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Nature Communications - 24 August 2017

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  Latest Correspondence    
Correspondence: The experimental requirements for a photon thermal diode OPEN
Bair V. Budaev
21 August 2017 | doi: 10.1038/ncomms16135
Applied physics  Mechanical engineering  Photonic devices 

Correspondence: Reply to ‘The experimental requirements for a photon thermal diode’ OPEN
Zhen Chen, Carlaton Wong, Sean Lubner, Shannon Yee, John Miller, Wanyoung Jang, Corey Hardin, Anthony Fong, Javier E. Garay & Chris Dames
21 August 2017 | doi: 10.1038/ncomms16136
Energy science and technology  Mechanical engineering 
  Latest Articles View all Articles  

Myosin efflux promotes cell elongation to coordinate chromosome segregation with cell cleavage OPEN
Emilie Montembault, Marie-Charlotte Claverie, Lou Bouit, Cedric Landmann, James Jenkins, Anna Tsankova, Clemens Cabernard & Anne Royou

Chromatid segregation must be coordinated with cytokinesis to preserve genomic stability. Here the authors show that cells clear trailing chromatids from the cleavage site in a two-step cell elongation and demonstrate the role of myosin efflux in the second phase.

23 August 2017 | doi: 10.1038/s41467-017-00337-6
Chromosome segregation  Cytokinesis 

Diffusive and arrested transport of atoms under tailored disorder OPEN
Fangzhao Alex An, Eric J. Meier & Bryce Gadway

Cold atom quantum simulation has had challenges in realising the tailored, dynamic types of disorder relevant to real materials. Here, the authors use synthetic momentum-space lattices to engineer spatially and dynamically controlled disorder to observe ballistic, diffusive, and arrested atomic transport.

23 August 2017 | doi: 10.1038/s41467-017-00387-w
Bose–Einstein condensates  Ultracold gases 

Extracellular-matrix-mediated osmotic pressure drives Vibrio cholerae biofilm expansion and cheater exclusion OPEN
Jing Yan, Carey D. Nadell, Howard A. Stone, Ned S. Wingreen & Bonnie L. Bassler

Most bacteria live in biofilms, surface-attached communities encased in an extracellular matrix. Here, Yan et al. show that matrix production in Vibrio cholerae increases the osmotic pressure within the biofilm, promoting biofilm expansion and physical exclusion of non-matrix producing cheaters.

23 August 2017 | doi: 10.1038/s41467-017-00401-1
Biofilms  Biomaterials  Cellular microbiology 

RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes OPEN
Joseph Abatemarco, Maen F. Sarhan, James M. Wagner, Jyun-Liang Lin, Leqian Liu, Wafa Hassouneh, Shuo-Fu Yuan, Hal S. Alper & Adam R. Abate

Screening libraries of genetically engineered microbes for secreted products is limited by the available assay throughput. Here the authors combine aptamer-based fluorescent detection with droplet microfluidics to achieve high throughput screening of yeast strains engineered for enhanced tyrosine or streptavidin production.

23 August 2017 | doi: 10.1038/s41467-017-00425-7
High-throughput screening  Microfluidics  Synthetic biology 

Flow-induced elongation of von Willebrand factor precedes tension-dependent activation OPEN
Hongxia Fu, Yan Jiang, Darren Yang, Friedrich Scheiflinger, Wesley P. Wong & Timothy A. Springer

Von Willebrand factor (VWF) is a blood protein involved in clotting and is proposed to be activated by flow, but the mechanism is unknown. Here the authors show that VWF is first converted from a compact to linear form by flow, and is subsequently activated to bind GPIbα in a tension-dependent manner.

23 August 2017 | doi: 10.1038/s41467-017-00230-2
Immunology  Single-molecule biophysics 

Live-cell p53 single-molecule binding is modulated by C-terminal acetylation and correlates with transcriptional activity OPEN
Alessia Loffreda, Emanuela Jacchetti, Sofia Antunes, Paolo Rainone, Tiziana Daniele, Tatsuya Morisaki, Marco E. Bianchi, Carlo Tacchetti & Davide Mazza

Both transcription binding kinetics and post-translational modifications of transcription factors are thought to play a role in the modulation of transcription. Here the authors use single-molecule tracking to directly demonstrate that p53 acetylation modulates promoter residence time and transcriptional activity.

22 August 2017 | doi: 10.1038/s41467-017-00398-7
Microscopy  Single-molecule biophysics  Transcription  Tumour-suppressor proteins 

Layered van der Waals crystals with hyperbolic light dispersion OPEN
M. N. Gjerding, R. Petersen, T. G. Pedersen, N. A. Mortensen & K. S. Thygesen

Natural hyperbolic materials retain the peculiar optical properties of traditional metamaterials whilst not requiring artificial structuring. Here, the authors perform a theoretical screening of a large class of natural materials with hyperbolic dispersion among the family of layered transition metal dichalcogenides.

