: 10.1038/s41467-017-01318-5
Analytical chemistry  Metabolomics  Statistical methods 

Non-canonical activation of OmpR drives acid and osmotic stress responses in single bacterial cells OPEN
Smarajit Chakraborty, Ricksen S. Winardhi, Leslie K. Morgan, Jie Yan & Linda J. Kenney

OmpR is a transcription factor activated in acid and osmotic responses of Gram-negative bacteria, leading to acidification of the bacterial cytoplasm. Here the authors use single cell pH imaging to define the role of OmpR-regulated genes in the acidification response to osmotic and acid stress of Salmonella and E. coli.

14 November 2017 | doi: 10.1038/s41467-017-02030-0
Biophysics  Microbiology  Stress signalling  Transcription factors 

Interfaces between hexagonal and cubic oxides and their structure alternatives OPEN
Hua Zhou, Lijun Wu, Hui-Qiong Wang, Jin-Cheng Zheng, Lihua Zhang, Kim Kisslinger, Yaping Li, Zhiqiang Wang, Hao Cheng, Shanming Ke, Yu Li, Junyong Kang & Yimei Zhu

The control over the crystallographic orientation at functional oxide interfaces is crucial to the performance of oxide-based electronics. Here, Zhou et al. provide a detailed insight into the thermodynamic and kinetic process of nucleation-mediated crystal growth at the ZnO and MgO interface.

14 November 2017 | doi: 10.1038/s41467-017-01655-5
Structural properties  Surfaces, interfaces and thin films  Transmission electron microscopy 

NitroSynapsin therapy for a mouse MEF2C haploinsufficiency model of human autism OPEN
Shichun Tu, Mohd Waseem Akhtar, Rosa Maria Escorihuela, Alejandro Amador-Arjona, Vivek Swarup, James Parker, Jeffrey D. Zaremba, Timothy Holland, Neha Bansal, Daniel R. Holohan, Kevin Lopez, Scott D. Ryan, Shing Fai Chan, Li Yan, Xiaofei Zhang, Xiayu Huang, Abdullah Sultan, Scott R. McKercher, Rajesh Ambasudhan, Huaxi Xu et al.

Human MEF2C haploinsufficiency results in Autism Spectrum Disorder (ASD), but it is unclear if the same is true in mice. Here, the authors show that Mef2c +/− mice have behavioral defects and neuronal abnormalities similar to ASD, and symptoms can be ameliorated with the new drug, NitroSynapsin.

14 November 2017 | doi: 10.1038/s41467-017-01563-8
Autism spectrum disorders  Genetics of the nervous system 

Impacts of hemispheric solar geoengineering on tropical cyclone frequency OPEN
Anthony C. Jones, James M. Haywood, Nick Dunstone, Kerry Emanuel, Matthew K. Hawcroft, Kevin I. Hodges & Andy Jones

Solar geoengineering has been proposed as a means of mitigating the warming effects of climate change, yet the consequences of such action remain uncertain. Here, using a general circulation model, the authors evaluate the effect of stratospheric aerosol injection on tropical cyclone activity.

14 November 2017 | doi: 10.1038/s41467-017-01606-0
Atmospheric science  Climate and Earth system modelling 

Heterogeneity in the Drosophila gustatory receptor complexes that detect aversive compounds OPEN
Ha Yeon Sung, Yong Taek Jeong, Ji Yeon Lim, Hyeyon Kim, Soo Min Oh, Sun Wook Hwang, Jae Young Kwon & Seok Jun Moon

Taste sensilla are Drosophila sensory organs containing taste neurons, which have differential tuning for bitter compounds. Here, the authors systematically examine what combinations of gustatory receptor genes confer a specific taste response profile in different bitter taste neurons.

14 November 2017 | doi: 10.1038/s41467-017-01639-5
Behavioural genetics  Neurophysiology  Taste receptors 

Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers OPEN
Manaswini Sivaramakrishnan, Kathleen D. McCarthy, Sébastien Campagne, Sylwia Huber, Sonja Meier, Angélique Augustin, Tobias Heckel, Hélène Meistermann, Melanie N. Hug, Pascale Birrer, Ahmed Moursy, Sarah Khawaja, Roland Schmucki, Nikos Berntenis, Nicolas Giroud, Sabrina Golling, Manuel Tzouros, Balazs Banfai, Gonzalo Duran-Pacheco, Jens Lamerz et al.

Small molecules correcting the splicing deficit of the survival of motor neuron 2 (SMN2) gene have been identified as having therapeutic potential. Here, the authors provide evidence that SMN2 mRNA forms a ribonucleoprotein complex that can be specifically targeted by these small molecules.

14 November 2017 | doi: 10.1038/s41467-017-01559-4
Alternative splicing  RNA  Target identification 

Strategies for feeding the world more sustainably with organic agriculture OPEN
Adrian Muller, Christian Schader, Nadia El-Hage Scialabba, Judith Brüggemann, Anne Isensee, Karl-Heinz Erb, Pete Smith, Peter Klocke, Florian Leiber, Matthias Stolze & Urs Niggli

Organic agriculture requires fewer inputs but produces lower yields than conventional farming. Here, via a modeling approach, Muller et al. predict that if food waste and meat consumption are reduced, organic agriculture could feed the world without requiring cropland expansion.

14 November 2017 | doi: 10.1038/s41467-017-01410-w
Agriculture  Environmental impact  Sustainability 

Myokine mediated muscle-kidney crosstalk suppresses metabolic reprogramming and fibrosis in damaged kidneys OPEN
Hui Peng, Qianqian Wang, Tanqi Lou, Jun Qin, Sungyun Jung, Vivekananda Shetty, Feng Li, Yanlin Wang, Xin-hua Feng, William E. Mitch, Brett H. Graham & Zhaoyong Hu

Progressive tubule cell damage results in defects in mitochondrial metabolism and exercise seems to be beneficial during chronic kidney disease. Here Peng et al. show that irisin, an exercise-induced myokine, improves kidney energy metabolism by inhibiting TGF-β type 1 receptors and ameliorates fibrosis.

14 November 2017 | doi: 10.1038/s41467-017-01646-6
Chronic kidney disease  Renal fibrosis 

Dynamic tuning of optical absorbers for accelerated solar-thermal energy storage OPEN
Zhongyong Wang, Zhen Tong, Qinxian Ye, Hang Hu, Xiao Nie, Chen Yan, Wen Shang, Chengyi Song, Jianbo Wu, Jun Wang, Hua Bao, Peng Tao & Tao Deng

Solar-thermal energy storage based on phase-change materials suffers from slow thermal-diffusion-based charging. Here the authors alleviate this issue by introducing optical absorbers and controlling their distribution to accelerate charging process and thus improve solar-thermal energy conversion.

14 November 2017 | doi: 10.1038/s41467-017-01618-w
Materials for energy and catalysis  Optical materials and structures 

A rapid cosmic-ray increase in BC 3372–3371 from ancient buried tree rings in China OPEN
F. Y. Wang, H. Yu, Y. C. Zou, Z. G. Dai & K. S. Cheng

14C can be absorbed by trees as a result of the interaction of cosmic rays produced by high-energy phenomena with the Earth’s atmosphere. Here, the authors observe a rapid increase of 14C in an ancient buried tree from BC 3372 to BC 3371, and suggest that it could originate from a large solar proton event.

14 November 2017 | doi: 10.1038/s41467-017-01698-8
High-energy astrophysics  Solar physics 

Iced photochemical reduction to synthesize atomically dispersed metals by suppressing nanocrystal growth OPEN
Hehe Wei, Kai Huang, Da Wang, Ruoyu Zhang, Binghui Ge, Jingyuan Ma, Bo Wen, Shuai Zhang, Qunyang Li, Ming Lei, Cheng Zhang, Joshua Irawan, Li-Min Liu & Hui Wu

Photochemical synthesis is a popular approach to fabricate metallic nanoparticles, however stabilizing individually-dispersed atoms by this method remains challenging. Here, the authors freeze their precursor solution prior to UV irradiation to obtain atomically-dispersed platinum catalysts with high electrocatalytic performance.

14 November 2017 | doi: 10.1038/s41467-017-01521-4
Electrocatalysis  Photochemistry  Synthesis and processing 

Both Nodal signalling and stochasticity select for prospective distal visceral endoderm in mouse embryos OPEN
Katsuyoshi Takaoka, Hiromi Nishimura & Hiroshi Hamada

In the mouse embryo, anterior-posterior polarity is established by distal visceral endoderm (DVE) at embryonic day 5.5 but how this arises is unclear. Here, the authors show that expression of Lefty1 earlier can define DVE, and that future DVE cells are selected by Nodal signalling and stochasticity.

14 November 2017 | doi: 10.1038/s41467-017-01625-x
Cell lineage  Embryology 

Antimicrobial peptides in frog poisons constitute a molecular toxin delivery system against predators OPEN
Constantijn Raaymakers, Elin Verbrugghe, Sophie Hernot, Tom Hellebuyck, Cecilia Betti, Cindy Peleman, Myriam Claeys, Wim Bert, Vicky Caveliers, Steven Ballet, An Martel, Frank Pasmans & Kim Roelants

To avoid being eaten, poisonous prey animals must rely on fast passage of toxins across a predator’s oral tissue, a major barrier to large molecules. Here, Raaymakers et al. show that antimicrobial peptides co secreted with frog toxins enhance intoxication of a snake predator by permeabilizing oral cell layers.

14 November 2017 | doi: 10.1038/s41467-017-01710-1
Animal physiology  Evolutionary ecology  Herpetology  Peptides 

A primacy code for odor identity OPEN
Christopher D. Wilson, Gabriela O. Serrano, Alexei A. Koulakov & Dmitry Rinberg

Odor identity remains stable despite changes in concentration yet the neural mechanisms are relatively unknown. Here the authors test a primacy coding model using an optogenetic masking paradigm in mice to show that a set of earliest activated receptors are sufficient to make decisions about odor identity across concentrations.

14 November 2017 | doi: 10.1038/s41467-017-01432-4
Olfactory bulb  Sensory processing 

The deep conservation of the Lepidoptera Z chromosome suggests a non-canonical origin of the W OPEN
Christelle Fraïsse, Marion A. L. Picard & Beatriz Vicoso

The canonical scenario of sex chromosome evolution is through the differentiation of ancestral pairs of autosomes. Here, Fraïsse and colleagues use a comparative genomic analysis that shows the deep conservation of the Z chromosome in Lepidoptera and supports a non-canonical origin of the W chromosome.

