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Nature Communications - 07 March 2018

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Two-electron spin correlations in precision placed donors in silicon OPEN
M. A. Broome, S. K. Gorman, M. G. House, S. J. Hile, J. G. Keizer, D. Keith, C. D. Hill, T. F. Watson, W. J. Baker, L. C. L. Hollenberg & M. Y. Simmons

Donor impurities in silicon are promising candidates as qubits but in order to create a large-scale quantum computer inter-qubit coupling must be introduced by precise positioning of the donors. Here the authors demonstrate the fabrication, manipulation and readout of a two qubit phosphorous donor device.

07 March 2018 | doi: 10.1038/s41467-018-02982-x
Physics  Qubits 

Surface energy of strained amorphous solids OPEN
Rafael D. Schulman, Miguel Trejo, Thomas Salez, Elie Raphaël & Kari Dalnoki-Veress

Whether or not amorphous solids exhibit strain-dependent surface energies, like those of crystalline materials, is still a matter of debate. Here, Schulman et al. monitor the contact angle of droplets on strained polymeric glasses and elastomers, which directly probes energy variation at the interfaces.

07 March 2018 | doi: 10.1038/s41467-018-03346-1
Surfaces, interfaces and thin films  Wetting 

Aerosol effects on cloud water amounts were successfully simulated by a global cloud-system resolving model OPEN
Yousuke Sato, Daisuke Goto, Takuro Michibata, Kentaroh Suzuki, Toshihiko Takemura, Hirofumi Tomita & Teruyuki Nakajima

Most global climate models overestimate the aerosol effect on cloud properties, but the reason for this is unclear. Here the authors show that using explicit representation of cloud microphysics, in global scale modelling, rather than parameterisations, reduces the overestimation.

07 March 2018 | doi: 10.1038/s41467-018-03379-6
Atmospheric science  Climate and Earth system modelling  Projection and prediction 

Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila OPEN
Fumiaki Obata, Clara O. Fons & Alex P. Gould

Low doses of harmful chemicals such as oxidants can have beneficial effects, in some cases mediated by increased expression of stress response genes. In this study, the authors show that low-dose oxidants increase the longevity of Drosophila via a different mechanism, remodelling of the microbiome.

07 March 2018 | doi: 10.1038/s41467-018-03070-w
Ageing  Drosophila  Microbiome 

Ultra-thin enzymatic liquid membrane for CO2 separation and capture OPEN
Yaqin Fu, Ying-Bing Jiang, Darren Dunphy, Haifeng Xiong, Eric Coker, Stan Chou, Hongxia Zhang, Juan M. Vanegas, Jonas G. Croissant, Joseph L. Cecchi, Susan B. Rempe & C. Jeffrey Brinker

Porous membranes show great promise for CO2 separation and capture, but are currently limited by a trade-off between permeance and selectivity. Here, the authors fabricate a bio-inspired, ultra-thin enzymatic liquid membrane that displays exceptional CO2 permeability and selectivity under ambient conditions.

07 March 2018 | doi: 10.1038/s41467-018-03285-x
Bioinspired materials  Carbon capture and storage  Chemical engineering  Materials chemistry 

A conserved interaction of the dynein light intermediate chain with dynein-dynactin effectors necessary for processivity OPEN
In-Gyun Lee, Mara A. Olenick, Malgorzata Boczkowska, Clara Franzini-Armstrong, Erika L. F. Holzbaur & Roberto Dominguez

A growing number of cargo-specific effector proteins are being identified that interact with both dynein and dynactin and form processive dynein-dynactin-effector complexes. Here the authors identify and characterize a conserved mechanism of interaction between dynein and unrelated effector proteins.

07 March 2018 | doi: 10.1038/s41467-018-03412-8
Dynein  X-ray crystallography 

Genome-wide analysis yields new loci associating with aortic valve stenosis OPEN
Anna Helgadottir , Gudmar Thorleifsson, Solveig Gretarsdottir, Olafur A. Stefansson, Vinicius Tragante, Rosa B. Thorolfsdottir, Ingileif Jonsdottir, Thorsteinn Bjornsson, Valgerdur Steinthorsdottir, Niek Verweij, Jonas B. Nielsen, Wei Zhou, Lasse Folkersen, Andreas Martinsson, Mahyar Heydarpour, Siddharth Prakash, Gylfi Oskarsson, Tomas Gudbjartsson, Arnar Geirsson, Isleifur Olafsson et al.

