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Nature Communications - 11 April 2018

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KAUST Discovery: Research into clean fuels

Fuel Combustion Chemist Mani Sarathy's research focuses on alternative fuels. He is working closely with atmospheric scientists to better grasp the fate of exhaust emissions. The research also examines the use of artificial intelligence and machine learning to improve combustion processes. 

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Emerging three-dimensional culture methods enable differentiated human stem cells to form into brain organoids or assembloids, which can be used to study evolution, development, and disease. 

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Computer-aided discovery of a metal–organic framework with superior oxygen uptake OPEN
Peyman Z. Moghadam, Timur Islamoglu, Subhadip Goswami, Jason Exley, Marcus Fantham, Clemens F. Kaminski, Randall Q. Snurr, Omar K. Farha & David Fairen-Jimenez

The emergence of thousands of metal–organic frameworks (MOFs) has created the challenge of finding promising structures for particular applications. Here, the authors present a tool for computer-aided material discovery where a large number of MOFs are screened, with the top-ranked structure synthesized for oxygen storage applications.

11 April 2018 | doi: 10.1038/s41467-018-03892-8
Chemical engineering  Metal–organic frameworks 

Supported black phosphorus nanosheets as hydrogen-evolving photocatalyst achieving 5.4% energy conversion efficiency at 353 K OPEN
Bin Tian, Bining Tian, Bethany Smith, M. C. Scott, Ruinian Hua, Qin Lei & Yue Tian

In order to displace fossil fuel technologies, it is crucial to develop efficient solar-to-fuel conversion materials using abundant, cheap elements. Here, the authors prepare few-layer black phosphorous with amorphous cobalt phosphide and produce hydrogen gas with light at high efficiencies.

11 April 2018 | doi: 10.1038/s41467-018-03737-4
Photocatalysis  Solar fuels  Synthesis and processing 

Somatic activating mutations in MAP2K1 cause melorheostosis OPEN
Heeseog Kang, Smita Jha, Zuoming Deng, Nadja Fratzl-Zelman, Wayne A. Cabral, Aleksandra Ivovic, Françoise Meylan, Eric P. Hanson, Eileen Lange, James Katz, Paul Roschger, Klaus Klaushofer, Edward W. Cowen, Richard M. Siegel, Joan C. Marini & Timothy Bhattacharyya

Melorheostosis is characterized by bone overgrowth and associated with pain and functional impairment. Here, the authors use whole exome sequencing to identify somatic mutations in MAP2K1 in affected bone of melorheostosis patients which is associated with increased proliferation but delayed differentiation of cultured osteoblasts.

11 April 2018 | doi: 10.1038/s41467-018-03720-z
Disease genetics  Endocrine system and metabolic diseases  Mechanisms of disease 

Towards a new approach to reveal dynamical organization of the brain using topological data analysis OPEN
Manish Saggar, Olaf Sporns, Javier Gonzalez-Castillo, Peter A. Bandettini, Gunnar Carlsson, Gary Glover & Allan L. Reiss

Approaches describing how the brain changes to accomplish cognitive tasks tend to rely on collapsed data. Here, authors present a new approach that maintains high dimensionality and use it to describe individual differences in how brain activity is represented and organized across different cognitive tasks.

11 April 2018 | doi: 10.1038/s41467-018-03664-4
Computational biology and bioinformatics  Neuroscience 

Conditional privatization of a public siderophore enables Pseudomonas aeruginosa to resist cheater invasion OPEN
Zhenyu Jin, Jiahong Li, Lei Ni, Rongrong Zhang, Aiguo Xia & Fan Jin

Pyoverdine is secreted by the opportunistic pathogen Pseudomonas aeruginosa to scavenge iron from its hosts. Here, the authors show that under stress conditions P. aeruginosa uses a ‘conditional privatization’ strategy, reserving pyoverdine intracellularly to protect against oxidative damage.

11 April 2018 | doi: 10.1038/s41467-018-03791-y
Bacterial evolution  Evolutionary theory  Experimental evolution 

Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants OPEN
Felix Wojcik, Geoffrey P. Dann, Leslie Y. Beh, Galia T. Debelouchina, Raphael Hofmann & Tom W. Muir

Ubiquitylation of H2B is associated with transcription and regulation of chromatin structure. Here, the authors perform an unbiased screen to identify the role of chromatin modifications on ubiquitylation of H2BK120 and characterize the crosstalk between H2BK120ub and H2A modifications and variants.

11 April 2018 | doi: 10.1038/s41467-018-03895-5
Enzyme mechanisms  Histone post-translational modifications  Histone variants  Nucleosomes 

High power surface emitting terahertz laser with hybrid second- and fourth-order Bragg gratings OPEN
Yuan Jin, Liang Gao, Ji Chen, Chongzhao Wu, John L. Reno & Sushil Kumar

Proper design of the gratings can enhance the efficiency of distributed-feedback and quantum cascade lasers. Here, Jin et al. use a hybrid grating system that superposes second- and fourth-order Bragg gratings and achieve high radiative efficiency and a single-lobe radiation pattern.

11 April 2018 | doi: 10.1038/s41467-018-03697-9
Quantum cascade lasers  Semiconductor lasers 

A fully reconfigurable waveguide Bragg grating for programmable photonic signal processing OPEN
Weifeng Zhang & Jianping Yao

Bragg gratings are versatile elements used to perform spectral filtering in optical circuits. Here, the authors develop a scalable, reconfigurable grating device which can be electrically tuned to actively change its behaviour and control of optical pathways, for use in photonic signal processing.

11 April 2018 | doi: 10.1038/s41467-018-03738-3
Integrated optics  Microwave photonics  Optoelectronic devices and components 

Synaptically silent sensory hair cells in zebrafish are recruited after damage OPEN
Qiuxiang Zhang, Suna Li, Hiu-Tung C. Wong, Xinyi J. He, Alisha Beirl, Ronald S. Petralia, Ya-Xian Wang & Katie S. Kindt

Hair cells of the inner ear are mechanosensors that detect sound, and synapse onto afferent neurons. Here, the authors used calcium imaging to find that not all hair cells are synaptically engaged, but after damage these silent cells are synaptically engaged.

11 April 2018 | doi: 10.1038/s41467-018-03806-8
Gap junctions  Hair cell  Sensory processing 

Chirality-controlled crystallization via screw dislocations OPEN
Baeckkyoung Sung, Alexis de la Cotte & Eric Grelet

Understanding why and how molecules transfer their chirality into helical superstructures, including crystals, remains a challenge. Here, the authors show that topological defects not only promote the growth, but also control the helical morphology of crystals formed by chiral rod-shaped particles.

11 April 2018 | doi: 10.1038/s41467-018-03745-4
Colloids  Liquid crystals  Self-assembly 

Macrophage-derived IL-1β/NF-κB signaling mediates parenteral nutrition-associated cholestasis OPEN
Karim C. El Kasmi, Padade M. Vue, Aimee L. Anderson, Michael W. Devereaux, Swati Ghosh, Natarajan Balasubramaniyan, Sophie A. Fillon, Carola Dahrenmoeller, Ayed Allawzi, Crystal Woods, Sarah McKenna, Clyde J. Wright, Linda Johnson, Angelo D’Alessandro, Julie A. Reisz, Eva Nozik-Grayck, Frederick J. Suchy & Ronald J. Sokol

The authors previously developed a mouse model of parenteral nutrition-associated cholestasis (PNAC) that is dependent on parenteral phytosterols and intestinal injury with DSS. Here they refine the model and show that PNAC pathology is dependent on recruitment of hepatic macrophages and IL-1 signaling.