22 August 2017 | doi: 10.1038/s41467-017-00412-y
Electronic properties and materials  Metamaterials  Nanophotonics and plasmonics 

Lapsyn controls branch extension and positioning of astrocyte-like glia in the Drosophila optic lobe OPEN
Benjamin Richier, Cristina de Miguel Vijandi, Stefanie Mackensen & Iris Salecker

How glial cells, such as astrocytes, acquire their characteristic morphology during development is poorly understood. Here the authors describe the morphogenesis of astrocyte-like glia in the Drosophila optic lobe, and through a RNAi screen, they identify a transmembrane LRR protein–Lapsyn–that plays a critical role in this process.

22 August 2017 | doi: 10.1038/s41467-017-00384-z
Development of the nervous system  Glial biology 

Interspecies nutrient extraction and toxin delivery between bacteria OPEN
Ofer Stempler, Amit K. Baidya, Saurabh Bhattacharya, Ganesh Babu Malli Mohan, Elhanan Tzipilevich, Lior Sinai, Gideon Mamou & Sigal Ben-Yehuda

Bacteria can exchange nutrients and macromolecules through tubular membranous structures called nanotubes. Here, the authors show that Bacillus subtilis can kill and prey on Bacillus megaterium by delivering a toxin and extracting nutrients in a nanotube-dependent manner.

22 August 2017 | doi: 10.1038/s41467-017-00344-7
Bacterial toxins  Bacteriology  Cellular microbiology  Microbial ecology 

SIRT7 antagonizes TGF-β signaling and inhibits breast cancer metastasis OPEN
Xiaolong Tang, Lei Shi, Ni Xie, Zuojun Liu, Minxian Qian, Fanbiao Meng, Qingyang Xu, Mingyan Zhou, Xinyue Cao, Wei-Guo Zhu & Baohua Liu

Metastatic disease is the major reason for breast cancer-related deaths; therefore, a better understanding of this process and its players is needed. Here the authors report the role of SIRT7 in inhibiting SMAD4-mediated breast cancer metastasis providing a possible therapeutic avenue.

22 August 2017 | doi: 10.1038/s41467-017-00396-9
Acetylation  Breast cancer 

Computational prediction of new auxetic materials OPEN
John Dagdelen, Joseph Montoya, Maarten de Jong & Kristin Persson

There are very few inorganic materials with auxetic homogenous Poisson’s ratio in polycrystalline form. Here authors develop an approach to screening materials databases for target properties such as negative Poisson’s ratio by using stability and structural motifs to predict new instances of homogenous auxetic behavior as well as a number of materials with near-zero Poisson’s ratio.

22 August 2017 | doi: 10.1038/s41467-017-00399-6
Computational methods  Materials for devices 

A three enzyme system to generate the Strychnos alkaloid scaffold from a central biosynthetic intermediate OPEN
Evangelos C. Tatsis, Inês Carqueijeiro, Thomas Dugé de Bernonville, Jakob Franke, Thu-Thuy T. Dang, Audrey Oudin, Arnaud Lanoue, Florent Lafontaine, Anna K. Stavrinides, Marc Clastre, Vincent Courdavault & Sarah E. O’Connor

The biosynthetic pathway of preakuammicine, a monoterpene precursor of the anti-cancer agent vinblastine, has remained largely unexplored. Here, the authors provide transcriptomic and biochemical data to identify two enzymes that, in tandem, convert strictosidine to akuammicine, the stable shunt product of preakuammicine.

22 August 2017 | doi: 10.1038/s41467-017-00154-x
Biocatalysis  Biosynthesis 

Tunable two-dimensional interfacial coupling in molecular heterostructures OPEN
Beibei Xu, Himanshu Chakraborty, Vivek K. Yadav, Zhuolei Zhang, Michael L. Klein & Shenqiang Ren

Two-dimensional van der Waals heterostructures are of interest due to their unique interlayer coupling and optoelectronic properties. Here authors develop a Langmuir-Blodgett method to organize charge transfer molecular heterostructures with externally tunable conductance and capacitance and broadband photoresponse.

22 August 2017 | doi: 10.1038/s41467-017-00390-1
Molecular self-assembly  Organic molecules in materials science 

Exit from quiescence displays a memory of cell growth and division OPEN
Xia Wang, Kotaro Fujimaki, Geoffrey C. Mitchell, Jungeun Sarah Kwon, Kimiko Della Croce, Chris Langsdorf, Hao Helen Zhang & Guang Yao

The quiescence-exit process is noisy even in genetically identical cells under the same environmental conditions. Here the authors show that the heterogeneity of quiescence exit reflects a memory of preceding cell growth at quiescence induction and immediate division history prior to quiescence entry.

22 August 2017 | doi: 10.1038/s41467-017-00367-0
Cell growth  Computer modelling 

Synthesis of quenchable amorphous diamond OPEN
Zhidan Zeng, Liuxiang Yang, Qiaoshi Zeng, Hongbo Lou, Hongwei Sheng, Jianguo Wen, Dean J. Miller, Yue Meng, Wenge Yang, Wendy L. Mao & Ho-kwang Mao

Diamond’s properties are dictated by its crystalline, fully tetrahedrally bonded structure. Here authors synthesize a bulk sp 3-bonded amorphous form of carbon under high pressure and temperature, show that it has bulk modulus comparable to crystalline diamond and that it can be recovered under ambient conditions.