14 November 2017 | doi: 10.1038/s41467-017-01663-5
Comparative genomics  Evolutionary genetics  Genome evolution 

GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection OPEN
Hua Yuan, Jinru Zhang, Yujuan Cai, Sheng Wu, Kui Yang, H. C. Stephen Chan, Wei Huang, Wen-Bing Jin, Yan Li, Yue Yin, Yasuhiro Igarashi, Shuguang Yuan, Jiahai Zhou & Gong-Li Tang

GyrI-like proteins are small-molecule binding proteins that are widely distributed in prokaryotes and eukaryotes, with functions that are poorly characterized. Here, the authors identify GyrI-like proteins as cyclopropanoid cyclopropyl hydrolases that can confer resistance to cytotoxic cyclopropanoid compounds.

14 November 2017 | doi: 10.1038/s41467-017-01508-1
Biosynthesis  Cellular microbiology  Hydrolases 

Transgenic Cavendish bananas with resistance to Fusarium wilt tropical race 4 OPEN
James Dale, Anthony James, Jean-Yves Paul, Harjeet Khanna, Mark Smith, Santy Peraza-Echeverria, Fernando Garcia-Bastidas, Gert Kema, Peter Waterhouse, Kerrie Mengersen & Robert Harding

The newly recognized Fusarium wilt pathogen tropical race 4 is threatening worldwide banana production. Here, the authors transform Cavendish bananas with a resistance gene, RGA2, from diploid banana or a nematode-derived gene, Ced9, and confer resistance to natural infection under field conditions.

14 November 2017 | doi: 10.1038/s41467-017-01670-6
Agricultural genetics  Field trials  Molecular engineering in plants 

The core-promoter factor TRF2 mediates a Fruitless action to masculinize neurobehavioral traits in Drosophila  OPEN
Zahid Sadek Chowdhury, Kosei Sato & Daisuke Yamamoto

fruitless (fru) is an important sex-determinant gene that controls the expression of neuroanatomical sex differences in Drosophila. Here the authors report that a core-promoter factor, TRF2, suppresses a male-type neurite specification through direct interaction with FruBM isoform at the robo1 target gene promoter.

14 November 2017 | doi: 10.1038/s41467-017-01623-z
Genetics  Neuroscience  Sexual dimorphism 

Imaging the transient heat generation of individual nanostructures with a mechanoresponsive polymer OPEN
Xueqin Chen, Qing Xia, Yue Cao, Qianhao Min, Jianrong Zhang, Zixuan Chen, Hong-Yuan Chen & Jun-Jie Zhu

Remote thermometers with a high spatiotemporal resolution are very desirable for applications in the life sciences, including photothermal therapy. Here, Chen et al. develop polymer coated gold nanorods with a temperature sensitivity of 80 mK and a 4 ms response time for thermometry in the life sciences.

14 November 2017 | doi: 10.1038/s41467-017-01614-0
Nanoparticles  Optical imaging  Surface plasmon resonance 

Mixed Weyl semimetals and low-dissipation magnetization control in insulators by spin–orbit torques OPEN
Jan-Philipp Hanke, Frank Freimuth, Chengwang Niu, Stefan Blügel & Yuriy Mokrousov

Electric-field control of magnetization switching is highly promising for low-dissipation spintronics. Here, the authors propose an electrically induced topological phase transition mediated by spin orbit torques as attractive way to control magnetization in absence of longitudinal charge currents.

14 November 2017 | doi: 10.1038/s41467-017-01138-7
Electronic properties and materials  Magnetic properties and materials  Quantum Hall  Spintronics 

O-GlcNAcylation of SIRT1 enhances its deacetylase activity and promotes cytoprotection under stress OPEN
Cuifang Han, Yuchao Gu, Hui Shan, Wenyi Mi, Jiahui Sun, Minghui Shi, Xinling Zhang, Xinzhi Lu, Feng Han, Qianhong Gong & Wengong Yu

SIRT1 is a stress sensor whose deacetylase activity is increased during cellular stress, but the molecular mechanism is unclear. Here, the authors show that O-GlcNAcylation of SIRT1 is elevated upon different stress stimuli and increases SIRT1 deacetylase activity, protecting cells from stress-induced apoptosis.

14 November 2017 | doi: 10.1038/s41467-017-01654-6
Glycobiology  Glycosylation  Stress signalling 

Accessibility of the histone H3 tail in the nucleosome for binding of paired readers OPEN
Jovylyn Gatchalian, Xiaodong Wang, Jinzen Ikebe, Khan L. Cox, Adam H. Tencer, Yi Zhang, Nathaniel L. Burge, Luo Di, Matthew D. Gibson, Catherine A. Musselman, Michael G. Poirier, Hidetoshi Kono, Jeffrey J. Hayes & Tatiana G. Kutateladze

The chromatin remodeller CHD4 contains two PHD finger reader domains that have been shown to bivalently recognize H3 histone tails. Here, the authors describe a mechanism by which the PHD fingers bind to the intact nucleosome core particle, revealing both cooperative and individual interactions.

14 November 2017 | doi: 10.1038/s41467-017-01598-x
Molecular biophysics  Nucleosomes 

A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells OPEN
Hyun Ju Lee, Deniz Bartsch, Cally Xiao, Santiago Guerrero, Gaurav Ahuja, Christina Schindler, James J. Moresco, John R. Yates III, Fátima Gebauer, Hisham Bazzi, Christoph Dieterich, Leo Kurian & David Vilchez

Unlike transcriptional regulation of hESC identity, little is known post-transcriptionally. Here, the authors show that the RNA binding protein CSDE1 regulates core components of hESC identity, neurectoderm commitment and neurogenesis to maintain pluripotency and prevent neural differentiation.

13 November 2017 | doi: 10.1038/s41467-017-01744-5
Developmental neurogenesis  Differentiation  Embryonic stem cells  Pluripotency  RNA decay 

Dengue virus-reactive CD8+ T cells mediate cross-protection against subsequent Zika virus challenge OPEN
Jinsheng Wen, Annie Elong Ngono, Jose Angel Regla-Nava, Kenneth Kim, Matthew J. Gorman, Michael S. Diamond & Sujan Shresta

Dengue virus-specific antibody and CD8+ T cells that cross-react with Zika virus have been described. Here, the authors establish a functionally protective role for cross-reactive dengue virus-specific CD8+ T cells during challenge with Zika virus.

13 November 2017 | doi: 10.1038/s41467-017-01669-z
Antibodies  CD8-positive T cells  Dengue virus  Viral infection 

Development of a genetic sensor that eliminates p53 deficient cells OPEN
Jovan Mircetic, Antje Dietrich, Maciej Paszkowski-Rogacz, Mechthild Krause & Frank Buchholz

TP53 is mutated in many cancers, a system to detect and selectively eliminate p53 mutant cells is an attractive therapeutic strategy. Here, the authors present a genetic sensor that can detect p53 activity and is coupled to the thymidine kinase gene, which can activate the drug Ganciclovir, resulting in cell death.

13 November 2017 | doi: 10.1038/s41467-017-01688-w
Biosensors  Cancer genomics  Targeted therapies 

Intratumoral CD40 activation and checkpoint blockade induces T cell-mediated eradication of melanoma in the brain OPEN
Manisha Singh, Christina Vianden, Mark J. Cantwell, Zhimin Dai, Zhilan Xiao, Meenu Sharma, Hiep Khong, Ashvin R. Jaiswal, Faisal Faak, Yared Hailemichael, L. M. E. Janssen, Uddalak Bharadwaj, Michael A. Curran, Adi Diab, Roland L. Bassett, David J. Tweardy, Patrick Hwu & Willem W. Overwijk

Treatment options for metastatic melanoma are limited. Here the authors show that combining an immunostimulant adenovirus, currently in clinical trials for leukemia, with immune checkpoints blockade (ICB) results in systemic eradication of ICB resistant melanoma tumours from both skin and brain of mice.

13 November 2017 | doi: 10.1038/s41467-017-01572-7
Cancer immunotherapy  Melanoma  Tumour immunology 

Self-probing spectroscopy of XUV photo-ionization dynamics in atoms subjected to a strong-field environment OPEN
Doron Azoury, Michael Krüger, Gal Orenstein, Henrik R. Larsson, Sebastian Bauch, Barry D. Bruner & Nirit Dudovich

Single photon ionization—one of the most fundamental light matter interactions—can be significantly altered in a strong-field environment. Here the authors demonstrate a self-probing spectroscopy technique, resolving the evolution of the interaction in helium atoms with attosecond precision.

13 November 2017 | doi: 10.1038/s41467-017-01723-w
Atomic and molecular interactions with photons  Attosecond science  Optical spectroscopy 

Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA OPEN
Yuan Tian, Mariana Babor, Jerome Lane, Veronique Schulten, Veena S. Patil, Grégory Seumois, Sandy L. Rosales, Zheng Fu, Gaelle Picarda, Julie Burel, Jose Zapardiel-Gonzalo, Rashika N. Tennekoon, Aruna D. De Silva, Sunil Premawansa, Gayani Premawansa, Ananda Wijewickrama, Jason A. Greenbaum, Pandurangan Vijayanand, Daniela Weiskopf, Alessandro Sette et al.

Memory T cells are essential for combating recurring infection by promoting prompt and effective immune responses. Here the authors show, via system biology approaches, that human CD4 memory T cells contains a CD45RA-rexpressing pool that can be further subsetted by the expression of GPR56 for distinct functionalities.

13 November 2017 | doi: 10.1038/s41467-017-01728-5
Antimicrobial responses  CD4-positive T cells  Immunological memory  Lymphocyte differentiation 

Regulation of angiotensin II actions by enhancers and super-enhancers in vascular smooth muscle cells OPEN
Sadhan Das, Parijat Senapati, Zhuo Chen, Marpadga A. Reddy, Rituparna Ganguly, Linda Lanting, Varun Mandi, Anita Bansal, Amy Leung, Selena Zhang, Ye Jia, Xiwei Wu, Dustin E. Schones & Rama Natarajan

The repertoire of tissue-specific distal regulators of gene transcription enhancers defines homeostasis or disease. Here, the authors reveal the enhancer and super-enhancer signature of vascular smooth muscle cells under normal and angiotensin II stimuli, providing new insight into the transcriptional regulation of vascular pathologies.