11 April 2018 | doi: 10.1038/s41467-018-03764-1
Gastrointestinal diseases  Kupffer cells  Paediatric research 

How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin OPEN
Michael B. Doud, Juhye M. Lee & Jesse D. Bloom

Influenza A virus can escape antibodies, but it is unclear how the ease of escape depends on the epitope targeted by an antibody. Here, the authors show that neutralization breadth is an imperfect indicator of the ease of viral escape by single mutations, and that antibodies targeting the stalk of hemagglutinin are harder to escape.

11 April 2018 | doi: 10.1038/s41467-018-03665-3
Antibodies  High-throughput screening  Influenza virus  Molecular evolution 

Inhibition of cancer stem cell like cells by a synthetic retinoid OPEN
Junwei Chen, Xin Cao, Quanlin An, Yao Zhang, Ke Li, Wenting Yao, Fuchun Shi, Yanfang Pan, Qiong Jia, Wenwen Zhou, Fang Yang, Fuxiang Wei, Ning Wang & Biao Yu

The discovery of efficient drugs is a main challenge in cancer therapy. Here, the authors report a synthetic retinoid, WYC-209 with anti-tumor and anti-metastatic activity mediated by the retinoic acid receptor signaling pathway.

11 April 2018 | doi: 10.1038/s41467-018-03877-7
Biophysics  Cancer therapy 

Srf destabilizes cellular identity by suppressing cell-type-specific gene expression programs OPEN
Takashi Ikeda, Takafusa Hikichi, Hisashi Miura, Hirofumi Shibata, Kanae Mitsunaga, Yosuke Yamada, Knut Woltjen, Kei Miyamoto, Ichiro Hiratani, Yasuhiro Yamada, Akitsu Hotta, Takuya Yamamoto, Keisuke Okita & Shinji Masui

The transcription factor Srf is a central regulator of immediate-early and actin cytoskeletal genes. Here the authors show that Srf is activated by repression of β-actin, promoting iPSC reprogramming of neural progenitor cells and hepatoblasts by repressing cell-type specific genes.

11 April 2018 | doi: 10.1038/s41467-018-03748-1
Actin  Reprogramming 

Controlling symmetry and localization with an artificial gauge field in a disordered quantum system OPEN
Clément Hainaut, Isam Manai, Jean-François Clément, Jean Claude Garreau, Pascal Szriftgiser, Gabriel Lemarié, Nicolas Cherroret, Dominique Delande & Radu Chicireanu

Periodically kicked rotors are useful in exploring localization phenomenon. Here the authors use ultracold Cs atoms kicked by short laser pulses and show that the periodic modulation results into interference signals as a signature of weak and strong localizations.

11 April 2018 | doi: 10.1038/s41467-018-03481-9
Matter waves and particle beams  Quantum mechanics  Quantum simulation  Ultracold gases 

Ultrastable metallic glasses formed on cold substrates OPEN
P. Luo, C. R. Cao, F. Zhu, Y. M. Lv, Y. H. Liu, P. Wen, H. Y. Bai, G. Vaughan, M. di Michiel, B. Ruta & W. H. Wang

Producing ultrastable metallic glasses has always been associated with substrates heated close to the glass transition temperature. Here, the authors show that reducing the deposition rate of the metallic glass on a cold substrate produces ultrastable metallic glasses with remarkably improved stability.

11 April 2018 | doi: 10.1038/s41467-018-03656-4
Design, synthesis and processing  Glasses  Mechanical properties  Metals and alloys 

Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle OPEN
Emily C. Hartman, Christopher M. Jakobson, Andrew H. Favor, Marco J. Lobba, Ester Álvarez-Benedicto, Matthew B. Francis & Danielle Tullman-Ercek

Self-assembling proteins have important applications in industrial technologies, but it is difficult to predict how mutations affect assembly. Here the authors present SyMAPS, coupling comprehensive codon mutagenesis with high-throughput sequencing, and apply it to bacteriophage capsid protein.

11 April 2018 | doi: 10.1038/s41467-018-03783-y
Drug delivery  Synthetic biology  Viral proteins 

Release of Staphylococcus aureus extracellular vesicles and their application as a vaccine platform OPEN
Xiaogang Wang, Christopher D. Thompson, Christopher Weidenmaier & Jean C. Lee

Extracellular vesicles (EVs) influence host-pathogen interactions, but EV biogenesis in gram-positive bacteria remains elusive. Here authors characterize EVs from Staphylococcus aureus and show that phenol-soluble modulins and autolysins promote EV biogenesis by disrupting the membrane and cell wall.

11 April 2018 | doi: 10.1038/s41467-018-03847-z
Pathogens  Preclinical research 

Constant strain accumulation rate between major earthquakes on the North Anatolian Fault OPEN
Ekbal Hussain, Tim J. Wright, Richard J. Walters, David P. S. Bekaert, Ryan Lloyd & Andrew Hooper

Accumulation of interseismic strain may now be constrained by satellite observations. Here, the authors show that strain accumulation rates on the North Anatolian Fault are constant for the interseismic period indicating that lower-crustal viscosities from postseismic studies are not representative.

11 April 2018 | doi: 10.1038/s41467-018-03739-2
Natural hazards  Tectonics 

Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections OPEN
Angela M. Early , Marc Lievens, Bronwyn L. MacInnis, Christian F. Ockenhouse, Sarah K. Volkman, Samuel Adjei, Tsiri Agbenyega, Daniel Ansong, Stacey Gondi, Brian Greenwood, Mary Hamel, Chris Odero, Kephas Otieno, Walter Otieno, Seth Owusu-Agyei, Kwaku Poku Asante, Hermann Sorgho, Lucas Tina, Halidou Tinto, Innocent Valea et al.

Host immune responses exert selective pressure on Plasmodium falciparum. Here, the authors show that allele-specific immunity impacts the antigenic diversity of individual malaria infections. This process partially explains the extreme amino acid diversity of many parasite antigens and suggests that vaccines should account for allele-specific immunity.

11 April 2018 | doi: 10.1038/s41467-018-03807-7
Malaria  Pathogens  Population genetics  Vaccines 

Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration OPEN
Akihito Harada, Kazumitsu Maehara, Yusuke Ono, Hiroyuki Taguchi, Kiyoshi Yoshioka, Yasuo Kitajima, Yan Xie, Yuko Sato, Takeshi Iwasaki, Jumpei Nogami, Seiji Okada, Tetsuro Komatsu, Yuichiro Semba, Tatsuya Takemoto, Hiroshi Kimura, Hitoshi Kurumizaka & Yasuyuki Ohkawa

Incorporation of histone H3 variant H3.3 into chromatin regulates transcription. Here the authors find that H3.3 sub-variant H3mm7 is required for skeletal muscle regeneration and that H3mm7 nucleosomes are unstable and exhibit higher mobility, with H3mm7 promoting open chromatin around promoters.

11 April 2018 | doi: 10.1038/s41467-018-03845-1
Histone analysis  Muscle stem cells  Next-generation sequencing  X-ray crystallography 

Combining CO2 reduction with propane oxidative dehydrogenation over bimetallic catalysts OPEN
Elaine Gomez, Shyam Kattel, Binhang Yan, Siyu Yao, Ping Liu & Jingguang G. Chen

The oxidative dehydrogenation of propane by CO2 (CO2-ODHP) can potentially fill the gap of propylene production while consuming a greenhouse gas. Here, the authors identify non-precious FeNi and precious NiPt catalysts supported on CeO2 as promising catalysts for CO2-ODHP and dry reforming, respectively, in flow reactor studies.