Aortic valve stenosis (AS) is the most common valvular heart disease. Here the authors identify two new AS loci that also associate with bicuspid aortic valve, aortic root diameter and/or coronary artery disease implicating both developmental abnormalities and atherosclerosis-like processes in AS.

07 March 2018 | doi: 10.1038/s41467-018-03252-6
Congenital heart defects  Genome-wide association studies  Heart development  Valvular disease 

Ionic liquid gating control of RKKY interaction in FeCoB/Ru/FeCoB and (Pt/Co)2/Ru/(Co/Pt)2 multilayers OPEN
Qu Yang, Lei Wang, Ziyao Zhou, Liqian Wang, Yijun Zhang, Shishun Zhao, Guohua Dong, Yuxin Cheng, Tai Min, Zhongqiang Hu, Wei Chen, Ke Xia & Ming Liu

Energy efficient control of magnetization in antiferromagnetic materials is one of the key ingredients for antiferromagnetic spintronics. Here the authors demonstrate voltage control of RKKY interaction and magnetization switching in synthetic antiferromagnetic multilayers by ionic liquid gating.

07 March 2018 | doi: 10.1038/s41467-018-03356-z
Ferroelectrics and multiferroics  Magnetic properties and materials 

Topological hybrid silicon microlasers OPEN
Han Zhao, Pei Miao, Mohammad H. Teimourpour, Simon Malzard, Ramy El-Ganainy, Henning Schomerus & Liang Feng

Topological effects, first observed in condensed matter physics, are now also studied in optical systems, extending the scope to active topological devices. Here, Zhao et al. combine topological physics with non-Hermitian photonics, demonstrating a topological microlaser on a silicon platform.

07 March 2018 | doi: 10.1038/s41467-018-03434-2
Semiconductor lasers  Silicon photonics 

Nitrogen fixation sustained productivity in the wake of the Palaeoproterozoic Great Oxygenation Event OPEN
Genming Luo, Christopher K. Junium, Gareth Izon, Shuhei Ono, Nicolas J. Beukes, Thomas J. Algeo, Ying Cui, Shucheng Xie & Roger E. Summons

The response of biogeochemical nitrogen cycle to Earth-surface oxygenation remains poorly known. Here, the authors show that aerobic nitrogen cycling was pervasive prior to the Great Oxygenation Event (GOE), but its evolution was complex, with diazotrophy prevailing and sustaining productivity after the GOE.

07 March 2018 | doi: 10.1038/s41467-018-03361-2
Element cycles  Marine chemistry 

Improving genetic prediction by leveraging genetic correlations among human diseases and traits OPEN
Robert M. Maier, Zhihong Zhu, Sang Hong Lee, Maciej Trzaskowski, Douglas M. Ruderfer, Eli A. Stahl, Stephan Ripke, Naomi R. Wray, Jian Yang, Peter M. Visscher & Matthew R. Robinson

Genetic prediction of complex traits so far has limited accuracy because of insufficient understanding of the genetic risk. Here, Maier et al. develop an improved method for trait prediction that makes use of genetic correlations between traits and apply it to summary statistics of psychiatric diseases.

07 March 2018 | doi: 10.1038/s41467-017-02769-6
Genome-wide association studies  Predictive medicine  Quantitative trait  Statistical methods 

Ice-volume-forced erosion of the Chinese Loess Plateau global Quaternary stratotype site OPEN
T. Stevens, J.-P. Buylaert, C. Thiel, G. Újvári, S. Yi, A. S. Murray, M. Frechen & H. Lu

A basic requirement for reconstructing past environmental change is accurate understanding of sediment age. Here, the authors show that the interpretation of a benchmark archive in China has been inaccurate, and that ice volume primarily controls desert dynamics, sediment preservation, and precipitation at the site.