22 August 2017 | doi: 10.1038/s41467-017-00395-w
Glasses  Mechanical properties 

BRCA locus-specific loss of heterozygosity in germline BRCA1 and BRCA2 carriers OPEN
Kara N. Maxwell, Bradley Wubbenhorst, Brandon M. Wenz, Daniel De Sloover, John Pluta, Lyndsey Emery, Amanda Barrett, Adam A. Kraya, Ioannis N. Anastopoulos, Shun Yu, Yuchao Jiang, Hao Chen, Nancy R. Zhang, Nicole Hackman, Kurt D’Andrea, Robert Daber, Jennifer J. D. Morrissette, Nandita Mitra, Michael Feldman, Susan M. Domchek et al.

Most tumours associated with germline BRCA1/BRCA2 loss of function mutations respond to DNA damaging agents, however, some do not. Herein, the authors identify that a subset of breast/ovarian tumors retain a normal allele, which is associated with decreased overall survival after DNA damage-inducing platinum chemotherapy.

22 August 2017 | doi: 10.1038/s41467-017-00388-9
Cancer genetics  Cancer genomics 

Acoustically actuated ultra-compact NEMS magnetoelectric antennas OPEN
Tianxiang Nan, Hwaider Lin, Yuan Gao, Alexei Matyushov, Guoliang Yu, Huaihao Chen, Neville Sun, Shengjun Wei, Zhiguang Wang, Menghui Li, Xinjun Wang, Amine Belkessam, Rongdi Guo, Brian Chen, James Zhou, Zhenyun Qian, Yu Hui, Matteo Rinaldi, Michael E. McConney, Brandon M. Howe et al.

The miniaturization of antennas beyond a wavelength is limited by designs which rely on electromagnetic resonances. Here, Nan et al. have developed acoustically actuated antennas that couple the acoustic resonance of the antenna with the electromagnetic wave, reducing the antenna footprint by up to 100.

22 August 2017 | doi: 10.1038/s41467-017-00343-8
Acoustics  Electrical and electronic engineering  Electronic devices  Ferroelectrics and multiferroics 

Fermion-induced quantum critical points OPEN
Zi-Xiang Li, Yi-Fan Jiang, Shao-Kai Jian & Hong Yao

Quantum phase transitions are governed by Landau-Ginzburg theory and the exceptions are rare. Here, Li et al. propose a type of Landau-forbidden quantum critical points induced by gapless fermions in two-dimensional Dirac semimetals.

22 August 2017 | doi: 10.1038/s41467-017-00167-6
Phase transitions and critical phenomena  Topological insulators 

CLEC5A is a critical receptor in innate immunity against Listeria infection OPEN
Szu-Ting Chen, Fei-Ju Li, Tzy-yun Hsu, Shu-Mei Liang, Yi-Chen Yeh, Wen-Yu Liao, Teh-Ying Chou, Nien-Jun Chen, Michael Hsiao, Wen-Bin Yang & Shie-Liang Hsieh

The lectin receptor CLEC5A is a pattern recognition receptor that has been shown to detect dengue and Japanese encephalitis virus. Here the authors show that CLEC5A is needed for optimal ROS production, NET formation and other immune responses to Listeria monocytogenes in mice.

21 August 2017 | doi: 10.1038/s41467-017-00356-3
Infection  Pattern recognition receptors 

Differential alternative splicing coupled to nonsense-mediated decay of mRNA ensures dietary restriction-induced longevity OPEN
Syed Shamsh Tabrez, Ravi Datta Sharma, Vaibhav Jain, Atif Ahmed Siddiqui & Arnab Mukhopadhyay

Alternative splicing coupled to nonsense-mediated decay (AS-NMD) is a conserved mechanism for post-transcriptional gene regulation. Here, the authors provide evidence that AS-NMD is enhanced during dietary restriction (DR) and is required for DR-mediated longevity assurance in C. elegans.

21 August 2017 | doi: 10.1038/s41467-017-00370-5
Ageing  Gene regulation  RNA splicing 

Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes OPEN
Vagheesh M. Narasimhan, Raheleh Rahbari, Aylwyn Scally, Arthur Wuster, Dan Mason, Yali Xue, John Wright, Richard C. Trembath, Eamonn R. Maher, David A. van Heel, Adam Auton, Matthew E. Hurles, Chris Tyler-Smith & Richard Durbin

Estimates of human mutation rates differ substantially based on the approach. Here, the authors present a multi-generational estimate from the autozygous segment in a non-European population that gives insight into the contribution of post-zygotic mutations and population-specific mutational processes.

21 August 2017 | doi: 10.1038/s41467-017-00323-y
Computational biology and bioinformatics  Genomics  Population genetics 

JunB promotes Th17 cell identity and restrains alternative CD4+ T-cell programs during inflammation OPEN
Tiffany M. Carr, Joshua D. Wheaton, Geoffrey M. Houtz & Maria Ciofani

AP-1 family transcription factors regulate CD4+ T helper cell differentiation. Here the authors show that the AP-1 member JunB is a nonredundant regulator of transcriptional programs that support Th17 cell identity and restrain alternative Th1 and Treg cell fates in inflammatory contexts of acute fungal infection and chronic autoimmunity.