13 November 2017 | doi: 10.1038/s41467-017-01629-7
Cardiovascular diseases  Epigenomics  Gene regulation  Transcriptional regulatory elements 

Region and cell-type resolved quantitative proteomic map of the human heart OPEN
Sophia Doll, Martina Dreßen, Philipp E. Geyer, Daniel N. Itzhak, Christian Braun, Stefanie A. Doppler, Florian Meier, Marcus-Andre Deutsch, Harald Lahm, Rüdiger Lange, Markus Krane & Matthias Mann

The human heart is composed of distinct regions and cell types, but relatively little is known about their specific protein composition. Here, the authors present a region- and cell type-specific proteomic map of the healthy human heart, revealing functional differences and potential cell type markers.

13 November 2017 | doi: 10.1038/s41467-017-01747-2
Atrial fibrillation  Mass spectrometry  Proteomics 

ER-associated degradation regulates Alzheimer’s amyloid pathology and memory function by modulating γ-secretase activity OPEN
Bing Zhu, LuLin Jiang, Timothy Huang, Yingjun Zhao, Tongfei Liu, Yongwang Zhong, Xiaoguang Li, Alexandre Campos, Kenneth Pomeroy, Eliezer Masliah, Dongxian Zhang & Huaxi Xu

Endoplasmic-reticulum associated degradation (ERAD) regulates protein homeostasis. Here the authors identify an ERAD component membralin, and show that it interacts with a member of the γ-secretase complex to regulate β-amyloid (Aβ) pathology and memory deficits in an Alzheimer’s disease model.

13 November 2017 | doi: 10.1038/s41467-017-01799-4
Alzheimer's disease  Endoplasmic reticulum 

Virtual photons in the ground state of a dissipative system OPEN
Simone De Liberato

Phenomena linked with ultrastrong coupling rely on the presence of virtual photons in the system’s ground state. In this article, using exact diagonalization, De Liberato shows that the population of ground state virtual photons is only quantitatively affected by losses.

13 November 2017 | doi: 10.1038/s41467-017-01504-5
Microresonators  Quantum optics  Single photons and quantum effects 

The multiple antibiotic resistance operon of enteric bacteria controls DNA repair and outer membrane integrity OPEN
Prateek Sharma, James R. J. Haycocks, Alistair D. Middlemiss, Rachel A. Kettles, Laura E. Sellars, Vito Ricci, Laura J. V. Piddock & David C. Grainger

Transcription factors MarR and MarA confer multidrug resistance in enteric bacteria by modulating efflux pump and porin expression. Here, Sharma et al. show that MarA also upregulates genes required for lipid trafficking and DNA repair, thus reducing antibiotic entry and quinolone-induced DNA damage.

13 November 2017 | doi: 10.1038/s41467-017-01405-7
Antibacterial drug resistance  Bacterial genetics  Transcription factors 

Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors OPEN
Emily A. Saunderson, Peter Stepper, Jennifer J. Gomm, Lily Hoa, Adrienne Morgan, Michael D. Allen, J. Louise Jones, John G. Gribben, Tomasz P. Jurkowski & Gabriella Ficz

“Although aberrant promoter DNA hypermethylation is a hallmark of cancer, it is not clear whether it is sufficient to drive transformation. Here, the authors use CRISPR-dCas9 to perform hit-and-run epigenetic editing, which prevents senescence entry in primary breast cells from healthy donors.”

13 November 2017 | doi: 10.1038/s41467-017-01078-2
Breast cancer  CRISPR-Cas systems  DNA methylation  Tumour-suppressor proteins 

Ist1 regulates ESCRT-III assembly and function during multivesicular endosome biogenesis in Caenorhabditis elegans embryos OPEN
E. B. Frankel, Raakhee Shankar, James J. Moresco, John R. Yates III, Niels Volkmann & Anjon Audhya

During the oocyte-to-embryo transition in C. elegans, multivesicular endosomes (MVEs) are formed rapidly. Using live imaging and electron microscopy, the authors here show that the ESCRT-III subunit Ist1 is required for normal MVE biogenesis in the early C. elegans embryo.

13 November 2017 | doi: 10.1038/s41467-017-01636-8
ESCRT  Multivesicular bodies 

Optically-controlled long-term storage and release of thermal energy in phase-change materials OPEN
Grace G. D. Han, Huashan Li & Jeffrey C. Grossman

Phase-change materials offer excellent thermal storage due to their high latent heat; however, they suffer from spontaneous heat loss. Han et al., use organic photo-switching dopants to introduce an activation energy barrier which enables controllable thermal energy release and retention.

13 November 2017 | doi: 10.1038/s41467-017-01608-y
Chemistry  Materials science  Solar thermal energy 

BRCA2 antagonizes classical and alternative nonhomologous end-joining to prevent gross genomic instability OPEN
Jinhua Han, Chunyan Ruan, Michael S. Y. Huen, Jiadong Wang, Anyong Xie, Chun Fu, Ting Liu & Jun Huang

The genomic instability phenotype characteristic of BRCA2-deficient cells is not fully mechanistically understood. Here the authors show BRCA2 inactivation destabilizes RPA-coated single-stranded DNA and leads to toxic non homologous end-joining events.

13 November 2017 | doi: 10.1038/s41467-017-01759-y
Double-strand DNA breaks  Stress signalling 

Mapping functional diversity from remotely sensed morphological and physiological forest traits OPEN
Fabian D. Schneider, Felix Morsdorf, Bernhard Schmid, Owen L. Petchey, Andreas Hueni, David S. Schimel & Michael E. Schaepman

As remote sensing technology improves, it is now possible to map fine-scale variation in plant functional traits. Schneider et al. remotely sense tree functional diversity, validate with field data, and reveal patterns of plant adaptation to the environment previously not retrievable from plot data

13 November 2017 | doi: 10.1038/s41467-017-01530-3
Biodiversity  Community ecology  Ecosystem ecology  Forest ecology 

Evidence of renal angiomyolipoma neoplastic stem cells arising from renal epithelial cells OPEN
Ana Filipa Gonçalves, Mojca Adlesic, Simone Brandt, Tomas Hejhal, Sabine Harlander, Lukas Sommer, Olga Shakhova, Peter J. Wild & Ian J. Frew

Renal angiomyolipomas (AML) contain a mix of clonal tumour cells. Here, through reverse tumour engineering experiments, mouse genetics and analyses of human AML tumours, the authors provide evidence that these mesenchymal tumours originate from renal proximal tubule epithelial cells.

13 November 2017 | doi: 10.1038/s41467-017-01514-3
Cancer stem cells  Renal cancer 

The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding OPEN
Nicolas Tarbouriech, Corinne Ducournau, Stephanie Hutin, Philippe J. Mas, Petr Man, Eric Forest, Darren J. Hart, Christophe N. Peyrefitte, Wim P. Burmeister & Frédéric Iseni

The catalytic subunit E9 of the vaccinia virus DNA polymerase forms a functional polymerase holoenzyme by interacting with the heterodimeric processivity factor A20/D4. Here the authors present the structure of full-length E9 and show that an insertion within its palm domain binds A20, in a mode different from other family B polymerases.

13 November 2017 | doi: 10.1038/s41467-017-01542-z
Enzyme mechanisms  X-ray crystallography 

Thermostable exoshells fold and stabilize recombinant proteins OPEN
Siddharth Deshpande, Nihar D. Masurkar, Vallerinteavide Mavelli Girish, Malan Desai, Goutam Chakraborty, Juliana M. Chan & Chester L. Drum

Improving recombinant protein expression and stabilization remains a significant challenge. Here, the authors engineer Archaeoglobus fulgidus ferritin as a thermostable exoshell to provide steric accommodation and charge complementation for recombinant proteins, which can improve yields by 100 fold.

13 November 2017 | doi: 10.1038/s41467-017-01585-2
Nanoparticles  Protein folding 

Quantification of flexoelectricity in PbTiO3/SrTiO3 superlattice polar vortices using machine learning and phase-field modeling OPEN
Q. Li, C. T. Nelson, S.-L. Hsu, A. R. Damodaran, L.-L. Li, A. K. Yadav, M. McCarter, L. W. Martin, R. Ramesh & S. V. Kalinin

Flexoelectric coupling between strain gradients and polarization influences the physics of ferroelectric devices but it is difficult to directly probe its effects. Here, Li et al. use principal component analysis to compare STEM images with phase-field modeling and extract the flexoelectric contributions.

13 November 2017 | doi: 10.1038/s41467-017-01733-8
Coarse-grained models  Ferroelectrics and multiferroics  Structural properties 

Highly selective nickel-catalyzed gem-difluoropropargylation of unactivated alkylzinc reagents OPEN
Lun An, Chang Xu & Xingang Zhang

Difluoroalkylated compounds find wide application in medicinal chemistry. Here, the authors describe the mild nickel-catalyzed difluoroalkylation of aliphatic alkylzinc reagents with gem-difluoropropargylbromides and show its utility in a number of post-synthetic transformations.

13 November 2017 | doi: 10.1038/s41467-017-01540-1
Homogeneous catalysis  Synthetic chemistry methodology  Reaction mechanisms 

Atomically-precise colloidal nanoparticles of cerium dioxide OPEN
Kylie J. Mitchell, Khalil A. Abboud & George Christou

Control over nanoparticle atomicity has not yet been extended to metal oxides. Here, the authors present the synthesis and X-ray crystal structures of a family of atomically precise ceria nanoclusters, a pivotal step for understanding the relationship between their atomic structure and reactivity.

13 November 2017 | doi: 10.1038/s41467-017-01672-4
Inorganic chemistry  Nanoparticle synthesis  Nanoparticles 

Carbon nanotubes as excitonic insulators OPEN
Daniele Varsano, Sandro Sorella, Davide Sangalli, Matteo Barborini, Stefano Corni, Elisa Molinari & Massimo Rontani

It has long been anticipated theoretically that semiconductors with small band gaps may form a correlated exciton insulator phase, but it has been difficult to find material realisations. Here, the authors predict numerically that zero-gap armchair carbon nanotubes could be exciton insulators.