07 March 2018 | doi: 10.1038/s41467-018-03329-2
Environmental impact  Palaeoclimate 

A transcriptome-wide association study identifies PALMD as a susceptibility gene for calcific aortic valve stenosis OPEN
Sébastien Thériault, Nathalie Gaudreault, Maxime Lamontagne, Mickael Rosa, Marie-Chloé Boulanger, David Messika-Zeitoun, Marie-Annick Clavel, Romain Capoulade, François Dagenais, Philippe Pibarot, Patrick Mathieu & Yohan Bossé

Progressive remodeling and calcification of the aortic valve leads to calcific aortic valve stenosis (CAVS) and, ultimately, heart failure. In a combined GWAS and TWAS approach, Thériault et al. identify PALMD as a candidate causal gene for CAVS, which is further supported by Mendelian randomization.

07 March 2018 | doi: 10.1038/s41467-018-03260-6
Gene expression profiling  Genome-wide association studies  Valvular disease 

Batch production of 6-inch uniform monolayer molybdenum disulfide catalyzed by sodium in glass OPEN
Pengfei Yang, Xiaolong Zou, Zhepeng Zhang, Min Hong, Jianping Shi, Shulin Chen, Jiapei Shu, Liyun Zhao, Shaolong Jiang, Xiebo Zhou, Yahuan Huan, Chunyu Xie, Peng Gao, Qing Chen, Qing Zhang, Zhongfan Liu & Yanfeng Zhang

Growth of large-area monolayer transition metal dichalcogenides is critical for their application but remains challenging. Here Yang et al. report rapid chemical vapor deposition of 6-inch monolayer molybdenum disulfide by sufficiently uniformly supplying the precursors and catalysts.

07 March 2018 | doi: 10.1038/s41467-018-03388-5
Synthesis and processing  Two-dimensional materials 

Itch/β-arrestin2-dependent non-proteolytic ubiquitylation of SuFu controls Hedgehog signalling and medulloblastoma tumorigenesis OPEN
Paola Infante , Roberta Faedda, Flavia Bernardi, Francesca Bufalieri, Ludovica Lospinoso Severini, Romina Alfonsi, Daniela Mazzà, Mariangela Siler, Sonia Coni, Agnese Po, Marialaura Petroni, Elisabetta Ferretti, Mattia Mori, Enrico De Smaele, Gianluca Canettieri, Carlo Capalbo, Marella Maroder, Isabella Screpanti, Marcel Kool, Stefan M. Pfister et al.

SuFu is a tumour suppressor in medulloblastoma and regulates Gli proteins in the Sonic Hedgehog pathway; however, the molecular mechanisms behind this regulation are unclear. Here, the authors show that the Itch/β-arrestin2 complex binds and ubiquitylates SuFu, facilitating the interaction with Gli3 and its conversion into the repressive form, thus counteracting medulloblastoma formation.

07 March 2018 | doi: 10.1038/s41467-018-03339-0
Cancer  Ubiquitylation 

Direct observation of orbital hybridisation in a cuprate superconductor OPEN
C. E. Matt , D. Sutter, A. M. Cook, Y. Sassa, M. Månsson, O. Tjernberg, L. Das, M. Horio, D. Destraz, C. G. Fatuzzo, K. Hauser, M. Shi, M. Kobayashi, V. N. Strocov, T. Schmitt, P. Dudin, M. Hoesch, S. Pyon, T. Takayama, H. Takagi et al.

The essential physics of cuprate superconductors is often described by single-band models. Here, Matt et al. report direct observation of a two-band electronic structure in La-based cuprates.

06 March 2018 | doi: 10.1038/s41467-018-03266-0
Condensed-matter physics  Electronic properties and materials  Superconducting properties and materials 

Toward a universal decoder of linguistic meaning from brain activation OPEN
Francisco Pereira, Bin Lou, Brianna Pritchett, Samuel Ritter, Samuel J. Gershman, Nancy Kanwisher, Matthew Botvinick & Evelina Fedorenko

Previous work decoding linguistic meaning from imaging data has generally been limited to a small number of semantic categories. Here, authors show that a decoder trained on neuroimaging data of single concepts sampling the semantic space can robustly decode meanings of semantically diverse new sentences with topics not encountered during training.