21 August 2017 | doi: 10.1038/s41467-017-00380-3
Gene regulation in immune cells  T-helper 17 cells 

Visualizing atomic-scale redox dynamics in vanadium oxide-based catalysts OPEN
Martin Ek, Quentin M. Ramasse, Logi Arnarson, Poul Georg Moses & Stig Helveg

Redox processes in metal oxide surfaces can exhibit structure sensitivities which are difficult to uncover. Here, the authors use atomic-resolution imaging to demonstrate facet dependent alterations in the surfaces of supported vanadium oxide upon reduction and oxidation.

21 August 2017 | doi: 10.1038/s41467-017-00385-y
Heterogeneous catalysis  Materials for energy and catalysis  Nanoparticles  Structural properties  Transmission electron microscopy 

In situ atomic-scale imaging of the metal/oxide interfacial transformation OPEN
Lianfeng Zou, Jonathan Li, Dmitri Zakharov, Eric A. Stach & Guangwen Zhou

Metal/oxide interfaces play an important role in heterogeneous catalysis and redox reactions, but their buried nature makes them difficult to study. Here, the authors use environmental transmission electron microscopy to probe the atomic-level transformations at Cu2O/Cu interfaces as they undergo redox reactions.

21 August 2017 | doi: 10.1038/s41467-017-00371-4
Structural properties  Surfaces, interfaces and thin films  Synthesis and processing  Transmission electron microscopy 

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry OPEN
Ben C. Collins, Christie L. Hunter, Yansheng Liu, Birgit Schilling, George Rosenberger, Samuel L. Bader, Daniel W. Chan, Bradford W. Gibson, Anne-Claude Gingras, Jason M. Held, Mio Hirayama-Kurogi, Guixue Hou, Christoph Krisp, Brett Larsen, Liang Lin, Siqi Liu, Mark P. Molloy, Robert L. Moritz, Sumio Ohtsuki, Ralph Schlapbach et al.

SWATH-mass spectrometry consists of a data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics on the scale of thousands of proteins. Here, using data generated by eleven groups worldwide, the authors show that SWATH-MS is capable of generating highly reproducible data across different laboratories.

21 August 2017 | doi: 10.1038/s41467-017-00249-5
Proteomic analysis  Proteomics 

Platelets reduce anoikis and promote metastasis by activating YAP1 signaling OPEN
Monika Haemmerle, Morgan L. Taylor, Tony Gutschner, Sunila Pradeep, Min Soon Cho, Jianting Sheng, Yasmin M. Lyons, Archana S. Nagaraja, Robert L. Dood, Yunfei Wen, Lingegowda S. Mangala, Jean M. Hansen, Rajesha Rupaimoole, Kshipra M. Gharpure, Cristian Rodriguez-Aguayo, Sun Young Yim, Ju-Seog Lee, Cristina Ivan, Wei Hu, Gabriel Lopez-Berestein et al.

Platelets have been associated with increased tumor growth and metastasis but the mechanistic details of this interaction are still unclear. Here the authors show that platelets improve anoikis resistance of cancer cells and increase metastasis by activating Yap through a RhoA/MYPT-PP1 pathway.

21 August 2017 | doi: 10.1038/s41467-017-00411-z
Mechanisms of disease  Ovarian cancer 

Activated protein C protects from GvHD via PAR2/PAR3 signalling in regulatory T-cells OPEN
Satish Ranjan, Alexander Goihl, Shrey Kohli, Ihsan Gadi, Mandy Pierau, Khurrum Shahzad, Dheerendra Gupta, Fabian Bock, Hongjie Wang, Haroon Shaikh, Thilo Kähne, Dirk Reinhold, Ute Bank, Ana C. Zenclussen, Jana Niemz, Tina M. Schnöder, Monika Brunner-Weinzierl, Thomas Fischer, Thomas Kalinski, Burkhart Schraven et al.

Graft-vs.-host disease is a complication of allogenic hematopoietic stem cell transplantation, and is associated with endothelial dysfunction. Here the authors show that activated protein C signals via PAR2/PAR3 to expand Treg cells, mitigating the disease in mice.

21 August 2017 | doi: 10.1038/s41467-017-00169-4
Allotransplantation  CD4-positive T cells  Graft-versus-host disease 

Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature OPEN
Sara Martins, Alvaro Montiel-Jorda, Anne Cayrel, Stéphanie Huguet, Christine Paysant-Le Roux, Karin Ljung & Grégory Vert

Moderate heat stimulates the growth of Arabidopsis shoots in an auxin-dependent manner. Here, Martins et al. show that elevated ambient temperature modifies root growth by reducing the BRI1 brassinosteroid-receptor protein level and downregulating brassinosteroid signaling.