11 April 2018 | doi: 10.1038/s41467-018-03793-w
Catalytic mechanisms  Chemical engineering  Heterogeneous catalysis 

Allosteric regulation alters carrier domain translocation in pyruvate carboxylase OPEN
Yumeng Liu, Melissa M. Budelier, Katelyn Stine & Martin St. Maurice

Carrier domain enzymes accomplish catalysis by physically transporting intermediates long distances between remote active sites. Here the authors describe a wide range of catalytically productive translocation events during catalysis by pyruvate carboxylase and suggest a basis for its allosteric activation.

11 April 2018 | doi: 10.1038/s41467-018-03814-8
Enzyme mechanisms  Multienzyme complexes 

PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition OPEN
Timothy J. Durham, Maxwell W. Libbrecht, J. Jeffry Howbert, Jeff Bilmes & William Stafford Noble

Assays to characterize the epigenome and interrogate chromatin state genome wide have so far been performed in a selected set of conditions. Here, Durham et al. develop a computational method based on tensor decomposition to impute missing experiments in collections of epigenomics experiments.

11 April 2018 | doi: 10.1038/s41467-018-03635-9
Epigenomics  Machine learning 

Performance of the Trioplex real-time RT-PCR assay for detection of Zika, dengue, and chikungunya viruses OPEN
Gilberto A. Santiago, Jesús Vázquez, Sean Courtney, Katia Y. Matías, Lauren E. Andersen, Candimar Colón, Angela E. Butler, Rebecca Roulo, John Bowzard, Julie M. Villanueva & Jorge L. Muñoz-Jordan

The Trioplex real-time RT-PCR assay was developed for detection of Zika virus infections in areas with dengue and chikungunya transmission. Here, Santiago et al. describe the optimization and clinical performance of the assay, showing high sensitivity for detection and differentiation of the three viruses.

11 April 2018 | doi: 10.1038/s41467-018-03772-1
Assay systems  Microbiology techniques  Viral infection 

Probing the strongly driven spin-boson model in a superconducting quantum circuit OPEN
L. Magazzù, P. Forn-Díaz, R. Belyansky, J.-L. Orgiazzi, M. A. Yurtalan, M. R. Otto, A. Lupascu, C. M. Wilson & M. Grifoni

Two-level systems interacting with a bosonic environment appear everywhere in physics. Here, the authors use a superconducting device to study this spin-boson model in the presence of coherent driving, showing that the drive enhances dissipation into the environment and can localize or delocalize the system.

11 April 2018 | doi: 10.1038/s41467-018-03626-w
Quantum physics  Superconducting devices 

Molecular basis for the folding of β-helical autotransporter passenger domains OPEN
Xiaojun Yuan, Matthew D. Johnson, Jing Zhang, Alvin W. Lo, Mark A. Schembri, Lakshmi C. Wijeyewickrema, Robert N. Pike, Gerard H. M. Huysmans, Ian R. Henderson & Denisse L. Leyton

Autotransporter passenger domains are presented on or released from the bacterial surface upon translocation through an outer membrane β-barrel anchor. Here the authors study the two E. coli autotransporters Pet and EspP and propose that the β-barrel anchor acts as a vector to nucleate the folding of the passenger domain.

11 April 2018 | doi: 10.1038/s41467-018-03593-2
Bacteriology  Membrane proteins 

Snap evaporation of droplets on smooth topographies OPEN
Gary G. Wells, Élfego Ruiz-Gutiérrez, Youen Le Lirzin, Anthony Nourry, Bethany V. Orme, Marc Pradas & Rodrigo Ledesma-Aguilar

Droplet evaporation control has applications in inkjet printing and surface patterning. Here, the authors show that on slippery curved substrates droplets evaporate by slowly retracting and then suddenly snapping, which can be exploited to design surfaces that control an evaporation sequence.

11 April 2018 | doi: 10.1038/s41467-018-03840-6
Applied mathematics  Fluidics  Phase transitions and critical phenomena  Wetting 

Eigenmode orthogonality breaking and anomalous dynamics in multimode nano-optomechanical systems under non-reciprocal coupling OPEN
Laure Mercier de Lépinay, Benjamin Pigeau, Benjamin Besga & Olivier Arcizet

Understanding the dynamics of nanomechanical probes is important for improving high-sensitivity force field sensing. Here, the authors study the vibrations of a suspended nanowire in the presence of a rotational optical force field which breaks the orthogonality of the nanoresonator eigenmodes.

11 April 2018 | doi: 10.1038/s41467-018-03741-8
Nanophotonics and plasmonics  Nanosensors  NEMS  Optomechanics 

Negative circular polarization emissions from WSe2/MoSe2 commensurate heterobilayers OPEN
Wei-Ting Hsu, Li-Syuan Lu, Po-Hsun Wu, Ming-Hao Lee, Peng-Jen Chen, Pei-Ying Wu, Yi-Chia Chou, Horng-Tay Jeng, Lain-Jong Li, Ming-Wen Chu & Wen-Hao Chang

The interlayer coupling in van der Waals heterostructures is sensitive to the interlayer atomic registry. Here, the authors investigate the polarisation properties of epitaxially grown, commensurate WSe2/MoSe2 heterobilayers with well-defined atomic registry, and observe negative, circularly polarized photoluminescence from interlayer excitons.

10 April 2018 | doi: 10.1038/s41467-018-03869-7
Two-dimensional materials 

Small tumor necrosis factor receptor biologics inhibit the tumor necrosis factor-p38 signalling axis and inflammation OPEN
Violet R. Mukaro, Alex Quach, Michelle E. Gahan, Bernadette Boog, Zhi H. Huang, Xiuhui Gao, Carol Haddad, Suresh Mahalingam, Charles S. Hii & Antonio Ferrante

Anti-TNF therapy has improved the treatment of inflammatory disease but can predispose to infection and malignancy. Here the authors show an anti-TNF biologic peptide that functionally and selectively targets the TNF-p38 pathway in multiple models of inflammation.

10 April 2018 | doi: 10.1038/s41467-018-03640-y
Biologics  Rheumatoid arthritis  Translational immunology  Tumour-necrosis factors 

Longer and more frequent marine heatwaves over the past century OPEN
Eric C. J. Oliver, Markus G. Donat, Michael T. Burrows, Pippa J. Moore, Dan A. Smale, Lisa V. Alexander, Jessica A. Benthuysen, Ming Feng, Alex Sen Gupta, Alistair J. Hobday, Neil J. Holbrook, Sarah E. Perkins-Kirkpatrick, Hillary A. Scannell, Sandra C. Straub & Thomas Wernberg

Marine heatwaves are climatic extremes with devastating and long-term impacts on marine ecosystems, fisheries and aquaculture. Here the authors use a range of ocean temperature observations to identify significant increases in marine heatwaves over the past century.

10 April 2018 | doi: 10.1038/s41467-018-03732-9
Natural hazards  Physical oceanography 

Massive mining of publicly available RNA-seq data from human and mouse OPEN
Alexander Lachmann, Denis Torre, Alexandra B. Keenan, Kathleen M. Jagodnik, Hoyjin J. Lee, Lily Wang, Moshe C. Silverstein & Avi Ma’ayan

Publicly available RNA-seq data is provided mostly in raw form, resulting in a barrier for integrative analyses. Here, Lachmann et al. develop a high-throughput processing infrastructure and search database (ARCHS4) that provides processed RNA-seq data for 187,946 publicly available mouse and human samples to support exploration and reuse.