06 March 2018 | doi: 10.1038/s41467-018-03068-4
Computational science  Neural decoding 

Gene-by-environment interactions in urban populations modulate risk phenotypes OPEN
Marie-Julie Favé, Fabien C. Lamaze, David Soave, Alan Hodgkinson, Héloïse Gauvin, Vanessa Bruat, Jean-Christophe Grenier, Elias Gbeha, Kimberly Skead, Audrey Smargiassi, Markey Johnson, Youssef Idaghdour & Philip Awadalla

Individuals with different genotypes may respond differently to environmental variation. Here, Favé et al. find substantial impacts of different environment exposures on the transcriptome and clinical endophenotypes when controlling for genetic ancestry by analyzing data from ∼1000 individuals from a founder population in Quebec.

06 March 2018 | doi: 10.1038/s41467-018-03202-2
Epidemiology  Gene regulation  Population genetics  Quantitative trait 

Saccade-synchronized rapid attention shifts in macaque visual cortical area MT OPEN
Tao Yao, Stefan Treue & B. Suresh Krishna

Saccades result in remapping the neural representation of a target object as well as its attentional modulation. Here the authors show that the trans-saccadic attentional shift is precisely synchronized with the saccade resulting in optimal maintenance of the locus of spatial attention.

06 March 2018 | doi: 10.1038/s41467-018-03398-3
Attention  Saccades 

Decapping protein EDC4 regulates DNA repair and phenocopies BRCA1 OPEN
Gonzalo Hernández , María José Ramírez, Jordi Minguillón, Paco Quiles, Gorka Ruiz de Garibay, Miriam Aza-Carmona, Massimo Bogliolo, Roser Pujol, Rosario Prados-Carvajal, Juana Fernández, Nadia García, Adrià López, Sara Gutiérrez-Enríquez, Orland Diez, Javier Benítez, Mónica Salinas, Alex Teulé, Joan Brunet, Paolo Radice, Paolo Peterlongo et al.

Mutations in BRCA1 are associated with an increased risk of breast and ovarian cancer. Here the authors show that EDC4, a component of P-bodies, is a member of the BRCA1 complex with roles in stimulating end resection at breaks.

06 March 2018 | doi: 10.1038/s41467-018-03433-3
Cancer  Double-strand DNA breaks  Genomic instability  RNA metabolism 

Flexibility in motor timing constrains the topology and dynamics of pattern generator circuits OPEN
Cengiz Pehlevan, Farhan Ali & Bence P. Ölveczky

Human speech and bird song requires the generation of precisely timed motor patterns. The authors show that zebra finches can learn to independently modify the duration of individual song segments and find that synfire chain networks are ideally suited to implement such flexible motor timing.

06 March 2018 | doi: 10.1038/s41467-018-03261-5
Computational neuroscience  Learning and memory  Reward 

Nanowire arrays restore vision in blind mice OPEN
Jing Tang, Nan Qin, Yan Chong, Yupu Diao, Yiliguma, Zhexuan Wang, Tian Xue, Min Jiang, Jiayi Zhang & Gengfeng Zheng

The restoration of light response using retinal prosthesis could be a way to restore vision following retinal degenerative disease. Here the authors develop gold-titania nanowire arrays that restore visual response in blind mice.

06 March 2018 | doi: 10.1038/s41467-018-03212-0
Biomedical engineering  Implants 

Asynchrony between Antarctic temperature and CO2 associated with obliquity over the past 720,000 years OPEN
Ryu Uemura, Hideaki Motoyama, Valérie Masson-Delmotte, Jean Jouzel, Kenji Kawamura, Kumiko Goto-Azuma, Shuji Fujita, Takayuki Kuramoto, Motohiro Hirabayashi, Takayuki Miyake, Hiroshi Ohno, Koji Fujita, Ayako Abe-Ouchi, Yoshinori Iizuka, Shinichiro Horikawa, Makoto Igarashi, Keisuke Suzuki, Toshitaka Suzuki & Yoshiyuki Fujii

The Antarctic temperature record displays a puzzling asynchrony with changes in CO2 through glacial cycles. Here, the authors show that a 720,000-year Antarctic temperature record is affected by variations in obliquity-induced local insolation that are associated with phase modulation of eccentricity cycle.