21 August 2017 | doi: 10.1038/s41467-017-00355-4
Brassinosteroid  Plant signalling 

ROCKII inhibition promotes the maturation of human pancreatic beta-like cells OPEN
Zaniar Ghazizadeh, Der-I Kao, Sadaf Amin, Brandoch Cook, Sahana Rao, Ting Zhou, Tuo Zhang, Zhaoying Xiang, Reyn Kenyon, Omer Kaymakcalan, Chengyang Liu, Todd Evans & Shuibing Chen

Our incomplete understanding of how pancreatic beta cells form limits the generation of beta-like cells from human pluripotent stem cells (hPSC). Here, the authors identify a ROCKII inhibitor H1152 as increasing insulin secreting cells from hPSCs and improving beta-cell maturation on transplantation in vivo.

21 August 2017 | doi: 10.1038/s41467-017-00129-y
Islets of Langerhans  Screening  Stem-cell differentiation 

Single molecule high-throughput footprinting of small and large DNA ligands OPEN
Maria Manosas, Joan Camunas-Soler, Vincent Croquette & Felix Ritort

Mapping the sequence specificity of DNA ligands remains a challenge, particularly for small drugs. Here the authors develop a parallelized single molecule magnetic tweezers approach using engineered DNA hairpins that can detect sequence selectivity, thermodynamics and kinetics of binding for small drugs and large proteins.

21 August 2017 | doi: 10.1038/s41467-017-00379-w
DNA  Molecular biophysics  Physical chemistry  Single-molecule biophysics 

Antiskyrmions stabilized at interfaces by anisotropic Dzyaloshinskii-Moriya interactions OPEN
Markus Hoffmann, Bernd Zimmermann, Gideon P. Müller, Daniel Schürhoff, Nikolai S. Kiselev, Christof Melcher & Stefan Blügel

Skyrmions, localized defects in the magnetization, can be stabilised in materials by the Dzyaloshinskii-Moriya interaction (DMI). Hoffmann et al. predict that, when the DMI is anisotropic, antiskyrmions can be formed and coexist with skyrmions, enabling studies and exploitation of their interactions.

21 August 2017 | doi: 10.1038/s41467-017-00313-0
Magnetic properties and materials  Spintronics  Surfaces, interfaces and thin films 

Timing of Smarcb1 and Nf2 inactivation determines schwannoma versus rhabdoid tumor development OPEN
Jeremie Vitte, Fuying Gao, Giovanni Coppola, Alexander R. Judkins & Marco Giovannini

SMARCB1 mutations predispose to rhabdoid tumors and schwannomas but the mechanisms underlying the tumor type specificity are unknown. Here the authors present new mouse models and show that early Smarcb1 loss causes rhabdoid tumors whereas loss at later stages combined with Nf2 gene inactivation causes shwannomas.

21 August 2017 | doi: 10.1038/s41467-017-00346-5
Cancer models  CNS cancer  Tumour-suppressor proteins 

Long-term consistency in chimpanzee consolation behaviour reflects empathetic personalities OPEN
Christine E. Webb, Teresa Romero, Becca Franks & Frans B. M. de Waal

Non-human animals are known to exhibit behaviours suggestive of empathy, but the development and maintenance of these traits is unexplored. Here, Webb and colleagues quantify individual consolation tendencies over 10 years across two chimpanzee groups and show evidence of consistent ‘empathetic personalities’.

18 August 2017 | doi: 10.1038/s41467-017-00360-7
Animal behaviour  Biological anthropology  Psychology 

Non-coding RNAs participate in the regulatory network of CLDN4 via ceRNA mediated miRNA evasion OPEN
Yong-xi Song, Jing-xu Sun, Jun-hua Zhao, Yu-chong Yang, Jin-xin Shi, Zhong-hua Wu, Xiao-wan Chen, Peng Gao, Zhi-feng Miao & Zhen-ning Wang

Non-coding RNAs can modify the expression of proteins in cancer networks. Here the authors reveal a regulatory network in gastric cancer whereby claudin-4 expression is reduced by specific miRNAs, which are in turn bound by specific lncRNAs acting as competing endogenous RNAs (ceRNAs), resulting in increased claudin-4 expression.

18 August 2017 | doi: 10.1038/s41467-017-00304-1
Gastric cancer  Long non-coding RNAs 

CD206+ M2-like macrophages regulate systemic glucose metabolism by inhibiting proliferation of adipocyte progenitors OPEN
Allah Nawaz, Aminuddin Aminuddin, Tomonobu Kado, Akiko Takikawa, Seiji Yamamoto, Koichi Tsuneyama, Yoshiko Igarashi, Masashi Ikutani, Yasuhiro Nishida, Yoshinori Nagai, Kiyoshi Takatsu, Johji Imura, Masakiyo Sasahara, Yukiko Okazaki, Kohjiro Ueki, Tadashi Okamura, Kumpei Tokuyama, Akira Ando, Michihiro Matsumoto, Hisashi Mori et al.