13 November 2017 | doi: 10.1038/s41467-017-01660-8
Carbon nanotubes and fullerenes  Electronic properties and materials 

Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy OPEN
Yicong Wu, Abhishek Kumar, Corey Smith, Evan Ardiel, Panagiotis Chandris, Ryan Christensen, Ivan Rey-Suarez, Min Guo, Harshad D. Vishwasrao, Jiji Chen, Jianyong Tang, Arpita Upadhyaya, Patrick J. La Riviere & Hari Shroff

Light-sheet fluorescence microscopy enables high resolution imaging of biological samples. Here the authors use reflective coverslips to obtain multiple sample views simultaneously, improving the speed of acquisition and resolution compared to dual-view selective plane illumination microscopy.

13 November 2017 | doi: 10.1038/s41467-017-01250-8
Cellular imaging  Light-sheet microscopy  Optical imaging 

Probing optical anisotropy of nanometer-thin van der waals microcrystals by near-field imaging OPEN
Debo Hu, Xiaoxia Yang, Chi Li, Ruina Liu, Ziheng Yao, Hai Hu, Stephanie N. Gilbert Corder, Jianing Chen, Zhipei Sun, Mengkun Liu & Qing Dai

The optical response of van der Waals layered crystals is strongly anisotropic. Here, the authors develop a nano-imaging technique to determine the in-plane and out-of-plane components of the anisotropic dielectric tensors in MoS2 and hBN, two representative van der Waals crystals.

13 November 2017 | doi: 10.1038/s41467-017-01580-7
Imaging and sensing  Nanophotonics and plasmonics  Nanoscale materials 

TRIM24 is an oncogenic transcriptional co-activator of STAT3 in glioblastoma OPEN
Deguan Lv, Yanxin Li, Weiwei Zhang, Angel A. Alvarez, Lina Song, Jianming Tang, Wei-Qiang Gao, Bo Hu, Shi-Yuan Cheng & Haizhong Feng

EGF receptor (EGFR) amplification and mutation are major drivers in glioma tumorigenesis but this mechanism is not well understood. Here, the authors show EGFR-upregulated H3K23ac binds TRIM24 which recruits STAT3, leading to activation of STAT3 signaling, enhancing EGFR-driven tumorigenesis.

13 November 2017 | doi: 10.1038/s41467-017-01731-w
CNS cancer 

Neuronal hyperactivity due to loss of inhibitory tone in APOE4 mice lacking Alzheimer’s disease-like pathology OPEN

The APOE4 allele is the leading risk factor for late-onset Alzheimer’s disease, but how it might contribute to the disease is not clear. Here the authors show that a mouse expressing the human APOE4 allele displays hyperactivity in the entorhinal cortex due to a decreased inhibitory tone, which may in part explain accelerated Alzheimer’s pathology in APOE4 carriers.

13 November 2017 | doi: 10.1038/s41467-017-01444-0
Alzheimer's disease  Hippocampus  Metabolism 

RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure OPEN
Oz Solomon, Ayelet Di Segni, Karen Cesarkas, Hagit T. Porath, Victoria Marcu-Malina, Orel Mizrahi, Noam Stern-Ginossar, Nitzan Kol, Sarit Farage-Barhom, Efrat Glick-Saar, Yaniv Lerenthal, Erez Y. Levanon, Ninette Amariglio, Ron Unger, Itamar Goldstein, Eran Eyal & Gidi Rechavi

Adenosine deaminase acting on RNA 1 (ADAR1) edits adenosine to inosine. Here the authors, using parallel analysis of RNA secondary structure sequencing, provide evidence that ADAR1 induces sequence-context-dependent RNA secondary structures changes, often leading to stabilization of the RNA duplex.

13 November 2017 | doi: 10.1038/s41467-017-01458-8
Computational biology and bioinformatics  Gene regulation  RNA 

An unusual endo-selective C-H hydroarylationof norbornene by the Rh(I)-catalyzed reactionof benzamides OPEN
Kaname Shibata, Satoko Natsui, Mamoru Tobisu, Yoshiya Fukumoto & Naoto Chatani

Investigating unusual organometallic pathways may help to efficiently control product selectivity in homogeneous catalysis. Here, the authors report the hydroarylation of aromatic amides with norbornene derivatives and propose the formation of a rhodium-carbene intermediate leading to rarely observed endo-products.

13 November 2017 | doi: 10.1038/s41467-017-01531-2
Homogeneous catalysis  Synthetic chemistry methodology  Stereochemistry 

Nanopore electric snapshots of an RNA tertiary folding pathway OPEN
Xinyue Zhang, Dong Zhang, Chenhan Zhao, Kai Tian, Ruicheng Shi, Xiao Du, Andrew J. Burcke, Jing Wang, Shi-Jie Chen & Li-Qun Gu

While RNA folding is critical for its function, study of this process is challenging. Here, the authors combine nanopore single-molecule manipulation with theoretical analysis to follow the folding of an RNA pseudoknot, monitoring the intermediate states and the kinetics of their interconversion.

13 November 2017 | doi: 10.1038/s41467-017-01588-z
Computational biophysics  Molecular modelling  Single-channel recording  Single-molecule biophysics 

mTOR intersects antibody-inducing signals from TACI in marginal zone B cells OPEN
Jordi Sintes, Maurizio Gentile, Shuling Zhang, Yolanda Garcia-Carmona, Giuliana Magri, Linda Cassis, Daniel Segura-Garzón, Alessandra Ciociola, Emilie K. Grasset, Sabrina Bascones, Laura Comerma, Marc Pybus, David Lligé, Irene Puga, Cindy Gutzeit, Bing He, Wendy DuBois, Marta Crespo, Julio Pascual, Anna Mensa et al.

Marginal zone B cells differentiate into plasma cells rapidly in response to T-cell-independent antigens, but how they do so is not clear. Here the authors show TACI cooperates with TLR signalling to drive mTOR activity and subsequent class switching and plasmablast differentiation.

13 November 2017 | doi: 10.1038/s41467-017-01602-4
Class switch recombination  Marginal zone B cells 

PLCγ-dependent mTOR signalling controls IL-7-mediated early B cell development OPEN
Mei Yu, Yuhong Chen, Hu Zeng, Yongwei Zheng, Guoping Fu, Wen Zhu, Ulrich Broeckel, Praful Aggarwal, Amy Turner, Geoffrey Neale, Cliff Guy, Nan Zhu, Hongbo Chi, Renren Wen & Demin Wang

IL-7R activation drives early B cell development, but the signalling is unclear. Here the authors show PLCγ is involved in IL-7R-induced mTOR activation via a DAG/PKC-dependent pathway, and that double deficiency of the two PLCγ isoforms arrests B cell development at the pre-pro-B stage in mice.

13 November 2017 | doi: 10.1038/s41467-017-01388-5
B-2 cells  Lymphopoiesis 

Balancing activity, stability and conductivity of nanoporous core-shell iridium/iridium oxide oxygen evolution catalysts OPEN
Yong-Tae Kim, Pietro Papa Lopes, Shin-Ae Park, A-Yeong Lee, Jinkyu Lim, Hyunjoo Lee, Seoin Back, Yousung Jung, Nemanja Danilovic, Vojislav Stamenkovic, Jonah Erlebacher, Joshua Snyder & Nenad M. Markovic

Production of affordable, clean hydrogen relies on efficient oxygen evolution, but improving catalytic performance for the reaction in acidic media is challenging. Here the authors show how tuning the nanoporous morphology of iridium/iridium oxide leads to an improvement in activity/stability, compared with conventional iridium-based oxides.

13 November 2017 | doi: 10.1038/s41467-017-01734-7
Electrocatalysis  Structural properties 

IL-2 imprints human naive B cell fate towards plasma cell through ERK/ELK1-mediated BACH2 repression OPEN
Nicolas Hipp, Hannah Symington, Cédric Pastoret, Gersende Caron, Céline Monvoisin, Karin Tarte, Thierry Fest & Céline Delaloy

T cells help B cells to differentiate into antibody-producing plasma cells. Here the authors show that T cells produce interleukin-2 to activate ERK/ELK1 and suppress BACH2 expression by modulating the BACH2 super-enhancer, thereby altering BACH2 downstream transcription programs for plasma cell differentiation.

13 November 2017 | doi: 10.1038/s41467-017-01475-7
Class switch recombination  Gene regulation in immune cells  Interleukins  Plasma cells 

Volcanism in slab tear faults is larger than in island-arcs and back-arcs OPEN
Luca Cocchi, Salvatore Passaro, Fabio Caratori Tontini & Guido Ventura

The volcanism of subduction settings concentrates in island-arcs and back-arc basins. Here, the authors show that the lithospheric tear faults bounding roll-backing slabs may focus huge volcanism with a volume of the erupted products exceeding that of the island-arcs edifices and back-arcs spreading centres.

13 November 2017 | doi: 10.1038/s41467-017-01626-w
Geodynamics  Geomagnetism  Volcanology 

Airway surface liquid pH is not acidic in children with cystic fibrosis OPEN
André Schultz, Ramaa Puvvadi, Sergey M. Borisov, Nicole C. Shaw, Ingo Klimant, Luke J. Berry, Samuel T. Montgomery, Thien Nguyen, Silvia M. Kreda, Anthony Kicic, Peter B. Noble, Brian Button & Stephen M. Stick

Modulation of airway surface liquid pH has been proposed as a therapy for cystic fibrosis, but whether pH is indeed altered in cystic fibrosis is controversial. Here, the authors develop a novel fibre-optic based pH measurement technology, and show that pH is not altered in children with cystic fibrosis.

10 November 2017 | doi: 10.1038/s41467-017-00532-5
Cystic fibrosis  Optical sensors  Respiration 

Electrostrictive microelectromechanical fibres and textiles OPEN
Tural Khudiyev, Jefferson Clayton, Etgar Levy, Noémie Chocat, Alexander Gumennik, Alexander M. Stolyarov, John Joannopoulos & Yoel Fink

Micro-electromechanical systems fabrication techniques are based on silicon micromachining processes, resulting in rigid and low aspect ratio structures. Here the authors demonstrate a flexible, high aspect ratio micro-electromechanical system in fibre enabled by an electrostrictive ferrorelaxor terpolymer layer.

10 November 2017 | doi: 10.1038/s41467-017-01558-5
Actuators  Applied optics  Electrical and electronic engineering 

Supramammillary glutamate neurons are a key node of the arousal system OPEN
Nigel P. Pedersen, Loris Ferrari, Anne Venner, Joshua L. Wang, Stephen B. G. Abbott, Nina Vujovic, Elda Arrigoni, Clifford B. Saper & Patrick M. Fuller

Supramammillary nucleus (SuM) neurons have been studied in the context of REM sleep but their possible role in mediating wakefulness is not known. Here the authors elucidate the distinct functional contributions of three subpopulations in the SuM on electrographical and behavioral arousal in mice using genetically targeted approaches.