06 March 2018 | doi: 10.1038/s41467-018-03328-3
Cryospheric science  Palaeoceanography  Palaeoclimate 

Photosystem II Subunit S overexpression increases the efficiency of water use in a field-grown crop OPEN
Katarzyna Głowacka, Johannes Kromdijk, Katherine Kucera, Jiayang Xie, Amanda P. Cavanagh, Lauriebeth Leonelli, Andrew D. B. Leakey, Donald R. Ort, Krishna K. Niyogi & Stephen P. Long

Availability of irrigation water will be an increasing barrier to global crop yield increases. Here the authors show transgenic tobacco plants overexpressing Photosystem II Subunit S have less stomatal opening in response to light and a 25% reduction in water loss per CO2 assimilated under replicated field trials.

06 March 2018 | doi: 10.1038/s41467-018-03231-x
Field trials  Molecular engineering in plants  Non-photochemical quenching 

Adoptive cancer immunotherapy using DNA-demethylated T helper cells as antigen-presenting cells OPEN
Alexei F. Kirkin, Karine N. Dzhandzhugazyan, Per Guldberg, Johnny Jon Fang, Rikke S. Andersen, Christina Dahl, Jann Mortensen, Tim Lundby, Aase Wagner, Ian Law, Helle Broholm, Line Madsen, Christer Lundell-Ek, Morten F. Gjerstorff, Henrik J. Ditzel, Martin R. Jensen & Walter Fischer

A critical determinant of tumor eradication by adoptive immunotherapy is the tumor associated antigen recognized by cytotoxic T lymphocytes. Here the authors generate ex vivo autologous cytotoxic T lymphocytes by exposure to antigens induced by DNA demethylation and report the results of a phase 1 trial of 25 patients with recurrent glioblastoma multiforme with tumor regression in three patients.

06 March 2018 | doi: 10.1038/s41467-018-03217-9
Cancer  Translational research 

Inverted valley polarization in optically excited transition metal dichalcogenides OPEN
Gunnar Berghäuser, Ivan Bernal-Villamil, Robert Schmidt, Robert Schneider, Iris Niehues, Paul Erhart, Steffen Michaelis de Vasconcellos, Rudolf Bratschitsch, Andreas Knorr & Ermin Malic

In atomically thin transition metal dichalcogenides, spin- and valley-polarised states can be addressed thanks to large spin–orbit coupling and circular dichroism. Here, the authors investigate theoretically and experimentally the decay dynamics of spin and valley polarisation in transition metal dichalcogenide monolayers.

06 March 2018 | doi: 10.1038/s41467-018-03354-1
Electronic devices  Nonlinear optics  Two-dimensional materials 

Disease-associated missense mutations in GluN2B subunit alter NMDA receptor ligand binding and ion channel properties OPEN
Laura Fedele, Joseph Newcombe, Maya Topf, Alasdair Gibb, Robert J. Harvey & Trevor G. Smart

N-methyl-d-aspartate-receptors (NMDARs) are glutamate receptors critical for synaptic transmission, plasticity, and cognition. Here, the authors look at four neurodevelopmental disease-related mutations of NMDAR, gaining insight into binding of Mg2+ and mechanism of memantine, an NMDAR antagonist.

06 March 2018 | doi: 10.1038/s41467-018-02927-4
Epilepsy  Ion channels in the nervous system 

Identification of single amino acid differences in uniformly charged homopolymeric peptides with aerolysin nanopore OPEN
Fabien Piguet, Hadjer Ouldali, Manuela Pastoriza-Gallego, Philippe Manivet, Juan Pelta & Abdelghani Oukhaled

Existing methods used for peptide analysis suffer from low sensitivity and specificity. Here the authors demonstrate the nanopore-based size-discrimination and purity analysis of short homopolymeric peptides with a single amino acid resolution.

06 March 2018 | doi: 10.1038/s41467-018-03418-2
Biophysical chemistry  Nanopores  Peptides  Single-molecule biophysics 

Current-driven dynamics and inhibition of the skyrmion Hall effect of ferrimagnetic skyrmions in GdFeCo films OPEN
Seonghoon Woo, Kyung Mee Song, Xichao Zhang, Yan Zhou, Motohiko Ezawa, Xiaoxi Liu, S. Finizio, J. Raabe, Nyun Jong Lee, Sang-Il Kim, Seung-Young Park, Younghak Kim, Jae-Young Kim, Dongjoon Lee, OukJae Lee, Jun Woo Choi, Byoung-Chul Min, Hyun Cheol Koo & Joonyeon Chang

Non-zero topological charge prevents the straight motion of ferromagnetic skyrmions and hinders their applications. Here, the authors report the stabilization and current-driven dynamics of skyrmions in GdFeCo films in which the ferrimagnetic skyrmions can move with high velocity and reduced skyrmion Hall angle.