Adipose tissue contains macrophages that can influence both local and systemic metabolism via the secretion of cytokines. Here, Nawaz et al. report that M2-like macrophages, present in adipose tissue, create a microenvironment that inhibits proliferation of adipocyte progenitors due to the secretion of TGF-β1

18 August 2017 | doi: 10.1038/s41467-017-00231-1
Macrophages  Medical research  Obesity 

Landscape of submitochondrial protein distribution OPEN
F.-Nora Vögtle, Julia M. Burkhart, Humberto Gonczarowska-Jorge, Cansu Kücükköse, Asli Aras Taskin, Dominik Kopczynski, Robert Ahrends, Dirk Mossmann, Albert Sickmann, René P. Zahedi & Chris Meisinger

Protein localization plays an important role in the regulation of cellular physiology. Here the authors use an integrated proteomics approach to localize proteins to the mitochondria and provide a detailed map of their specific localization within the organelle.

18 August 2017 | doi: 10.1038/s41467-017-00359-0
Mitochondria  Proteomics 

Atg4 proteolytic activity can be inhibited by Atg1 phosphorylation OPEN
Jana Sánchez-Wandelmer, Franziska Kriegenburg, Sabrina Rohringer, Martina Schuschnig, Rubén Gómez-Sánchez, Bettina Zens, Susana Abreu, Ralph Hardenberg, David Hollenstein, Jieqiong Gao, Christian Ungermann, Sascha Martens, Claudine Kraft & Fulvio Reggiori

The protease Atg4 mediates Atg8 lipidation, required for autophagosome biogenesis, but also triggers Atg8 release from the membranes, however is unclear how these steps are coordinated. Here the authors show that phosphorylation by Atg1 inhibits Atg4 at autophagosome formation sites.

18 August 2017 | doi: 10.1038/s41467-017-00302-3
Macroautophagy  Vacuole 

Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin OPEN
Aleix Bayona-Feliu, Anna Casas-Lamesa, Oscar Reina, Jordi Bernués & Fernando Azorín

While structural importance of linker histone H1 in packaging eukaryotic genome into chromatin is well known, its biological function remains poorly understood. Here the authors reveal that Drosophila linker histone H1 prevents DNA:RNA hybrids accumulation and genome instability in heterochromatin.

18 August 2017 | doi: 10.1038/s41467-017-00338-5
Chromatin  DNA damage and repair 

Mass production of bulk artificial nacre with excellent mechanical properties OPEN
Huai-Ling Gao, Si-Ming Chen, Li-Bo Mao, Zhao-Qiang Song, Hong-Bin Yao, Helmut Cölfen, Xi-Sheng Luo, Fu Zhang, Zhao Pan, Yu-Feng Meng, Yong Ni & Shu-Hong Yu

Artificial materials that replicate the mechanical properties of nacre represent important structural materials, but are difficult to produce in bulk. Here, the authors exploit the bottom-up assembly of 2D nacre-mimetic films to fabricate 3D bulk artificial nacre with an optimized architecture and excellent mechanical properties.

18 August 2017 | doi: 10.1038/s41467-017-00392-z
Bioinspired materials  Mechanical properties  Structural properties 

Sequential conformational transitions and α-helical supercoiling regulate a sensor histidine kinase OPEN

Sensor histidine kinases (SHK) consist of sensor, linker and kinase modules and different models for SHK signal transduction have been proposed. Here the authors present nano- to millisecond time-resolved X-ray scattering measurements, which reveal a structural mechanism for kinase domain activation in SHK.

18 August 2017 | doi: 10.1038/s41467-017-00300-5
Biophysics  Computational biophysics  Kinases  Structural biology 

Tree height strongly affects estimates of water-use efficiency responses to climate and CO2 using isotopes OPEN
R. J. W. Brienen, E. Gloor, S. Clerici, R. Newton, L. Arppe, A. Boom, S. Bottrell, M. Callaghan, T. Heaton, S. Helama, G. Helle, M. J. Leng, K. Mielikäinen, M. Oinonen & M. Timonen

Intrinsic water-use efficiency (W i ) reconstructions using tree rings often disregard developmental changes in W i as trees age. Here, the authors compare W i across varying tree sizes at a fixed CO2 level and show that ignoring developmental changes impacts conclusions on trees’ W i responses to CO2 or climate.

18 August 2017 | doi: 10.1038/s41467-017-00225-z
Carbon cycle  Stable isotope analysis 

A reversible phospho-switch mediated by ULK1 regulates the activity of autophagy protease ATG4B OPEN
N. Pengo, A. Agrotis, K. Prak, J. Jones & R. Ketteler

Upon autophagy induction, LC3 is cleaved by the protease ATG4 and conjugated to the autophagosomal membrane; however, its removal is mediated by the same protease. Here the authors show that ULK1-mediated phosphorylation and PP2A-mediated dephosphorylation of ATG4 regulates its cellular activity to control LC3 processing.

18 August 2017 | doi: 10.1038/s41467-017-00303-2
Macroautophagy  Phosphorylation 

Giant onsite electronic entropy enhances the performance of ceria for water splitting OPEN
S. Shahab Naghavi, Antoine A. Emery, Heine A. Hansen, Fei Zhou, Vidvuds Ozolins & Chris Wolverton

Solid-state entropy of reduction increases the thermodynamic efficiency of ceria for two-step thermochemical water splitting. Here, the authors report a large and different source of entropy, the onsite electronic configurational entropy arising from coupling between orbital and spin angular momenta in f orbitals.