10 April 2018 | doi: 10.1038/s41467-018-03751-6
Computer science  Data integration  Data processing 

The ASIC3/P2X3 cognate receptor is a pain-relevant and ligand-gated cationic channel OPEN
Gabriele Stephan, Lumei Huang, Yong Tang, Sandra Vilotti, Elsa Fabbretti, Ye Yu, Wolfgang Nörenberg, Heike Franke, Flóra Göröncsér, Beáta Sperlágh, Anke Dopychai, Ralf Hausmann, Günther Schmalzing, Patrizia Rubini & Peter Illes

Two subclasses of ligand-gated ion channels (ASIC3 and P2X3) are both present at sensory neurons and might be therefore subject to receptor crosstalk. Here authors use electrophysiology, biochemistry and co-immunoprecipitation to show that the two ion channels interact and affect P2X3 currents.

10 April 2018 | doi: 10.1038/s41467-018-03728-5
Cellular neuroscience  Ion channels in the nervous system  Molecular neuroscience 

Magnetically-driven phase transformation strengthening in high entropy alloys OPEN
Changning Niu, Carlyn R. LaRosa, Jiashi Miao, Michael J. Mills & Maryam Ghazisaeidi

Medium entropy alloy CoCrNi has better mechanical properties than high entropy alloys such as CrMnFeCoNi, but why that is remains unclear. Here, the authors show that a nanostructured phase at lattice defects in CoCrNi causes its extraordinary properties, while it is magnetically frustrated and suppressed in CrMnFeCoNi.

10 April 2018 | doi: 10.1038/s41467-018-03846-0
Atomistic models  Metals and alloys  Phase transitions and critical phenomena 

Single-site catalyst promoters accelerate metal-catalyzed nitroarene hydrogenation OPEN
Liang Wang, Erjia Guan, Jian Zhang, Junhao Yang, Yihan Zhu, Yu Han, Ming Yang, Cheng Cen, Gang Fu, Bruce C. Gates & Feng-Shou Xiao

Understanding of the structures and roles of catalyst promoters markedly lags behind the understanding of the structures and roles of catalytic sites. Here, the authors address this challenge by incorporating a single-site promoter—tin—on a TiO2 surface to enhance the catalytic activity of various metals on the TiO2 in selective hydrogenation of nitroarenes.

10 April 2018 | doi: 10.1038/s41467-018-03810-y
Catalyst synthesis  Catalytic mechanisms  Heterogeneous catalysis 

Burned forests impact water supplies OPEN
Dennis W. Hallema, Ge Sun, Peter V. Caldwell, Steven P. Norman, Erika C. Cohen, Yongqiang Liu, Kevin D. Bladon & Steven G. McNulty

Wildland fire seasons in the United States are getting longer, yet the impacts of fire on water availability at the regional scale are unclear. Here the authors show that fire increased annual river flow throughout the West, while prescribed burns in the subtropical Southeast had limited impact on river flow.

10 April 2018 | doi: 10.1038/s41467-018-03735-6
Environmental impact  Hydrology  Natural hazards  Water resources 

Matriptase-2 deficiency protects from obesity by modulating iron homeostasis OPEN
Alicia R. Folgueras, Sandra Freitas-Rodríguez, Andrew J. Ramsay, Cecilia Garabaya, Francisco Rodríguez, Gloria Velasco & Carlos López-Otín

Iron homeostasis dysfunctions have been associated with several metabolic disorders including obesity, steatosis and diabetes. Here the authors demonstrate that the hepcidin repressor matriptase-2 regulates adiposity and its deficiency protects mice against obesity and promotes lipolysis.

10 April 2018 | doi: 10.1038/s41467-018-03853-1
Fat metabolism  Metabolic syndrome 

Characterization of PIK3CA and PIK3R1 somatic mutations in Chinese breast cancer patients OPEN
Li Chen, Liu Yang, Ling Yao, Xia-Ying Kuang, Wen-Jia Zuo, Shan Li, Feng Qiao, Yi-Rong Liu, Zhi-Gang Cao, Shu-Ling Zhou, Xiao-Yan Zhou, Wen-Tao Yang, Jin-Xiu Shi, Wei Huang, Xin Hu & Zhi-Ming Shao

The PI3K pathway is altered across various cancer types. Here the authors use amplicon exon sequencing to analyze the landscape of somatic mutations affecting the PI3K pathway specifically in breast cancer patients in China.

10 April 2018 | doi: 10.1038/s41467-018-03867-9
Breast cancer  Cancer genomics 

Transposon-modified antigen-specific T lymphocytes for sustained therapeutic protein delivery in vivo OPEN
Richard T. O’Neil, Sunandan Saha, Ruth Ann Veach, Richard C. Welch, Lauren E. Woodard, Cliona M. Rooney & Matthew H. Wilson

Delivery of therapeutic proteins to patients may be costly to administer, and often requires repeated injections. Here, the authors use antigen-specific T cells expressing erythropoietin, and show that following transfer in mice, cell expansion and erythropoietin production can be boosted by vaccination, raising the haematocrit.

10 April 2018 | doi: 10.1038/s41467-018-03787-8
Erythropoietin  Gene delivery  T cells 

Horn-like space-coiling metamaterials toward simultaneous phase and amplitude modulation OPEN
Reza Ghaffarivardavagh, Jacob Nikolajczyk, R. Glynn Holt, Stephan Anderson & Xin Zhang

Acoustic metasurfaces can be used to control acoustic waves, but generally they focus on phase control which limits potential functionality. Here, Ghaffarivardavagh et al. analytically develop a horn-like space coiling acoustic metasurface to control both the amplitude and phase of acoustic radiation patterns.

10 April 2018 | doi: 10.1038/s41467-018-03839-z
Acoustics  Mechanical engineering 

NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network OPEN
David J. Anderson , David I. Kaplan, Katrina M. Bell, Katerina Koutsis, John M. Haynes, Richard J. Mills, Dean G. Phelan, Elizabeth L. Qian, Ana Rita Leitoguinho, Deevina Arasaratnam, Tanya Labonne, Elizabeth S. Ng, Richard P. Davis, Simona Casini, Robert Passier, James E. Hudson, Enzo R. Porrello, Mauro W. Costa, Arash Rafii, Clare L. Curl et al.

A gene regulatory network, including the transcription factor Nkx2-5, regulates cardiac development. Here, the authors show that on deletion of NKX2-5 from human embryonic stem cells, there is impaired cardiomyogenesis and changes in action potentials, and that this is regulated via HEY2.

10 April 2018 | doi: 10.1038/s41467-018-03714-x
Congenital heart defects  Development  Differentiation 

Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome OPEN
Yanan Zhu, Wei Li Wang, Daqi Yu, Qi Ouyang, Ying Lu & Youdong Mao

The 26S proteasome consists of a core particle that is capped at each side by a regulatory particle. Here the authors present cryo-EM structures of the activated human 26S proteasome holoenzyme in three alternative open-gate states, which provides mechanistic insights into gate opening and dynamic remodeling of the substrate–translocation pathway.

10 April 2018 | doi: 10.1038/s41467-018-03785-w
Cryoelectron microscopy  Proteases 

Crab spiders impact floral-signal evolution indirectly through removal of florivores OPEN
Anina C. Knauer, Moe Bakhtiari & Florian P. Schiestl

Crab spiders can reduce pollination and thus have been suggested to select against the floral traits that attract them. Here, the authors instead find evidence of local adaptation of buckler mustard plants to increase attraction of crab spiders by emission of the floral volatile β-ocimene when infested by florivores.

10 April 2018 | doi: 10.1038/s41467-018-03792-x
Ecological networks  Evolution 

Extraordinary pseudocapacitive energy storage triggered by phase transformation in hierarchical vanadium oxides OPEN
Bo-Tian Liu, Xiang-Mei Shi, Xing-You Lang, Lin Gu, Zi Wen, Ming Zhao & Qing Jiang

Pseudocapacitive materials could enable high-performance electrochemical supercapacitors, but their practical capacitance and power density remain low. Here the authors show that in situ phase transformation triggers extraordinary pseudocapacitive energy storage in metallic isomeric vanadium oxides.