10 November 2017 | doi: 10.1038/s41467-017-01004-6
Disorders of consciousness  Hippocampus  Neural circuits  Wakefulness 

Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy OPEN
Mikihiro Shibata, Hiroshi Nishimasu, Noriyuki Kodera, Seiichi Hirano, Toshio Ando, Takayuki Uchihashi & Osamu Nureki

CRISPR RNA-guided endonuclease Cas9 recognizes and cleaves the double-stranded DNA complementary to the RNA guide. Here the authors use high-speed atomic force micropcopy (HS-AFM) to visualize the conformational dynamics of Cas9 during its DNA targeting and cleavage processes.

10 November 2017 | doi: 10.1038/s41467-017-01466-8
Enzyme mechanisms  Nucleases  Single-molecule biophysics  X-ray crystallography 

Cooperative polariton dynamics in feedback-coupled cavities OPEN
Bimu Yao, Y. S. Gui, J. W. Rao, S. Kaur, X. S. Chen, W. Lu, Y. Xiao, H. Guo, K. -P. Marzlin & C. -M. Hu

Rabi oscillations of magnons typically do not have few photon control of single spin quantum systems. Here, the authors use a feedback cavity architecture to increase magnon-photon cooperativity, enabling increased control of light-matter interactions in magnonic systems via cooperative polariton dynamics.

10 November 2017 | doi: 10.1038/s41467-017-01796-7
Condensed-matter physics  Polaritons  Quantum optics 

Probing dopant segregation in distinct cation sites at perovskite oxide polycrystal interfaces OPEN
Hye-In Yoon, Dong-Kyu Lee, Hyung Bin Bae, Gi-Young Jo, Hee-Suk Chung, Jin-Gyu Kim, Suk-Joong L. Kang & Sung-Yoon Chung

Space-charges in polycrystalline materials can drive segregation of dopants, however an in-depth understanding of this process is still missing. Here, the authors show that in polycrystalline perovskites the space-charge segregation and interfacial structure are nearly identical irrespective of the interface type.

10 November 2017 | doi: 10.1038/s41467-017-01134-x
Ceramics  Chemical physics  Solid-state chemistry  Surfaces, interfaces and thin films 

Allogeneic stem cell transplantation in fully MHC-matched Mauritian cynomolgus macaques recapitulates diverse human clinical outcomes OPEN
Benjamin J. Burwitz, Helen L. Wu, Shaheed Abdulhaqq, Christine Shriver-Munsch, Tonya Swanson, Alfred W. Legasse, Katherine B. Hammond, Stephanie L. Junell, Jason S. Reed, Benjamin N. Bimber, Justin M. Greene, Gabriela M. Webb, Mina Northrup, Wolfram Laub, Paul Kievit, Rhonda MacAllister, Michael K. Axthelm, Rebecca Ducore, Anne Lewis, Lois M. A. Colgin et al.

Rhesus macaques are not ideal for studying response to allogeneic hematopoietic stem cell transplant (allo-HSCT) owing to complex MHC genetics that prevent full MHC-matching. Here the authors show that inbred Mauritian-origin cynomolgus macaques are a superior preclinical model of allogeneic stem cell transplantation that mimics diverse clinical outcomes of human allo-HSCT.

10 November 2017 | doi: 10.1038/s41467-017-01631-z
Allotransplantation  Infectious diseases 

Live imaging molecular changes in junctional tension upon VE-cadherin in zebrafish OPEN
Anne Karine Lagendijk, Guillermo A. Gomez, Sungmin Baek, Daniel Hesselson, William E. Hughes, Scott Paterson, Daniel E. Conway, Heinz-Georg Belting, Markus Affolter, Kelly A. Smith, Martin A. Schwartz, Alpha S. Yap & Benjamin M. Hogan

Mechanical forces play a crucial role during morphogenesis, but how these are sensed and transduced in vivo is not fully understood. Here the authors apply a FRET tension sensor to live zebrafish and study changes in VE-cadherin tension at endothelial cell-cell junctions during arterial maturation.

10 November 2017 | doi: 10.1038/s41467-017-01325-6
Angiogenesis  Cadherins  Mechanotransduction 

Novel genetically encoded fluorescent probes enable real-time detection of potassium in vitro and in vivo OPEN
Helmut Bischof, Markus Rehberg, Sarah Stryeck, Katharina Artinger, Emrah Eroglu, Markus Waldeck-Weiermair, Benjamin Gottschalk, Rene Rost, Andras T. Deak, Tobias Niedrist, Nemanja Vujic, Hanna Lindermuth, Ruth Prassl, Brigitte Pelzmann, Klaus Groschner, Dagmar Kratky, Kathrin Eller, Alexander R. Rosenkranz, Tobias Madl, Nikolaus Plesnila et al.

K+ plays an important role in physiology and disease, but the lack of high specificity K+ sensors limits our understanding of its spatiotemporal dynamics. Here the authors develop genetically-encoded FRET-based probes able to quantify K+ concentration in body fluids, cells and specific organelles.

10 November 2017 | doi: 10.1038/s41467-017-01615-z
Fluorescence imaging  Sensors and probes  Wide-field fluorescence microscopy 

Dual protein kinase and nucleoside kinase modulators for rationally designed polypharmacology OPEN
Kahina Hammam, Magali Saez-Ayala, Etienne Rebuffet, Laurent Gros, Sophie Lopez, Berengere Hajem, Martine Humbert, Emilie Baudelet, Stephane Audebert, Stephane Betzi, Adrien Lugari, Sebastien Combes, Sebastien Letard, Nathalie Casteran, Colin Mansfield, Alain Moussy, Paulo De Sepulveda, Xavier Morelli & Patrice Dubreuil

Masitinib is a protein kinase inhibitor that sensitises refractory pancreatic adenocarcinoma cells to treatment with the nucleoside analog gemcitabine. Here the authors show that Masitinib activates deoxycytidine kinase to enhance phosphorylation of nucleoside analogue pro-drugs, increasing their potency.

10 November 2017 | doi: 10.1038/s41467-017-01582-5
Kinases  Small molecules  Target identification 

A thermostable Cas9 with increased lifetime in human plasma OPEN
Lucas B. Harrington, David Paez-Espino, Brett T. Staahl, Janice S. Chen, Enbo Ma, Nikos C. Kyrpides & Jennifer A. Doudna

While current CRISPR-Cas9 tools have revolutionized genome editing, they are not suitable for applications at elevated temperatures. Here, the authors characterize GeoCas9 from Geobacillus stearothermophilus, which is active up to 70°C and is stable in human plasma.

10 November 2017 | doi: 10.1038/s41467-017-01408-4
CRISPR-Cas9 genome editing  Genetic engineering 

Origin of the omnipotence of eukaryotic release factor 1 OPEN
Christoffer Lind, Ana Oliveira & Johan Åqvist

The eukaryotic release factor eRF1 is able to recognize the three stop codons UAA, UAG and UGA with high accuracy, while discriminating against near-cognate codons. Here the authors use molecular dynamic simulation to provide insight into the molecular basis behind the remarkable codon specificity of eRF1.

10 November 2017 | doi: 10.1038/s41467-017-01757-0
Biocatalysis  Computational biology and bioinformatics  Ribosome 

Giant thermal expansion and α-precipitation pathways in Ti-alloys OPEN
Matthias Bönisch, Ajit Panigrahi, Mihai Stoica, Mariana Calin, Eike Ahrens, Michael Zehetbauer, Werner Skrotzki & Jürgen Eckert

Complex phase transformations in β-stabilised titanium alloys can dramatically change their α and β microstructures, providing tailorability for aerospace or biomaterial applications. Here the authors show that Ti-Nb alloys exhibit giant thermal expansions and identify two new pathways that lead to α phase formation.

10 November 2017 | doi: 10.1038/s41467-017-01578-1
Aerospace engineering  Metals and alloys  Phase transitions and critical phenomena 

Multicolor lineage tracing reveals clonal architecture and dynamics in colon cancer OPEN
Sebastian Lamprecht, Eva Marina Schmidt, Cristina Blaj, Heiko Hermeking, Andreas Jung, Thomas Kirchner & David Horst

The clonal architecture of colon cancer and the relevance of tumor cell subpopulations for clonal outgrowth are poorly understood. Here, the authors describe the clonal architecture and dynamics in human colon cancer by using a multicolor lineage tracing approach in colon cancer xenografts.

10 November 2017 | doi: 10.1038/s41467-017-00976-9
Cancer models  Cancer stem cells 

The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA OPEN
S. Austin Hammond, René L. Warren, Benjamin P. Vandervalk, Erdi Kucuk, Hamza Khan, Ewan A. Gibb, Pawan Pandoh, Heather Kirk, Yongjun Zhao, Martin Jones, Andrew J. Mungall, Robin Coope, Stephen Pleasance, Richard A. Moore, Robert A. Holt, Jessica M. Round, Sara Ohora, Branden V. Walle, Nik Veldhoen, Caren C. Helbing et al.

The globally-distributed Ranidae (true frogs) are the largest frog family. Here, Hammond et al. present a draft genome of the North American bullfrog, Rana (Lithobates) catesbeiana, as a foundation for future understanding of true frog genetics as amphibian species face difficult environmental challenges.

10 November 2017 | doi: 10.1038/s41467-017-01316-7
Genomics  Herpetology  Long non-coding RNAs  Sequence annotation 

Human sperm steer with second harmonics of the flagellar beat OPEN
Guglielmo Saggiorato, Luis Alvarez, Jan F. Jikeli, U. Benjamin Kaupp, Gerhard Gompper & Jens Elgeti

The mechanism allowing sperm to steer is not fully understood. The authors find that superposition of two harmonic waves breaks the flagellar beat symmetry temporally rather than spatially, and that this mechanism is enhanced by the sexual hormone progesterone, which changes the motility pattern.

10 November 2017 | doi: 10.1038/s41467-017-01462-y
Biological physics  Cell migration  Cellular motility 

Orthogonal navigation of multiple visible-light-driven artificial microswimmers OPEN
Jing Zheng, Baohu Dai, Jizhuang Wang, Ze Xiong, Ya Yang, Jun Liu, Xiaojun Zhan, Zhihan Wan & Jinyao Tang

The ability to direct microwimmers along a particular trajectory is advantageous for targeted drug delivery and manufacturing at the microscale. Here Zheng et al. use different types of light-absorbing dyes to enable selective activation of different microswimmers independently from each other.