18 August 2017 | doi: 10.1038/s41467-017-00381-2
Computational methods  Electronic structure  Energy modelling 

Protection and consolidation of stone heritage by self-inoculation with indigenous carbonatogenic bacterial communities OPEN
Fadwa Jroundi, Mara Schiro, Encarnación Ruiz-Agudo, Kerstin Elert, Inés Martín-Sánchez, María Teresa González-Muñoz & Carlos Rodriguez-Navarro

Salt weathering enhanced by global warming and environmental pollution is increasingly threatening stone monuments and artworks. Here, the authors present a bacterial self-inoculation approach with indigenous carbonatogenic bacteria and find that this technique consolidates and protects salt damaged stone.

17 August 2017 | doi: 10.1038/s41467-017-00372-3
Applied microbiology  Biogeochemistry  Biomineralization 

Three-dimensional imaging of vortex structure in a ferroelectric nanoparticle driven by an electric field OPEN
D. Karpov, Z. Liu, T. dos Santos Rolo, R. Harder, P. V. Balachandran, D. Xue, T. Lookman & E. Fohtung

Imaging of topological states of matter such as vortex configurations has generally been limited to 2D surface effects. Here Karpov et al. study the volumetric structure and dynamics of a vortex core mediated by electric-field induced structural phase transition in a ferroelectric BaTiO3 nanoparticle.

17 August 2017 | doi: 10.1038/s41467-017-00318-9
Imaging techniques  Nanoparticles  Phase transitions and critical phenomena  Structural properties 

The non-coding RNA BC1 regulates experience-dependent structural plasticity and learning OPEN

Brain cytoplasmic (BC1) RNA is a non-coding RNA that has been implicated in translational regulation, seizure, and anxiety. Here, the authors show that in the cortex, BC1 RNA is required for sensory deprivation-induced structural plasticity of dendritic spines, as well as for correct sensory learning and social behaviors.

17 August 2017 | doi: 10.1038/s41467-017-00311-2
Neurological disorders  Neuroscience 

Extrinsic mechanical forces mediate retrograde axon extension in a developing neuronal circuit OPEN
M. A. Breau, I. Bonnet, J. Stoufflet, J. Xie, S. De Castro & S. Schneider-Maunoury

How neuronal migration and axon growth coordinate during development is only partially understood. Here the authors use quantitative imaging to characterise the morphogenesis of the zebrafish olfactory placode and report an unexpected phenomenon, whereby axons extend through the passive movement of neuron cell bodies away from tethered axon tips.

17 August 2017 | doi: 10.1038/s41467-017-00283-3
Axon and dendritic guidance  Cell migration  Morphogenesis  Neural circuits  Olfactory system 

Shift current photovoltaic effect in a ferroelectric charge-transfer complex OPEN
M. Nakamura, S. Horiuchi, F. Kagawa, N. Ogawa, T. Kurumaji, Y. Tokura & M. Kawasaki

The bulk photovoltaics refers to an effect whereby electrons move directionally in non-centrosymmetric crystals upon light radiation. Here, Nakamura et al. observe this effect in a ferroelectric organic charge-transfer complex, which shows large diffusion distance of photogenerated electrons over 200 µm.

17 August 2017 | doi: 10.1038/s41467-017-00250-y
Ferroelectrics and multiferroics  Solar cells 

Controlled radical fluorination of poly(meth)acrylic acids in aqueous solution OPEN
Yucheng Dong, Zhentao Wang & Chaozhong Li

Fluorinated alkenes have very poor reactivity in copolymerizations with non-fluorinated polar monomers. Here the authors show silver-catalyzed decarboxylative radical fluorination of poly(acrylic acid) with Selectfluor in water at room temperature to form poly(vinyl fluoride-co-acrylic acid) copolymers.

17 August 2017 | doi: 10.1038/s41467-017-00376-z
Homogeneous catalysis  Synthetic chemistry methodology  Polymer synthesis 

Liquid–liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau OPEN
Susmitha Ambadipudi, Jacek Biernat, Dietmar Riedel, Eckhard Mandelkow & Markus Zweckstetter

Tau forms aggregates in the brains of Alzheimer patients. Here, the authors identify conditions, where the microtubule-binding repeats of Tau undergo a phosphorylation-dependent liquid–liquid phase separation, leading to molecular crowding in the formed Tau liquid droplets and characterize them by NMR and other biophysical methods.

17 August 2017 | doi: 10.1038/s41467-017-00480-0
Molecular neuroscience  Solution-state NMR 

Dendritic calcium spikes are clearly detectable at the cortical surface OPEN
Mototaka Suzuki & Matthew E. Larkum

Surface EEG recordings are thought to primarily detect synaptic activity. Here the authors devise an optogenetic method to evoke dendritic calcium spikes in layer 5 pyramidal cells of the rat somatosensory cortex, and report that optogenetically evoked, as well as sensory-evoked dendritic calcium spikes make a significant contribution to surface EEG recordings.