10 April 2018 | doi: 10.1038/s41467-018-03700-3
Energy science and technology  Energy storage  Materials science  Nanoscale materials  Renewable energy 

A NIGT1-centred transcriptional cascade regulates nitrate signalling and incorporates phosphorus starvation signals in Arabidopsis OPEN
Yoshie Maeda, Mineko Konishi, Takatoshi Kiba, Yasuhito Sakuraba, Naoya Sawaki, Tomohiro Kurai, Yoshiaki Ueda, Hitoshi Sakakibara & Shuichi Yanagisawa

Plants respond to nutrients by modulating gene expression. Here, the authors show that nitrate suppresses NRT2.1 nitrate transporter expression via NIGT1 transcriptional repressors and that phosphate starvation enhances this pathway via PHR1, thus linking phosphorus and nitrogen signalling.

10 April 2018 | doi: 10.1038/s41467-018-03832-6
Plant signalling 

Response of carbon cycle to drier conditions in the mid-Holocene in central China OPEN
Xianyu Huang, Richard D. Pancost, Jiantao Xue, Yansheng Gu, Richard P. Evershed & Shucheng Xie

The effect of Asian summer monsoon hydrological changes on key biogeochemical processes remains poorly understood. Here, using a suite of biomarkers, the authors reconstruct palaeohydrological conditions during the Holocene and show that the peatland carbon cycle is strongly sensitive to paleohydrological changes.

10 April 2018 | doi: 10.1038/s41467-018-03804-w
Carbon cycle  Limnology 

ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration OPEN
Jie Wang, Cristina Zibetti, Peng Shang, Srinivasa R. Sripathi, Pingwu Zhang, Marisol Cano, Thanh Hoang, Shuli Xia, Hongkai Ji, Shannath L. Merbs, Donald J. Zack, James T. Handa, Debasish Sinha, Seth Blackshaw & Jiang Qian

Age-related macular degeneration (AMD) leads to dysfunctional retinal pigment epithelium (RPE) and vision loss. Here, the authors perform ATAC-seq to study chromatin accessibility and find that differentially accessible regions are enriched for photoreceptor and RPE-specific transcription factors in AMD

10 April 2018 | doi: 10.1038/s41467-018-03856-y
Epigenomics  Functional genomics  Macular degeneration 

Endogenous modulation of human visual cortex activity improves perception at twilight OPEN
Lorenzo Cordani, Enzo Tagliazucchi, Céline Vetter, Christian Hassemer, Till Roenneberg, Jörg H. Stehle & Christian A. Kell

Visual perception depends on light—which changes according to time of day—but the accompanying neural changes are unknown. Here, authors use fMRI to describe the brain dynamics underlying visual perception and find that sensory areas change their activity to compensate for lower light at dawn and dusk.

10 April 2018 | doi: 10.1038/s41467-018-03660-8
Circadian rhythms and sleep  Sensory processing 

Generation and characterization of ultrathin free-flowing liquid sheets OPEN
Jake D. Koralek, Jongjin B. Kim, Petr Brůža, Chandra B. Curry, Zhijiang Chen, Hans A. Bechtel, Amy A. Cordones, Philipp Sperling, Sven Toleikis, Jan F. Kern, Stefan P. Moeller, Siegfried H. Glenzer & Daniel P. DePonte

X-ray spectroscopy is a tool used for the investigation of aqueous solutions but the strong absorption of water means that very thin liquid sheets are needed for accurate analysis. Here the authors produce free-flowing liquid sheets 2 orders of magnitude thinner than sheets obtained with existing techniques.

10 April 2018 | doi: 10.1038/s41467-018-03696-w
Infrared spectroscopy  Microfluidics  Microscopy  Physics 

Distinct molecular pathways mediate Mycn and Myc-regulated miR-17-92 microRNA action in Feingold syndrome mouse models OPEN
Fatemeh Mirzamohammadi, Anastasia Kozlova, Garyfallia Papaioannou, Elena Paltrinieri, Ugur M. Ayturk & Tatsuya Kobayashi

Feingold syndrome is a skeletal dysplasia caused by mutations in MYCN or MIR17HG, but it is not clear if these mutations lead to pathology via a common molecular mechanism. Here, the authors show that mutations in MIR17HG lead to upregulated TGF-β signaling in limb mesenchymal cells, while mutations in MYCN downregulate PI3K signaling.

10 April 2018 | doi: 10.1038/s41467-018-03788-7
miRNAs  Musculoskeletal abnormalities  Transforming growth factor beta 

Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations OPEN
Libin Ye, Chris Neale, Adnan Sljoka, Brent Lyda, Dmitry Pichugin, Nobuyuki Tsuchimura, Sacha T. Larda, Régis Pomès, Angel E. García, Oliver P. Ernst, Roger K. Sunahara & R. Scott Prosser

G protein-coupled receptors (GPCRs) are membrane receptors and are important drug targets, whose regulation by cations is poorly understood. Here authors use NMR to elucidate effects of cations on functional states of the GPCR, adenosine A2Areceptor (A2AR).

10 April 2018 | doi: 10.1038/s41467-018-03314-9
G protein-coupled receptors  Solution-state NMR 

Species-specific host factors rather than virus-intrinsic virulence determine primate lentiviral pathogenicity OPEN
Simone Joas , Erica H. Parrish, Clement W. Gnanadurai, Edina Lump, Christina M. Stürzel, Nicholas F. Parrish, Gerald H. Learn, Ulrike Sauermann, Berit Neumann, Kerstin Mätz Rensing, Dietmar Fuchs, James M. Billingsley, Steven E. Bosinger, Guido Silvestri, Cristian Apetrei, Nicolas Huot, Thalia Garcia-Tellez, Michaela Müller-Trutwin, Dominik Hotter, Daniel Sauter et al.

In contrast to HIV, simian immunodeficiency viruses (SIV) do not cause disease in their hosts, and the reasons for this are unclear. Here, Joas et al. incorporate two putative HIV virulence factors into SIV and study effects in infected monkeys, suggesting that species-specific host factors are responsible for HIV pathogenesis.

10 April 2018 | doi: 10.1038/s41467-018-03762-3
Chronic inflammation  HIV infections  Retrovirus  Viral pathogenesis 

A high-strength silicide phase in a stainless steel alloy designed for wear-resistant applications OPEN
D. Bowden, Y. Krysiak, L. Palatinus, D. Tsivoulas, S. Plana-Ruiz, E. Sarakinou, U. Kolb, D. Stewart & M. Preuss

Wear- and corrosion-resistant hardfacing steels rely on carbon for strengthening. Here, the authors report an ultra-high strength silicide phase that could lead to a new class of silicide-strengthened stainless steels and alternative coatings for nuclear applications.

10 April 2018 | doi: 10.1038/s41467-018-03875-9
Mechanical properties  Metals and alloys  Structure of solids and liquids  Transmission electron microscopy 

Observation of elastic topological states in soft materials OPEN
Shuaifeng Li, Degang Zhao, Hao Niu, Xuefeng Zhu & Jianfeng Zang

Here the authors present an experimental observation of topological states in soft elastic metamaterials. They show reversibility in topological phases by changing filling ratio, tension and/or compression, while also demonstrating tunability of topological interface states by mechanical deformation.

10 April 2018 | doi: 10.1038/s41467-018-03830-8
Acoustics  Mechanical engineering 

Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater OPEN
Xuming Zhou , Xuanmin Guang, Di Sun, Shixia Xu, Mingzhou Li, Inge Seim, Wencai Jie, Linfeng Yang, Qianhua Zhu, Jiabao Xu, Qiang Gao, Alaattin Kaya, Qianhui Dou, Bingyao Chen, Wenhua Ren, Shuaicheng Li, Kaiya Zhou, Vadim N. Gladyshev, Rasmus Nielsen, Xiaodong Fang et al.