10 November 2017 | doi: 10.1038/s41467-017-01778-9
Colloids  Molecular machines and motors  Nanoscale devices 

Nanoscale design of polarization in ultrathin ferroelectric heterostructures OPEN
Gabriele De Luca, Nives Strkalj, Sebastian Manz, Corinne Bouillet, Manfred Fiebig & Morgan Trassin

Ferroelectric heterostructures exhibit a range of functional properties; however control of their growth remains a challenge. De  Luca et al., demonstrate in-situ optical second harmonic generation to monitor and tailor the polarisation and growth of multilayer barium titanate and bismuth ferrite films.

10 November 2017 | doi: 10.1038/s41467-017-01620-2
Ferroelectrics and multiferroics  Surfaces, interfaces and thin films 

Symmetry control of nanorod superlattice driven by a governing force OPEN
Yujia Liang, Yong Xie, Dongxue Chen, Chuanfei Guo, Shuai Hou, Tao Wen, Fengyou Yang, Ke Deng, Xiaochun Wu, Ivan I. Smalyukh & Qian Liu

Shape complementarity is the primary way to control the symmetry of nanoparticle assemblies. Here, the authors introduce a governing force that dominates symmetry control of nanorod superlattices, using it to obtain an unexpected and highly thermostable tetragonal lattice.

10 November 2017 | doi: 10.1038/s41467-017-01111-4
Nanoparticles  Self-assembly  Surface chemistry 

Semisynthetic fluorescent pH sensors for imaging exocytosis and endocytosis OPEN
Magalie Martineau, Agila Somasundaram, Jonathan B. Grimm, Todd D. Gruber, Daniel Choquet, Justin W. Taraska, Luke D. Lavis & David Perrais

Existing pH-sensitive red fluorescent protein probes don’t perform well in monitoring exocytosis and endocytosis. Here, the authors combine organic dyes with self-labeling tags or antibodies to develop semisynthetic protein conjugates that can image synaptic vesicle fusion events in living cells.

10 November 2017 | doi: 10.1038/s41467-017-01752-5
Exocytosis  Fluorescence imaging  Sensors and probes  Synaptic vesicle exocytosis 

Phospholipid flippase ATP11C is endocytosed and downregulated following Ca2+-mediated protein kinase C activation OPEN
Hiroyuki Takatsu, Masahiro Takayama, Tomoki Naito, Naoto Takada, Kazuya Tsumagari, Yasushi Ishihama, Kazuhisa Nakayama & Hye-Won Shin

ATP11C is a flippase that uses ATP hydrolysis to translocate phospholipids at the plasma membrane. Here, the authors show that the activation of Ca2+-dependent protein kinase C increases ATP11C endocytosis thus downregulating phospholipid translocation.

10 November 2017 | doi: 10.1038/s41467-017-01338-1
Calcium signalling  Endocytosis 

Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging OPEN
Denis Ptchelkine, Ashley Gillum, Tomohiro Mochizuki, Soizick Lucas-Staat, Ying Liu, Mart Krupovic, Simon E. V. Phillips, David Prangishvili & Juha T. Huiskonen

The rod-shaped virus APBV1 is among the most thermostable viruses known. Here, Ptchelkine et al. determine its structure at near-atomic resolution, show that the DNA is packed as left-handed superhelix and identify extended hydrophobic interfaces that likely contribute to the extreme thermostability of the capsid.

10 November 2017 | doi: 10.1038/s41467-017-01668-0
Archaea  Electron microscopy  Virus structures 

Global patterns of nitrate storage in the vadose zone OPEN
M. J. Ascott, D. C. Gooddy, L. Wang, M. E. Stuart, M. A. Lewis, R. S. Ward & A. M. Binley

Current global-scale nitrogen (N) budgets quantifying anthropogenic impacts on the N cycle do not explicitly consider nitrate storage in the vadose zone. Here, using estimates of depth to groundwater and nitrate leaching between 1900–2000, the authors show that the vadose zone is an important store of nitrate.

10 November 2017 | doi: 10.1038/s41467-017-01321-w
Element cycles  Hydrogeology  Hydrology 

KSRP specifies monocytic and granulocytic differentiation through regulating miR-129 biogenesis and RUNX1 expression OPEN
Hongmei Zhao, Xiaoshuang Wang, Ping Yi, Yanmin Si, Puwen Tan, Jinrong He, Shan Yu, Yue Ren, Yanni Ma, Junwu Zhang, Dong Wang, Fang Wang & Jia Yu

RNA-binding proteins (RBPs) regulate RNA activity and are implicated in haematopoietic malignancies, but their role in myeloid cell specification is unclear. Here, the authors show a role for the RBP KSRP in promoting granulocyte fate over monocyte fate through the biogenesis of miR-129 and a decrease in RUNX1.

10 November 2017 | doi: 10.1038/s41467-017-01425-3
Differentiation  miRNAs  Myelopoiesis  RNA 

Natural variation of YELLOW SEEDLING1 affects photosynthetic acclimation of Arabidopsis thaliana  OPEN
Roxanne van Rooijen, Willem Kruijer, René Boesten, Fred A. van Eeuwijk, Jeremy Harbinson & Mark G. M. Aarts

Natural genetic variation of photosynthesis is an underexplored resource for plant genetic improvement. Here, the authors find allelic variations of YS1 affect Arabidopsis photosynthesis acclimation using genome-wide association study, reverse genetics, and quantitative complementation approaches.

10 November 2017 | doi: 10.1038/s41467-017-01576-3
Genome-wide association studies  Natural variation in plants  Photosystem II 

A glimpse of gluons through deeply virtual compton scattering on the proton OPEN
M. Defurne, A. Martí Jiménez-Argüello, Z. Ahmed, H. Albataineh, K. Allada, K. A. Aniol, V. Bellini, M. Benali, W. Boeglin, P. Bertin, M. Brossard, A. Camsonne, M. Canan, S. Chandavar, C. Chen, J.-P. Chen, C. W. de Jager, R. de Leo, C. Desnault, A. Deur et al.

It remains a challenge to find the structure and the distribution of the constituents of nucleons. Here the authors use a scattering method to get information about the gluons and quarks inside a proton and separate the contribution of Bethe-Heitler from the deeply virtual Compton scattering process.

10 November 2017 | doi: 10.1038/s41467-017-01819-3
Experimental nuclear physics  Experimental particle physics  Phenomenology 

Outflow of cerebrospinal fluid is predominantly through lymphatic vessels and is reduced in aged mice OPEN
Qiaoli Ma, Benjamin V. Ineichen, Michael Detmar & Steven T. Proulx

It is believed that the bulk of cerebrospinal fluid (CSF) drains through arachnoid projections from the subarachnoid space to the dural venous sinuses. Here the authors show that the major outflow pathway for CSF in mice are lymphatic vessels and that this drainage decreases as the mice age.

10 November 2017 | doi: 10.1038/s41467-017-01484-6
Brain  Fluorescence imaging  Neuro–vascular interactions 

Resistance to cancer immunotherapy mediated by apoptosis of tumor-infiltrating lymphocytes OPEN
Jingjing Zhu, Céline G. Powis de Tenbossche, Stefania Cané, Didier Colau, Nicolas van Baren, Christophe Lurquin, Anne-Marie Schmitt-Verhulst, Peter Liljeström, Catherine Uyttenhove & Benoit J. Van den Eynde

Cancer immunotherapy is ineffective in a subset of patients. Here the authors show that, in a mouse model of melanoma, resistance to immune checkpoint inhibitors relies on loss of tumor-specific T cells through FasL-mediated apoptosis triggered by polymorphonuclear-myeloid-derived suppressor cells.

10 November 2017 | doi: 10.1038/s41467-017-00784-1
Cancer immunotherapy  Melanoma  Tumour immunology 

Structural basis of arrestin-3 activation and signaling OPEN
Qiuyan Chen, Nicole A. Perry, Sergey A. Vishnivetskiy, Sandra Berndt, Nathaniel C. Gilbert, Ya Zhuo, Prashant K. Singh, Jonas Tholen, Melanie D. Ohi, Eugenia V. Gurevich, Chad A. Brautigam, Candice S. Klug, Vsevolod V. Gurevich & T. M. Iverson

While arrestins are mainly associated with GPCR signaling, arrestin-3 can signal independently of receptor interaction. Here the authors present the structure of arrestin-3 bound to inositol hexakisphosphate (IP6) and propose a model for arrestin-3 activation.

10 November 2017 | doi: 10.1038/s41467-017-01218-8
Cell signalling  G protein-coupled receptors  X-ray crystallography 

Identification of a peptide recognizing cerebrovascular changes in mouse models of Alzheimer’s disease OPEN
Aman P. Mann, Pablo Scodeller, Sazid Hussain, Gary B. Braun, Tarmo Mölder, Kadri Toome, Rajesh Ambasudhan, Tambet Teesalu, Stuart A. Lipton & Erkki Ruoslahti

Cerebrovascular changes and astrogliosis occur in Alzheimer’s disease (AD). Using an in vivo phage display technique, the authors identified a peptide that upon systematic administration, can home to brain endothelial cells and astrocytes in mouse models of AD at the early stages of the disease.

10 November 2017 | doi: 10.1038/s41467-017-01096-0
Alzheimer's disease  Neuro–vascular interactions 

Direct catalytic hydrogenation of CO2 to formate over a Schiff-base-mediated gold nanocatalyst OPEN
Qinggang Liu, Xiaofeng Yang, Lin Li, Shu Miao, Yong Li, Yanqin Li, Xinkui Wang, Yanqiang Huang & Tao Zhang

Bicarbonate reduction is a bottleneck step of the CO2 hydrogenation to formic acid in alkaline solution. Here, the authors show a highly active Schiff-base-modified gold nanocatalyst for the efficient reduction of CO2 to formic acid under relatively mild conditions.