17 August 2017 | doi: 10.1038/s41467-017-00282-4
Neuroscience  Physiology 

G9a regulates breast cancer growth by modulating iron homeostasis through the repression of ferroxidase hephaestin OPEN
Ya-fang Wang, Jie Zhang, Yi Su, Yan-yan Shen, Dong-xian Jiang, Ying-yong Hou, Mei-yu Geng, Jian Ding & Yi Chen

G9a is a histone methyltransferase highly expressed in several cancers including breast cancer. Here the authors propose a mechanism through which G9a promotes breast cancer by regulating iron metabolism through the repression of ferroxidase hephaestin.

17 August 2017 | doi: 10.1038/s41467-017-00350-9
Cancer epigenetics  Cell growth 

Black phosphorus ink formulation for inkjet printing of optoelectronics and photonics OPEN

Atomically thin black phosphorus shows promise for optoelectronics and photonics, yet its instability under environmental conditions and the lack of well-established large-area synthesis protocols hinder its applications. Here, the authors demonstrate a stable black phosphorus ink suitable for printed ultrafast lasers and photodetectors.

17 August 2017 | doi: 10.1038/s41467-017-00358-1
Electronic devices  Electronic properties and devices 

The genetic basis of natural variation in a phoretic behavior OPEN
Daehan Lee, Heeseung Yang, Jun Kim, Shannon Brady, Stefan Zdraljevic, Mostafa Zamanian, Heekyeong Kim, Young-ki Paik, Leonid Kruglyak, Erik C. Andersen & Junho Lee

Nematodes use a characteristic set of movements, called nictation, to hitchhike on more mobile animals. Here, Lee et al. identify a genetic locus in the nematode Caenorhabditis elegans that underlies nictation and contributes to successful hitchhiking, but at expense of reduced offspring production.

17 August 2017 | doi: 10.1038/s41467-017-00386-x
Animal behaviour  Genetic variation  Quantitative trait 

Specialized odorant receptors in social insects that detect cuticular hydrocarbon cues and candidate pheromones OPEN
Gregory M. Pask, Jesse D. Slone, Jocelyn G. Millar, Prithwiraj Das, Jardel A. Moreira, Xiaofan Zhou, Jan Bello, Shelley L. Berger, Roberto Bonasio, Claude Desplan, Danny Reinberg, Jürgen Liebig, Laurence J. Zwiebel & Anandasankar Ray

Cuticular hydrocarbons (CHC) mediate the interactions between individuals in eusocial insects, but the sensory receptors for CHCs are unclear. Here the authors show that in ants such as H. saltator, the 9-exon subfamily of odorant receptors (HsOrs) responds to CHCs, and ectopic expression of HsOrs in Drosophila neurons imparts responsiveness to CHCs.

17 August 2017 | doi: 10.1038/s41467-017-00099-1
Olfactory receptors  Social behaviour 
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  Latest Erratum    
Erratum: E3 Ubiquitin ligase ZNRF4 negatively regulates NOD2 signalling and induces tolerance to MDP OPEN
Pradeep Bist , Wan Shoo Cheong, Aylwin Ng, Neha Dikshit, Bae Hoon Kim, Niyas Kudukkil Pulloor, Hanif Javanmard Khameneh, Matija Hedl, Avinash R. Shenoy, Vanniarajan Balamuralidhar, Najib Bin Abdul Malik, Michelle Hong, Albert Neutzner, Keh-Chuang Chin, Koichi S. Kobayashi, Antonio Bertoletti, Alessandra Mortellaro, Clara Abraham, John D. MacMicking, Ramnik J. Xavier et al.
18 August 2017 | doi: 10.1038/ncomms16141
Antimicrobial responses  Bacterial infection  Chronic inflammation  NOD-like receptors 
  Latest Corrigenda    
Corrigendum: The extracellular interactome of the human adenovirus family reveals diverse strategies for immunomodulation OPEN
Nadia Martinez-Martin, Sree R. Ramani, Jason A. Hackney, Irene Tom, Bernd J. Wranik, Michelle Chan, Johnny Wu, Maciej T. Paluch, Kentaro Takeda, Philip E. Hass, Hilary Clark & Lino C. Gonzalez
21 August 2017 | doi: 10.1038/ncomms16150
Adenovirus  Immunotherapy  Virus–host interactions 

Corrigendum: Adrenergic-mediated loss of splenic marginal zone B cells contributes to infection susceptibility after stroke OPEN
Laura McCulloch, Craig J. Smith & Barry W. McColl
18 August 2017 | doi: 10.1038/ncomms16151
Bacterial infection  Marginal zone B cells  Stroke 

Corrigendum: Mitochondrial ATP transporter depletion protects mice against liver steatosis and insulin resistance OPEN
18 August 2017 | doi: 10.1038/ncomms16143
Energy metabolism  Non-alcoholic fatty liver disease  Transporters 
  Latest Retraction    
Retraction: A photon thermal diode OPEN
Zhen Chen, Carlaton Wong, Sean Lubner, Shannon Yee, John Miller, Wanyoung Jang, Corey Hardin, Anthony Fong, Javier E. Garay & Chris Dames
21 August 2017 | doi: 10.1038/ncomms16134
Applied physics  Electronics, photonics and device physics  Statistical physics, thermodynamics and nonlinear dynamics 

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