Whales, dolphins and porpoises are adapted to various aquatic habitats. Here, Zhou et al. show that polymorphisms associated with renal function and the urea cycle have undergone selection in the freshwater Yangtze finless porpoise and provide genomic evidence of incipient speciation.

10 April 2018 | doi: 10.1038/s41467-018-03722-x
Evolutionary genetics  Population genetics  Speciation  Zoology 

Quantum metrology with quantum-chaotic sensors OPEN
Lukas J. Fiderer & Daniel Braun

Enhanced sensing using quantum systems generally relies on preparation of highly non-classical states, such as entangled or squeezed states. Here the authors propose a different approach, based on hypersensitivity of quantum-chaotic dynamics with respect to parameters of the system.

10 April 2018 | doi: 10.1038/s41467-018-03623-z
Quantum mechanics  Quantum metrology 

Entropy favors heterogeneous structures of networks near the rigidity threshold OPEN
Le Yan

The mechanical and thermodynamic properties of amorphous materials are governed by their disordered network at microscales, but the detail remains elusive. Yan shows that the vibrational entropy induces a floppy-rigid phase separation near the rigidity onset and thus favors heterogeneous structures.

10 April 2018 | doi: 10.1038/s41467-018-03859-9
Phase transitions and critical phenomena  Structure of solids and liquids 

The fluorination effect of fluoroamphiphiles in cytosolic protein delivery OPEN
Zhenjing Zhang, Wanwan Shen, Jing Ling, Yang Yan, Jingjing Hu & Yiyun Cheng

Proteins can serve as means of medical treatment, but their efficient delivery to cells is difficult. Here, the authors present a type of polymers, fluoroamphiphiles, acting as chemical chaperones that can facilitate the import of proteins into the inner compartment, i.e. cytosol, of cells.

10 April 2018 | doi: 10.1038/s41467-018-03779-8
Biomaterials – cells  Biomaterials – proteins  Protein delivery 

Model evidence for a seasonal bias in Antarctic ice cores OPEN
Michael P. Erb, Charles S. Jackson, Anthony J. Broccoli, David W. Lea, Paul J. Valdes, Michel Crucifix & Pedro N. DiNezio

Periodic changes in the tilt of the Earth’s axis alter the distribution of incoming solar radiation. Here, the authors show that the temperature response to this forcing seemingly differs in models and Antarctic ice cores, with a better agreement reached if ice cores are recording a seasonally weighted signal.

10 April 2018 | doi: 10.1038/s41467-018-03800-0
Atmospheric dynamics  Palaeoclimate 

In situ X-ray imaging of defect and molten pool dynamics in laser additive manufacturing OPEN
Chu Lun Alex Leung, Sebastian Marussi, Robert C. Atwood, Michael Towrie, Philip J. Withers & Peter D. Lee

Additive manufacturing of metals is now widely available, but the interaction of the metal powder with the laser remains unclear. Here, the authors use X-rays to image melt features and pore behaviour during laser melting of powders.

10 April 2018 | doi: 10.1038/s41467-018-03734-7
Design, synthesis and processing  Imaging techniques  Metals and alloys 

Increased formate overflow is a hallmark of oxidative cancer OPEN
Johannes Meiser, Anne Schuster, Matthias Pietzke, Johan Vande Voorde, Dimitris Athineos, Kristell Oizel, Guillermo Burgos-Barragan, Niek Wit, Sandeep Dhayade, Jennifer P. Morton, Emmanuel Dornier, David Sumpton, Gillian M. Mackay, Karen Blyth, Ketan J. Patel, Simone P. Niclou & Alexei Vazquez

Serine catabolism to formate supplies one-carbon units for biosynthesis. Here the authors show that formate production in murine cancers with high oxidative metabolism exceeds the biosynthetic demand and that high formate levels promotes invasion of cancer cells.

10 April 2018 | doi: 10.1038/s41467-018-03777-w
Cancer metabolism  Cell invasion  Metabolic pathways 

Designable ultra-smooth ultra-thin solid-electrolyte interphases of three alkali metal anodes OPEN
Yu Gu, Wei-Wei Wang, Yi-Juan Li, Qi-Hui Wu, Shuai Tang, Jia-Wei Yan, Ming-Sen Zheng, De-Yin Wu, Chun-Hai Fan, Wei-Qiang Hu, Zhao-Bin Chen, Yuan Fang, Qing-Hong Zhang, Quan-Feng Dong & Bing-Wei Mao

The dendrite growth of alkali metal anodes leads to charge/discharge cycling instability. Here, the authors show that electrochemical polishing can yield near-perfect anodes of three alkali metals by constructing smooth and thin solid-electrolyte interphase layers.

09 April 2018 | doi: 10.1038/s41467-018-03466-8
Batteries  Electrochemistry 

Stimulus dependent diversity and stereotypy in the output of an olfactory functional unit OPEN
Ezequiel M. Arneodo, Kristina B. Penikis, Neil Rabinowitz, Angela Licata, Annika Cichy, Jingji Zhang, Thomas Bozza & Dmitry Rinberg

Mitral/tufted (MT) cells connect to a single glomerulus and receive inputs from sensory neurons expressing the same odorant receptor. Here the authors report that sister MT cells connected to the M72 glomerulus exhibit variable responses to most M72 ligands but respond in a reproducible and stereotyped way to a high-affinity M72 ligand.

09 April 2018 | doi: 10.1038/s41467-018-03837-1
Olfactory system  Sensory processing 

Contraction of basal filopodia controls periodic feather branching via Notch and FGF signaling OPEN
Dongyang Cheng, Xiaoli Yan, Guofu Qiu, Juan Zhang, Hanwei Wang, Tingting Feng, Yarong Tian, Haiping Xu, Meiqing Wang, Wanzhong He, Ping Wu, Randall B Widelitz, Cheng-Ming Chuong & Zhicao Yue

Keratinocytes are organised into a periodic pattern in feather branching, but how this is regulated is unclear. Here, the authors show that there is a coordinated change in cell shape and adherence, mediated by Notch, FGF signalling and Rho GTPases, which in turn regulates feather branching.

09 April 2018 | doi: 10.1038/s41467-018-03801-z
Filopodia  Morphogenesis 

Systematic design and experimental demonstration of bianisotropic metasurfaces for scattering-free manipulation of acoustic wavefronts OPEN
Junfei Li, Chen Shen, Ana Díaz-Rubio, Sergei A. Tretyakov & Steven A. Cummer

Acoustic bianisotropy does not exist in natural materials but can be designed with acoustic metamaterials. Here, Li et al. utilized acoustic bianisotropy and develop a practical metamaterial with improved transmission efficiency which outperforms the Generalized Snell’s Law.

09 April 2018 | doi: 10.1038/s41467-018-03778-9
Acoustics  Surfaces, interfaces and thin films 

Archean phosphorus liberation induced by iron redox geochemistry OPEN
Barry Herschy, Sae Jung Chang, Ruth Blake, Aivo Lepland, Heather Abbott-Lyon, Jacqueline Sampson, Zachary Atlas, Terence P. Kee & Matthew A. Pasek

Phosphorus is presumed to have been a limiting nutrient in the Archean ocean due to binding to iron oxides. Here, the authors show the heating of iron with phosphate results in the reduction of phosphate to the ion phosphite, which is solubilized and ameliorates the issue of a low Archean phosphorus supply.