10 November 2017 | doi: 10.1038/s41467-017-01673-3
Carbon capture and storage  Catalytic mechanisms  Chemical hydrogen storage  Heterogeneous catalysis 

Purcell-enhanced quantum yield from carbon nanotube excitons coupled to plasmonic nanocavities OPEN
Yue Luo, Ehsaneh D. Ahmadi, Kamran Shayan, Yichen Ma, Kevin S. Mistry, Changjian Zhang, James Hone, Jeffrey L. Blackburn & Stefan Strauf

Single-walled carbon nanotubes offer exciting optoelectronic applications but generally suffer from low quantum yields. Here, Luo et al. demonstrate that coupling nanotubes to plasmonic antennas can lead to large Purcell enhancement and corresponding increase in quantum yield as well as plasmonic thermometry at the single molecule level.

10 November 2017 | doi: 10.1038/s41467-017-01777-w
Carbon nanotubes and fullerenes  Nanophotonics and plasmonics  Optical materials  Single photons and quantum effects 

Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB OPEN
Simon N. Willis, Julie Tellier, Yang Liao, Stephanie Trezise, Amanda Light, Kristy O’Donnell, Lee Ann Garrett-Sinha, Wei Shi, David M. Tarlinton & Stephen L. Nutt

Although important for early development, PU.1 is dispensable for mature B cell function, possibly owing to compensation by the related transcription factor SpiB. Here the authors show PU.1 and SpiB are collectively required for humoral immunity, through regulation of germinal centre formation and plasma cell differentiation.

10 November 2017 | doi: 10.1038/s41467-017-01605-1
Antibodies  Gene regulation in immune cells 

Tsg101 chaperone function revealed by HIV-1 assembly inhibitors OPEN
Madeleine Strickland, Lorna S. Ehrlich, Susan Watanabe, Mahfuz Khan, Marie-Paule Strub, Chi-Hao Luan, Michael D. Powell, Jonathan Leis, Nico Tjandra & Carol A. Carter

Tsg101 is a component of the host cellular ESCRT machinery and is required for HIV-1 replication. Here, the authors show that disruption of ubiquitin binding of the Tsg101 UEV domain through commonly used drugs arrests virus assembly, which might facilitate the development of potent HIV inhibitors.

09 November 2017 | doi: 10.1038/s41467-017-01426-2
Antivirals  Solution-state NMR 

A water-soluble nucleolin aptamer-paclitaxel conjugate for tumor-specific targeting in ovarian cancer OPEN
Fangfei Li, Jun Lu, Jin Liu, Chao Liang, Maolin Wang, Luyao Wang, Defang Li, Houzong Yao, Qiulong Zhang, Jia Wen, Zong-Kang Zhang, Jie Li, Quanxia Lv, Xiaojuan He, Baosheng Guo, Daogang Guan, Yuanyuan Yu, Lei Dang, Xiaohao Wu, Yongshu Li et al.

Paclitaxel, a first line chemotherapeutic drug, suffers from poor water solubility and low tissue selectivity. Here, the authors report a water-soluble nucleolin aptamer-paclitaxel conjugate that selectively accumulates in ovarian tumor issues displaying reduced toxicity and improved activity profiles.

09 November 2017 | doi: 10.1038/s41467-017-01565-6
DNA and RNA  Drug delivery  Drug development 

Depleted depletion drives polymer swelling in poor solvent mixtures OPEN
Debashish Mukherji, Carlos M. Marques, Torsten Stuehn & Kurt Kremer

Whilst polymer collapse in a single poor solvent is well understood, polymer swelling in mixtures of two repulsive solvents is surprising. Here, the authors unveil the microscopic origin of collapse-swelling-collapse behaviour, showing how it emerges at constant pressure when a balance of depletion interactions is achieved.

09 November 2017 | doi: 10.1038/s41467-017-01520-5
Chemical physics  Colloids  Polymers 

AIP limits neurotransmitter release by inhibiting calcium bursts from the ryanodine receptor OPEN
Bojun Chen, Ping Liu, Edward J. Hujber, Yan Li, Erik M. Jorgensen & Zhao-Wen Wang

In this work the authors show that AIP (aryl hydrocarbon receptor-interacting protein), a gene frequently mutated in association with pituitary tumors, regulates neurotransmitter release by inhibiting calcium release from ryanodine receptors.

09 November 2017 | doi: 10.1038/s41467-017-01704-z
Neurophysiology  Synaptic vesicle exocytosis 

Organocatalytic enantio- and diastereoselective cycloetherification via dynamic kinetic resolution of chiral cyanohydrins OPEN
Naoki Yoneda, Yuki Fujii, Akira Matsumoto, Keisuke Asano & Seijiro Matsubara

Enantioselective synthesis of six-membered oxacycles with multiple stereogenic centres is essential for the discovery of new therapeutic agents. Here the authors show organocatalytic cycloetherification for the highly enantio- and diastereoselective synthesis of tetrahydropyrans.

09 November 2017 | doi: 10.1038/s41467-017-01099-x
Drug development  Drug discovery and development  Organocatalysis  Stereochemistry 

A mechanism for FtsZ-independent proliferation in Streptomyces  OPEN
Fernando Santos-Beneit, David M. Roberts, Stuart Cantlay, Joseph R. McCormick & Jeff Errington

Protein FtsZ plays key roles in cell division and is essential in most bacterial species; exceptions include streptomycetes, which grow from the cell tip and form branched hyphae. Here, Santos-Beneit et al. show that branching allows FtsZ-independent proliferation in Streptomyces venezuelae.

09 November 2017 | doi: 10.1038/s41467-017-01596-z
Bacteriology  Cell division  Cellular microbiology 

Thermal crumpling of perforated two-dimensional sheets OPEN
David Yllanes, Sourav S. Bhabesh, David R. Nelson & Mark J. Bowick

Two-dimensional elastic membranes show great potential as functional materials, but how to engineer them with tunable mechanical properties remains challenging. Here, Yllanes et al. propose a method to induce the onset of crumpling transition in graphene-like sheets by simply altering their geometries.

09 November 2017 | doi: 10.1038/s41467-017-01551-y
Condensed-matter physics  Soft materials 

Spatio-temporally separated cortical flows and spindle geometry establish physical asymmetry in fly neural stem cells OPEN
Chantal Roubinet, Anna Tsankova, Tri Thanh Pham, Arnaud Monnard, Emmanuel Caussinus, Markus Affolter & Clemens Cabernard

Asymmetric cell division can generate daughter cells with cell size asymmetry, but the underlying mechanisms are not clear. Here the authors show that spatiotemporally controlled Myosin flows together with spindle asymmetry and positioning control cleavage furrow position and cortical expansion to establish physical asymmetry.

09 November 2017 | doi: 10.1038/s41467-017-01391-w
Cytokinesis  Mitosis 

Total morphosynthesis of biomimetic prismatic-type CaCO3 thin films OPEN
Chuanlian Xiao, Ming Li, Bingjun Wang, Ming-Feng Liu, Changyu Shao, Haihua Pan, Yong Lu, Bin-Bin Xu, Siwei Li, Da Zhan, Yuan Jiang, Ruikang Tang, Xiang Yang Liu & Helmut Cölfen

The exterior layers of mollusk shells are prismatic in nature, endowing them with stiffness and wear resistance. Inspired by these biominerals, here, Jiang and colleagues grow structurally similar prismatic-type CaCO3 thin films with comparable stiffness and hardness.

09 November 2017 | doi: 10.1038/s41467-017-01719-6
Biomineralization  Materials chemistry  Structural materials 

Polymorphic regenerated silk fibers assembled through bioinspired spinning OPEN
Shengjie Ling, Zhao Qin, Chunmei Li, Wenwen Huang, David L. Kaplan & Markus J. Buehler

Natural silk fibers are produced using a simple and green approach compared to alternative synthetic methods. Here, the authors show a bioinspired approach to spin regenerated silk fibers using anisotropic liquid crystals and dry spinning, resulting in remarkably robust fibers.

09 November 2017 | doi: 10.1038/s41467-017-00613-5
Bioinspired materials  Biological fluorescence  Environmental impact  Mechanical engineering  Synthesis and processing 

Electromagnetic scattering laws in Weyl systems OPEN
Ming Zhou, Lei Ying, Ling Lu, Lei Shi, Jian Zi & Zongfu Yu

Scattering characteristics are important optical properties but they depend strongly on the relative electromagnetic size and environment of a particle. Here, the authors study the frequency-dependence of the scattering cross section for a scatterer located inside a photonic Weyl system.

09 November 2017 | doi: 10.1038/s41467-017-01533-0
Optical physics  Photonic crystals 

Supramolecular networks stabilise and functionalise black phosphorus OPEN
Vladimir V. Korolkov, Ivan G. Timokhin, Rolf Haubrichs, Emily F. Smith, Lixu Yang, Sihai Yang, Neil R. Champness, Martin Schröder & Peter H. Beton

Few-layered black phosphorus has been exploited in transistors and other devices, but its poor stability under ambient conditions remains problematic. Here, a UK-Swiss collaboration show that a monolayer-thick supramolecular hydrogen-bonded network can protect a black phosphorus surface for over a month.

09 November 2017 | doi: 10.1038/s41467-017-01797-6
Scanning probe microscopy  Surface assembly  Two-dimensional materials 

Membrane curvature induced by proximity of anionic phospholipids can initiate endocytosis OPEN
Takashi Hirama, Stella M. Lu, Jason G. Kay, Masashi Maekawa, Michael M. Kozlov, Sergio Grinstein & Gregory D. Fairn

The plasma membrane is enriched in phosphatidylserine (PtdSer) mostly localized at the inner leaflet, which is predicted to induce membrane curvature. Here the authors show that membrane curvature induced by the proximity of anionic phospholipids can induce endocytosis and that cholesterol limits spontaneous curvature.

09 November 2017 | doi: 10.1038/s41467-017-01554-9
Cell biology  Membrane biophysics 

Observation of transverse spin Nernst magnetoresistance induced by thermal spin current in ferromagnet/non-magnet bilayers OPEN
Dong-Jun Kim, Chul-Yeon Jeon, Jong-Guk Choi, Jae Wook Lee, Srivathsava Surabhi, Jong-Ryul Jeong, Kyung-Jin Lee & Byong-Guk Park

Pure spin current generated thermally in nonmagnetic materials known as spin Nernst effect has not been demonstrated experimentally. Here, the authors report the observation of spin Nernst effect by studying the thermally-induced transverse magnetoresistance in ferromagnet/non-magnet heavy metal bilayers

09 November 2017 | doi: 10.1038/s41467-017-01493-5
Magnetic properties and materials  Spintronics 

Developmental diet regulates Drosophila lifespan via lipid autotoxins OPEN
M. Irina Stefana, Paul C. Driscoll, Fumiaki Obata, Ana Raquel Pengelly, Clare L. Newell, James I. MacRae & Alex P. Gould

The diet consumed during development can have long-lasting effects on adult physiology. Here, the authors show that developmental undernutrition in Drosophila extends lifespan by inhibiting the production of toxic lipids, called autotoxins, on the adult body surface.