06 March 2018 | doi: 10.1038/s41467-018-03378-7
Magnetic properties and materials  Spintronics 

The role of confined collagen geometry in decreasing nucleation energy barriers to intrafibrillar mineralization OPEN
Doyoon Kim, Byeongdu Lee, Stavros Thomopoulos & Young-Shin Jun

Nucleation in highly confined gaps shows distinctly different behavior from nucleation in extrafibrillar spaces. Here, using in situ X-ray scattering and classical nucleation theory, the authors show how confined geometry reduces energy barriers to intrafibrillar mineralization of collagen.

06 March 2018 | doi: 10.1038/s41467-018-03041-1
Biomaterials  Biomineralization 

Convergent genomic signatures of domestication in sheep and goats OPEN
Florian J. Alberto , Frédéric Boyer, Pablo Orozco-terWengel, Ian Streeter, Bertrand Servin, Pierre de Villemereuil, Badr Benjelloun, Pablo Librado, Filippo Biscarini, Licia Colli, Mario Barbato, Wahid Zamani, Adriana Alberti, Stefan Engelen, Alessandra Stella, Stéphane Joost, Paolo Ajmone-Marsan, Riccardo Negrini, Ludovic Orlando, Hamid Reza Rezaei et al.

The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.

06 March 2018 | doi: 10.1038/s41467-018-03206-y
Evolutionary genetics  Genetic variation 

Andean surface uplift constrained by radiogenic isotopes of arc lavas OPEN
Erin M. Scott, Mark B. Allen, Colin G. Macpherson, Ken J. W. McCaffrey, Jon P. Davidson, Christopher Saville & Mihai N. Ducea

Multiple complex tectonic and climatic processes have formed the Andes, which today provides a unique ecological niche. Here, Scott et al. investigate how the chemical composition of lavas from stratovolcanoes can be used to give insight on the uplift of the Andes over the last 200 million years.

06 March 2018 | doi: 10.1038/s41467-018-03173-4
Geochemistry  Geodynamics  Geomorphology  Tectonics 

Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome OPEN
Yi Hu, Jon G. Sanders, Piotr Łukasik, Catherine L. D’Amelio, John S. Millar, David R. Vann, Yemin Lan, Justin A. Newton, Mark Schotanus, Daniel J. C. Kronauer, Naomi E. Pierce, Corrie S. Moreau, John T. Wertz, Philipp Engel & Jacob A. Russell

Gut bacteria are prevalent across insects including ants, but their precise roles are often unclear. Here, Hu et al. show that microbes aid ants by recycling nitrogen into bio-available amino acids. This function is conserved across the turtle ants, suggesting an ancient nutritional mutualism.

06 March 2018 | doi: 10.1038/s41467-018-03357-y
Evolutionary ecology  Microbial ecology  Microbiome  Symbiosis 

Discrete energy levels of Caroli-de Gennes-Matricon states in quantum limit in FeTe0.55Se0.45 OPEN
Mingyang Chen, Xiaoyu Chen, Huan Yang, Zengyi Du, Xiyu Zhu, Enyu Wang & Hai-Hu Wen

Despite predicted decades ago, the discrete Caroli-de Gennes-Matricon states are difficult to observe. Here, Chen et al. observe discrete states appearing near zero bias at the vortex center of FeTe0.55Se0.45, strongly suggesting a Caroli-de Gennes-Matricon state.

06 March 2018 | doi: 10.1038/s41467-018-03404-8
Electronic properties and materials  Superconducting properties and materials 

ARMMs as a versatile platform for intracellular delivery of macromolecules OPEN
Qiyu Wang, Jiujiu Yu, Tatenda Kadungure, Joseph Beyene, Hong Zhang & Quan Lu

One of the challenges of biologic drug therapy is delivery into target cells and tissues. Here the authors present ARMMs (arrestin domain containing protein 1 mediated microvesicles) as a versatile platform for packaging and delivery of a myriad of molecules, including p53, RNAs and CRISPR-Cas9.