09 April 2018 | doi: 10.1038/s41467-018-03835-3
Element cycles  Chemical origin of life 

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons OPEN
Alex de Mendoza, Amandine Bonnet, Dulce B. Vargas-Landin, Nanjing Ji, Fei Hong, Feng Yang, Ling Li, Koichi Hori, Jahnvi Pflueger, Sam Buckberry, Hiroyuki Ohta, Nedeljka Rosic, Pascale Lesage, Senjie Lin & Ryan Lister

Cytosine methyltransferases (DNMTs) often silence transposons in eukaryotic genomes. Here the authors describe the recurrent acquisition of DNMTs by transposons from two distantly-related eukaryotes and suggest that methylation of CG dinucleotides by transposon DNMTs could modify the host epigenome in dinoflagellates.

09 April 2018 | doi: 10.1038/s41467-018-03724-9
DNA methylation  Epigenomics  Molecular evolution  Transposition 

Drought drives rapid shifts in tropical rainforest soil biogeochemistry and greenhouse gas emissions OPEN
Christine S. O’Connell, Leilei Ruan & Whendee L. Silver

Drought impacts on tropical forest soil carbon and greenhouse gas dynamics are poorly understood. Here, the authors investigate the impacts of the 2015 drought in a forest in Puerto Rico and find that it caused shifts in soil carbon dioxide and methane emissions and led to a decrease in available phosphorus.

09 April 2018 | doi: 10.1038/s41467-018-03352-3
Carbon cycle  Element cycles  Environmental impact  Forest ecology 

Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia OPEN
Jayaram Vijayakrishnan , James Studd, Peter Broderick, Ben Kinnersley, Amy Holroyd, Philip J. Law, Rajiv Kumar, James M. Allan, Christine J. Harrison, Anthony V. Moorman, Ajay Vora, Eve Roman, Sivaramakrishna Rachakonda, Sally E. Kinsey, Eamonn Sheridan, Pamela D. Thompson, Julie A. Irving, Rolf Koehler, Per Hoffmann, Markus M. Nöthen et al.

While GWAS have uncovered susceptibility loci for B-cell precursor acute lymphoblastic leukemia (BCP-ALL), much of the heritable risk remains undiscovered. Here, the authors perform a meta-analysis of two existing BCP-ALL GWAS together with an unpublished GWAS to identify risk loci at 8q24.21 and 2q22.3.

09 April 2018 | doi: 10.1038/s41467-018-03178-z
Genome-wide association studies  Paediatric cancer 

Quantitative 3D determination of self-assembled structures on nanoparticles using small angle neutron scattering OPEN
Zhi Luo, Domenico Marson, Quy K. Ong, Anna Loiudice, Joachim Kohlbrecher, Aurel Radulescu, Anwen Krause-Heuer, Tamim Darwish, Sandor Balog, Raffaella Buonsanti, Dmitri I. Svergun, Paola Posocco & Francesco Stellacci

The ligand shell of a nanoparticle remains difficult to resolve, as the available characterization methods provide only qualitative information. Here, the authors introduce an approach based on small-angle neutron scattering that can quantitatively reveal the organization of ligands in mixed-monolayer nanoparticles.

09 April 2018 | doi: 10.1038/s41467-018-03699-7
Characterization and analytical techniques  Molecular self-assembly  Nanoparticles 

Endocycle-related tubular cell hypertrophy and progenitor proliferation recover renal function after acute kidney injury OPEN
Elena Lazzeri , Maria Lucia Angelotti, Anna Peired, Carolina Conte, Julian A. Marschner, Laura Maggi, Benedetta Mazzinghi, Duccio Lombardi, Maria Elena Melica, Sara Nardi, Elisa Ronconi, Alessandro Sisti, Giulia Antonelli, Francesca Becherucci, Letizia De Chiara, Ricardo Romero Guevara, Alexa Burger, Beat Schaefer, Francesco Annunziato, Hans-Joachim Anders et al.

The recovery of function upon acute kidney injury is thought to involve tubular cell dedifferentiation and proliferation. Here the authors show that Pax2+ progenitors regenerate tubules via cell division while other tubular cells support function recovery by undergoing hypertrophy through endoreplication.

09 April 2018 | doi: 10.1038/s41467-018-03753-4
Acute kidney injury  Regeneration 

Origin of large plasticity and multiscale effects in iron-based metallic glasses OPEN
Baran Sarac, Yurii P. Ivanov, Andrey Chuvilin, Thomas Schöberl, Mihai Stoica, Zaoli Zhang & Jürgen Eckert

Iron-based bulk metallic glasses are remarkably plastic, but the origin of their plasticity remains challenging to isolate. Here, the authors use high resolution microscopy to show that nanocrystals are dispersed within the glass and form hard and soft zones that are responsible for enhancing ductility.

06 April 2018 | doi: 10.1038/s41467-018-03744-5
Glasses  Mechanical properties  Transmission electron microscopy 

Lipid binding promotes the open conformation and tumor-suppressive activity of neurofibromin 2 OPEN
Krishna Chinthalapudi, Vinay Mandati, Jie Zheng, Andrew J. Sharff, Gerard Bricogne, Patrick R. Griffin, Joseph Kissil & Tina Izard

Neurofibromin 2 (NF2) is a tumour suppressor that inhibits cell growth. Here the authors combine functional, biochemical, and structural studies and show that lipid-bound NF2 adopts an open conformation and that NF2 lipid binding is required for inhibition of cell proliferation.

06 April 2018 | doi: 10.1038/s41467-018-03648-4
Cell biology  X-ray crystallography 

De novo reconstruction of human adipose transcriptome reveals conserved lncRNAs as regulators of brown adipogenesis OPEN
Chunming Ding, Yen Ching Lim, Sook Yoong Chia, Arcinas Camille Esther Walet, Shaohai Xu, Kinyui Alice Lo, Yanling Zhao, Dewen Zhu, Zhihui Shan, Qingfeng Chen, Melvin Khee-Shing Leow, Dan Xu & Lei Sun

Long non-coding RNAs are known to regulate mouse white adipose tissue development and brown adipose tissue program expression. Here, the authors construct a roadmap for human long non-coding RNAs expressed in fetal brown adipose tissue, adult omental and subcutaneous white adipose tissues.

06 April 2018 | doi: 10.1038/s41467-018-03754-3
Computational biology and bioinformatics  Long non-coding RNAs 

Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements OPEN
William H. Hudson, Ian Mitchelle S. de Vera, Jerome C. Nwachukwu, Emily R. Weikum, Austin G. Herbst, Qin Yang, David L. Bain, Kendall W. Nettles, Douglas J. Kojetin & Eric A. Ortlund

Glucocorticoid receptor (GR) regulates immunity and inflammation but the mechanisms by which GR represses proinflammatory genes are still being debated. Here the authors use a multidisciplinary approach and show that GR binds to a cryptic site within genome-wide NFκB DNA response elements to repress pro-inflammatory genes.

06 April 2018 | doi: 10.1038/s41467-018-03780-1
NMR spectroscopy  Transcriptional regulatory elements  X-ray crystallography 

Origin of vertical orientation in two-dimensional metal halide perovskites and its effect on photovoltaic performance OPEN
Alexander Z. Chen, Michelle Shiu, Jennifer H. Ma, Matthew R. Alpert, Depei Zhang, Benjamin J. Foley, Detlef-M. Smilgies, Seung-Hun Lee & Joshua J. Choi

It is desirable to align the two-dimensional perovskite layers vertical to the electrodes to maximize device performance but the formation mechanism is unclear. Here Chen et al. reveal that the film formation starts at the liquid-air interface and is thus independent of the choice of substrates.