09 November 2017 | doi: 10.1038/s41467-017-01740-9
Ageing  Drosophila 

Label-free automated three-dimensional imaging of whole organs by microtomy-assisted photoacoustic microscopy OPEN
Terence T. W. Wong, Ruiying Zhang, Chi Zhang, Hsun-Chia Hsu, Konstantin I. Maslov, Lidai Wang, Junhui Shi, Ruimin Chen, K. Kirk Shung, Qifa Zhou & Lihong V. Wang

The state-of-the-art three-dimensional biomedical imaging often requires specific tissue preparation that may alter the physical properties of the specimen causing loss of information. Here Wong et al. develop a microtomy-assisted photoacoustic microscopy that allows imaging of biological samples without labelling agents and with reduced sectioning.

09 November 2017 | doi: 10.1038/s41467-017-01649-3
Imaging  Microscopy 

ATR kinase inhibition induces unscheduled origin firing through a Cdc7-dependent association between GINS and And-1 OPEN
Tatiana Moiseeva, Brian Hood, Sandy Schamus, Mark J. O’Connor, Thomas P. Conrads & Christopher J. Bakkenist

ATR kinase activity is essential for slowing replication forks and preventing DNA replication in cells with DNA damage. Here the authors show that ATR inhibition leads to Cdc7 phosphorylation of GINS, leading to origin firing.

09 November 2017 | doi: 10.1038/s41467-017-01401-x
Checkpoint signalling  Kinases 

Influenza virus genome reaches the plasma membrane via a modified endoplasmic reticulum and Rab11-dependent vesicles OPEN
Isabel Fernández de Castro Martin, Guillaume Fournier, Martin Sachse, Javier Pizarro-Cerda, Cristina Risco & Nadia Naffakh

Transport of neo-synthesized influenza A virus viral ribonucleoproteins (vRNPs) from the nucleus to the plasma membrane involves Rab 11 but the mechanism is unclear. Here the authors show that vRNPs are transported through a modified Rab11-positive endoplasmic reticulum and Rab11-dependent vesicles.

09 November 2017 | doi: 10.1038/s41467-017-01557-6
Endoplasmic reticulum  Influenza virus 

Structural insights into DNA cleavage activation of CRISPR-Cas9 system OPEN
Cong Huai, Gan Li, Ruijie Yao, Yingyi Zhang, Mi Cao, Liangliang Kong, Chenqiang Jia, Hui Yuan, Hongyan Chen, Daru Lu & Qiang Huang

CRISPR-Cas9 is widely used for genome engineering but structural data for the DNA cleavage step are still incomplete. Here, the authors present the cryo-EM structure of a ternary Cas9-sgRNA-target DNA complex, perform MD simulations and discuss implications for the Cas9 DNA cleavage mechanism.

09 November 2017 | doi: 10.1038/s41467-017-01496-2
CRISPR-Cas systems  Cryoelectron microscopy  Enzyme mechanisms 

Assessing the impact of imperfect adherence to artemether-lumefantrine on malaria treatment outcomes using within-host modelling OPEN
Joseph D. Challenger, Katia Bruxvoort, Azra C. Ghani & Lucy C. Okell

Artemether lumefantrine is widely used for the treatment of uncomplicated malaria. The impact of imperfect patient adherence to the six-dose regimen is hard to assess. Using adherence data for unsupervised patients, the authors model how suboptimal adherence affects treatment outcomes.

09 November 2017 | doi: 10.1038/s41467-017-01352-3
Computational models  Malaria  Parasitology 

Re-designing Interleukin-12 to enhance its safety and potential as an anti-tumor immunotherapeutic agent OPEN
Pengju Wang, Xiaozhu Li, Jiwei Wang, Dongling Gao, Yuenan Li, Haoze Li, Yongchao Chu, Zhongxian Zhang, Hongtao Liu, Guozhong Jiang, Zhenguo Cheng, Shengdian Wang, Jianzeng Dong, Baisui Feng, Louisa S. Chard, Nicholas R. Lemoine & Yaohe Wang

Interleukin-12 (IL-12) is a potent immunotherapeutic agent.

09 November 2017 | doi: 10.1038/s41467-017-01385-8
Cancer models  Cancer therapy  Immunization  Pancreatic cancer 

DNA methylation at enhancers identifies distinct breast cancer lineages OPEN
Thomas Fleischer, Xavier Tekpli, Anthony Mathelier, Shixiong Wang, Daniel Nebdal, Hari P. Dhakal, Kristine Kleivi Sahlberg, Ellen Schlichting, Anne-Lise Børresen-Dale, Elin Borgen, Bjørn Naume, Ragnhild Eskeland, Arnoldo Frigessi, Jörg Tost, Antoni Hurtado & Vessela N. Kristensen

Breast cancers are classified based on gene expression profiles but it is well known that DNA methylation patterns are also altered. Here the authors, by combining genome-wide DNA methylation and gene expression analysis, identify transcriptional networks regulated by DNA methylation at enhancers able to separate specific breast cancer subtypes.

09 November 2017 | doi: 10.1038/s41467-017-00510-x
Breast cancer  Cancer epigenetics 

In situ real-time gravimetric and viscoelastic probing of surface films formation on lithium batteries electrodes OPEN
Vadim Dargel, Netanel Shpigel, Sergey Sigalov, Prasant Nayak, Mikhael D. Levi, Leonid Daikhin & Doron Aurbach

The solid-electrolyte interphase formed on Li-battery electrodes strongly affects their cycling performance, however the mechanical properties of the surface films are not well-known. Here the authors report a sensitive gravimetric/viscoelastic method to probe surface film formation on composite electrodes, coupled with Li-ion intercalation.

09 November 2017 | doi: 10.1038/s41467-017-01722-x
Batteries  Characterization and analytical techniques 

PINK1-mediated phosphorylation of LETM1 regulates mitochondrial calcium transport and protects neurons against mitochondrial stress OPEN
En Huang, Dianbo Qu, Tianwen Huang, Nicoletta Rizzi, Wassamon Boonying, Dorothy Krolak, Paolo Ciana, John Woulfe, Christine Klein, Ruth S. Slack, Daniel Figeys & David S. Park

Mutations in the mitochondrial kinase PINK1 result in familial Parkinson’s disease. Here the authors show that LETM1, a mitochondrial inner membrane protein, is a substrate of PINK1 that regulates Ca2+ handling in mitochondria in response to mitochondrial toxins.

09 November 2017 | doi: 10.1038/s41467-017-01435-1
Parkinson's disease  Phosphorylation 

The self-healing of defects induced by the hydriding phase transformation in palladium nanoparticles OPEN
A. Ulvestad & A. Yau

Nanoscale materials commonly have improved properties over their bulk counterparts. Here, the authors use Bragg coherent diffractive imaging to reveal that Pd nanoparticles can self-heal crystallographic defects induced during the hydriding phase transformation, making them more resistant to strain-induced damage.

09 November 2017 | doi: 10.1038/s41467-017-01548-7
Condensed-matter physics  Materials for energy and catalysis  Nanoscale materials 

Effect of nitrogen atom positioning on the trade-off between emissive and photocatalytic properties of carbon dots OPEN
Santanu Bhattacharyya, Florian Ehrat, Patrick Urban, Roland Teves, Regina Wyrwich, Markus Döblinger, Jochen Feldmann, Alexander S. Urban & Jacek K. Stolarczyk

Carbon dots are an emergent class of nanomaterials that hold promise for innovations in imaging, sensing, and catalytic technologies. Here, Stolarczyk and colleagues control the nitrogen-atom content and location within carbon dots, reporting the resulting impact on emissivity and photocatalytic behaviour.

09 November 2017 | doi: 10.1038/s41467-017-01463-x
Nanoparticles  Photocatalysis  Synthesis and processing 

Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1 OPEN
Tianlong Zhang, Rong Wang, Zhijing Wang, Xiangxiang Wang, Fang Wang & Jianping Ding

Activated Rag GTPases recruit mTORC1 to lysosomes. Here the authors present the crystal structure of the Ragulator complex and identify the binding sites for the Roadblock domains of Rag GTPases, which gives insights how Rag GTPases are tethered to the lysosomal membrane.

09 November 2017 | doi: 10.1038/s41467-017-01567-4
TOR signalling  X-ray crystallography 

Prevalence and detection of low-allele-fraction variants in clinical cancer samples OPEN
Hyun-Tae Shin, Yoon-La Choi, Jae Won Yun, Nayoung K. D. Kim, Sook-Young Kim, Hyo Jeong Jeon, Jae-Yong Nam, Chung Lee, Daeun Ryu, Sang Cheol Kim, Kyunghee Park, Eunjin Lee, Joon Seol Bae, Dae Soon Son, Je-Gun Joung, Jeeyun Lee, Seung Tae Kim, Myung-Ju Ahn, Se-Hoon Lee, Jin Seok Ahn et al.

High-throughput sequencing is used to identify somatic variants in cancer patients. Here, the authors perform panel-based profiling of 5095 clinical samples and demonstrate that many clinically-actionable variants have low variant allele fractions, requiring assays with high detection sensitivity.

09 November 2017 | doi: 10.1038/s41467-017-01470-y
Cancer genetics  Oncology  Targeted resequencing 
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Erratum: Organocatalyzed synthesis of fluorinated poly(aryl thioethers) OPEN
Nathaniel H. Park, Gabriel dos Passos Gomes, Mareva Fevre, Gavin O. Jones, Igor V. Alabugin & James L. Hedrick
13 November 2017 | doi: 10.1038/s41467-017-01129-8
Polymer synthesis  Polymerization mechanisms 
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Corrigendum: Infrared light excites cells by changing their electrical capacitance OPEN
Mikhail G. Shapiro, Kazuaki Homma, Sebastian Villarreal, Claus-Peter Richter & Francisco Bezanilla
10 November 2017 | doi: 10.1038/ncomms16148
Electrophysiology  Membrane biophysics 
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