06 March 2018 | doi: 10.1038/s41467-018-03390-x
Molecular engineering  Protein delivery 

Context-dependent interactions and the regulation of species richness in freshwater fish OPEN
Andrew S. MacDougall, Eric Harvey, Jenny L. McCune, Karin A. Nilsson, Joseph Bennett, Jennifer Firn, Timothy Bartley, James B. Grace, Jocelyn Kelly, Tyler D. Tunney, Bailey McMeans, Shin-Ichiro S. Matsuzaki, Taku Kadoya, Ellen Esch, Kevin Cazelles, Nigel Lester & Kevin S. McCann

Species richness patterns are driven by biotic and abiotic factors, the relative strengths of which are unclear. Here, the authors test how species interactions or environmental traits influence fish richness across over 700 Canadian lakes, showing a surprisingly small role of negative interactions.

06 March 2018 | doi: 10.1038/s41467-018-03419-1
Biogeography  Community ecology  Freshwater ecology  Limnology 

Anisotropic photoemission time delays close to a Fano resonance OPEN
Claudio Cirelli , Carlos Marante, Sebastian Heuser, C. L. M. Petersson, Álvaro Jiménez Galán, Luca Argenti, Shiyang Zhong, David Busto, Marcus Isinger, Saikat Nandi, Sylvain Maclot, Linnea Rading, Per Johnsson, Mathieu Gisselbrecht, Matteo Lucchini, Lukas Gallmann, J. Marcus Dahlström, Eva Lindroth, Anne L’Huillier, Fernando Martín et al.

Ionization time delays are of interest in understanding the photoionization mechanism in atoms and molecules in ultra-short time scales. Here the authors investigate the angular dependence of photoionization time delays in the presence of an autoionizing resonance in argon atom using RABBITT technique.

06 March 2018 | doi: 10.1038/s41467-018-03009-1
Atomic and molecular interactions with photons  Attosecond science  High-harmonic generation 

Experimental observation of photonic nodal line degeneracies in metacrystals OPEN
Wenlong Gao, Biao Yang, Ben Tremain, Hongchao Liu, Qinghua Guo, Lingbo Xia, Alastair P. Hibbins & Shuang Zhang

Nodal lines are 1D band crossings forming a ring in the Brillouin zone which can spawn Weyl points. Here, using a cut-wire metacrystal designed for gigahertz frequencies, Gao et al. observe photonic nodal line degeneracies as well as the photonic Weyl points arising from them.

05 March 2018 | doi: 10.1038/s41467-018-03407-5
Metamaterials  Sub-wavelength optics 

Microhomology-assisted scarless genome editing in human iPSCs OPEN
Shin-Il Kim, Tomoko Matsumoto, Harunobu Kagawa, Michiko Nakamura, Ryoko Hirohata, Ayano Ueno, Maki Ohishi, Tetsushi Sakuma, Tomoyoshi Soga, Takashi Yamamoto & Knut Woltjen

Positive selection for gene targeting is a common and reliable method to generate isogenic disease models in human pluripotent stem cells. Here, the authors present engineered selection markers which achieve scarless excision by CRISPR-Cas9 and microhomology mediated end-joining.

05 March 2018 | doi: 10.1038/s41467-018-03044-y
CRISPR-Cas9 genome editing  Genetic engineering  Stem-cell biotechnology 

Uncovering the balance of forces driving microtubule aster migration in C. elegans zygotes OPEN
A. De Simone, A. Spahr, C. Busso & P. Gönczy

Microtubule asters are positioned precisely within cells by forces generated by molecular motors, but it is unclear how these are integrated in space and time. Here the authors perform in vivo drag measurements and genetic manipulations to determine the balance of forces that position microtubule asters in C. elegans zygotes.