06 April 2018 | doi: 10.1038/s41467-018-03757-0
Solar cells  Two-dimensional materials 

On-chip temporal focusing of elastic waves in a phononic crystal waveguide OPEN
M. Kurosu, D. Hatanaka, K. Onomitsu & H. Yamaguchi

Here the authors demonstrate the temporal control of ultrasonic wave propagation in a one-dimensional phononic crystal waveguide. Four-wave mixing experiments are implemented, providing a platform on which to realize novel nonlinear phenomena in the system.

06 April 2018 | doi: 10.1038/s41467-018-03726-7
Acoustics  Mechanical engineering 

Optimal diversification strategies in the networks of related products and of related research areas OPEN
Aamena Alshamsi, Flávio L. Pinheiro & Cesar A. Hidalgo

The probability that a region will develop a particular research activity increases with the number of similar activities in neighboring regions. Here the authors analyze diffusion strategies and show that it is not only important to know which activities to target but also when to target them.

06 April 2018 | doi: 10.1038/s41467-018-03740-9
Complex networks  Economics 

Control of laser plasma accelerated electrons for light sources OPEN
T. André , I. A. Andriyash, A. Loulergue, M. Labat, E. Roussel, A. Ghaith, M. Khojoyan, C. Thaury, M. Valléau, F. Briquez, F. Marteau, K. Tavakoli, P. N’Gotta, Y. Dietrich, G. Lambert, V. Malka, C. Benabderrahmane, J. Vétéran, L. Chapuis, T. El Ajjouri et al.

Electron beam quality in accelerators is crucial for light source application. Here the authors demonstrate beam conditioning of laser plasma electrons thanks to a specific transport line enabling the control of divergence, energy, steering and dispersion and the application to observe undulator radiation.

06 April 2018 | doi: 10.1038/s41467-018-03776-x
Free-electron lasers  Plasma-based accelerators 

Structural rearrangements of the histone octamer translocate DNA OPEN
Silvija Bilokapic, Mike Strauss & Mario Halic

Nucleosomes are dynamic and can move along DNA in an uncatalyzed manner but little is known about the mechanisms of histone octamer translocation. Here the authors present cryo-EM structures of nucleosomes in differently organized histone octamer and DNA states and show how histone octamers translocate DNA.

06 April 2018 | doi: 10.1038/s41467-018-03677-z
Chromatin remodelling  Chromatin structure  Cryoelectron microscopy  Nucleosomes 

A giant amphipathic helix from a perilipin that is adapted for coating lipid droplets OPEN
Alenka Čopič, Sandra Antoine-Bally, Manuel Giménez-Andrés, César La Torre Garay, Bruno Antonny, Marco M. Manni, Sophie Pagnotta, Jeanne Guihot & Catherine L. Jackson

Lipid droplets are cellular organelles important for cellular homeostasis and their disruption has been implicated in many diseases. Here the authors use a large amphipathic helix from perilipin 4 to uncover parameters important for specific lipid droplet targeting and stabilization of the oil core.

06 April 2018 | doi: 10.1038/s41467-018-03717-8
Lipoproteins  Membrane biophysics  Organelles 

In situ X-ray scattering observation of two-dimensional interfacial colloidal crystallization OPEN
Longlong Wu, Xiao Wang, Geng Wang & Gang Chen

Colloids adsorbed at fluid interfaces can self-assemble into crystal, but the detail remains largely unknown due to experimental challenges. Using in situ X-ray scattering, Wu et al. show that out-of-plane electrostatic force induces in-plane capillary attraction between like-charged particles.

06 April 2018 | doi: 10.1038/s41467-018-03767-y
Self-assembly  Surfaces, interfaces and thin films 
  Latest Author Corrections    
Author Correction: Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia OPEN
Manon Bonneau, Celestine Atyame, Marwa Beji, Fabienne Justy, Martin Cohen-Gonsaud, Mathieu Sicard & Mylène Weill
11 April 2018 | doi: 10.1038/s41467-018-03799-4
Evolutionary biology  Evolutionary genetics  Molecular evolution 

Author Correction: The genetic prehistory of the Baltic Sea region OPEN
Alissa Mittnik , Chuan-Chao Wang, Saskia Pfrengle, Mantas Daubaras, Gunita Zariņa, Fredrik Hallgren, Raili Allmäe, Valery Khartanovich, Vyacheslav Moiseyev, Mari Tõrv, Anja Furtwängler, Aida Andrades Valtueña, Michal Feldman, Christos Economou, Markku Oinonen, Andrejs Vasks, Elena Balanovska, David Reich, Rimantas Jankauskas, Wolfgang Haak et al.
11 April 2018 | doi: 10.1038/s41467-018-03872-y
Evolutionary biology  Evolutionary genetics  Genomics  Population genetics 

Author Correction: Watt-level 10-gigahertz solid-state laser enabled by self-defocusing nonlinearities in an aperiodically poled crystal OPEN
A. S. Mayer, C. R. Phillips & U. Keller
11 April 2018 | doi: 10.1038/s41467-018-03816-6
Mode-locked lasers  Solid-state lasers 

Author Correction: CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing OPEN
Xueni Li, Shiheng Liu, Jiansen Jiang, Lingdi Zhang, Sara Espinosa, Ryan C. Hill, Kirk C. Hansen, Z. Hong Zhou & Rui Zhao
11 April 2018 | doi: 10.1038/s41467-018-03708-9
Cryoelectron microscopy  RNA-binding proteins  RNA splicing 
  Latest Publisher Corrections    
Publisher Correction: Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity OPEN
Will J. R. Stone , Joseph J. Campo, André Lin Ouédraogo, Lisette Meerstein-Kessel, Isabelle Morlais, Dari Da, Anna Cohuet, Sandrine Nsango, Colin J. Sutherland, Marga van de Vegte-Bolmer, Rianne Siebelink-Stoter, Geert-Jan van Gemert, Wouter Graumans, Kjerstin Lanke, Adam D. Shandling, Jozelyn V. Pablo, Andy A. Teng, Sophie Jones, Roos M. de Jong, Amanda Fabra-García et al.
11 April 2018 | doi: 10.1038/s41467-018-03769-w
Antibodies  Biomarkers  Parasite host response 

Publisher Correction: Triparental plants provide direct evidence for polyspermy induced polyploidy OPEN
Thomas Nakel, Dawit G. Tekleyohans, Yanbo Mao, Golo Fuchert, Dieu Vo & Rita Groß-Hardt
11 April 2018 | doi: 10.1038/s41467-018-03823-7
Evolutionary biology  Fertilization  Plant evolution 

Publisher Correction: Rotating robots move collectively and self-organize OPEN
Christian Scholz, Michael Engel & Thorsten Pöschel
11 April 2018 | doi: 10.1038/s41467-018-03873-x
Phase transitions and critical phenomena  Statistical physics 

Publisher Correction: Recent progress and perspectives of space electric propulsion systems based on smart nanomaterials OPEN
I. Levchenko, S. Xu, G. Teel, D. Mariotti, M. L. R. Walker & M. Keidar
10 April 2018 | doi: 10.1038/s41467-018-03818-4
Aerospace engineering  Nanoscale materials 

Publisher Correction: ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma OPEN
Shujun Han, Yibo Ren, Wangxiao He, Huadong Liu, Zhe Zhi, Xinliang Zhu, Tielin Yang, Yu Rong, Bohan Ma, Timothy J. Purwin, Zhenlin Ouyang, Caixia Li, Xun Wang, Xueqiang Wang, Huizi Yang, Yan Zheng, Andrew E. Aplin, Jiankang Liu & Yongping Shao
06 April 2018 | doi: 10.1038/s41467-018-03710-1
Cancer  Cell signalling 

Adolescence Collection

Exploring the science of adolescence and its far-reaching implications for societal challenges 

Access the Collection online 
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