05 March 2018 | doi: 10.1038/s41467-018-03118-x
Cytoskeleton  Intracellular movement  Mitotic spindle 

A browser-based tool for visualization and analysis of diffusion MRI data OPEN
Jason D. Yeatman, Adam Richie-Halford, Josh K. Smith, Anisha Keshavan & Ariel Rokem

Data sharing is an important component of reproducible research, but meaningful data sharing can be difficult. Here authors describe a new open source tool, AFQ-Browser, that builds an interactive website allowing visualization and exploratory data analysis of published diffusion MRI data.

05 March 2018 | doi: 10.1038/s41467-018-03297-7
Bioinformatics  Cognitive neuroscience  Human behaviour 

Cancer-associated fibroblasts induce antigen-specific deletion of CD8 + T Cells to protect tumour cells OPEN
Matthew A. Lakins, Ehsan Ghorani, Hafsa Munir, Carla P. Martins & Jacqueline D. Shields

Tumours employ a variety of strategies to induce immune suppression. Here the authors show that cancer-associated fibroblasts process and cross-present tumour-antigens to T-cells resulting in antigen-specific T cell death and dysfunction via upregulation of both cell death and immune checkpoint signals.

05 March 2018 | doi: 10.1038/s41467-018-03347-0
Antigen processing and presentation  Cancer microenvironment  Immunosurveillance 

Reagent-controlled regiodivergent ring expansions of steroids OPEN
Manwika Charaschanya & Jeffrey Aubé

Late-stage diversification of natural products is an important starting point for drug discovery. Here, the authors use chiral reagents to perform the regiocontrolled ring expansion of steroid precursors and achieve more than 100 isomerically pure analogs with spatial and functional diversity.

05 March 2018 | doi: 10.1038/s41467-018-03248-2
Diversity-oriented synthesis  Synthetic chemistry methodology  Natural product synthesis 

Life times of metastable states guide regulatory signaling in transcriptional riboswitches OPEN
Christina Helmling, Dean-Paulos Klötzner, Florian Sochor, Rachel Anne Mooney, Anna Wacker, Robert Landick, Boris Fürtig, Alexander Heckel & Harald Schwalbe

Riboswitches are RNA-based regulatory elements, which regulate downstream gene expression by binding of small molecular weight ligands. Here the authors demonstrate the molecular mechanism of a transcriptional riboswitch that integrates changes in transcription rates, metabolite concentration, and kinetic on- and off-rates of ligand binding.

05 March 2018 | doi: 10.1038/s41467-018-03375-w
Riboswitches  RNA  Solution-state NMR 

Direct conversion of injury-site myeloid cells to fibroblast-like cells of granulation tissue OPEN
Mithun Sinha, Chandan K. Sen, Kanhaiya Singh, Amitava Das, Subhadip Ghatak, Brian Rhea, Britani Blackstone, Heather M. Powell, Savita Khanna & Sashwati Roy

At the site of injury, macrophages exit their characteristic phenotype undergoing direct conversion to fibroblasts. Keratinocyte-derived miR-21, packaged in extracellular vesicles, enables such plasticity which accounts for the vast majority of all fibroblasts in the granulation tissue.

05 March 2018 | doi: 10.1038/s41467-018-03208-w
Inflammation  miRNAs  Monocytes and macrophages 

Elucidating anionic oxygen activity in lithium-rich layered oxides OPEN
Jing Xu, Meiling Sun, Ruimin Qiao, Sara E. Renfrew, Lu Ma, Tianpin Wu, Sooyeon Hwang, Dennis Nordlund, Dong Su, Khalil Amine, Jun Lu, Bryan D. McCloskey, Wanli Yang & Wei Tong

A reversible oxygen redox process contributes extra capacity and understanding this behavior is of high importance. Here, aided by resonant inelastic X-ray scattering, the authors reveal the distinctive anionic oxygen activity of battery electrodes with different transition metals.

05 March 2018 | doi: 10.1038/s41467-018-03403-9
Batteries  Electrochemistry 

In situ atomic-scale observation of oxidation and decomposition processes in nanocrystalline alloys OPEN
Jinming Guo, Georg Haberfehlner, Julian Rosalie, Lei Li, María Jazmin Duarte, Gerald Kothleitner, Gerhard Dehm, Yunbin He, Reinhard Pippan & Zaoli Zhang

Oxygen contamination during the mixing of precursor powders for nanocrystalline materials affects alloy microstructure, but exactly how remains unclear. Here, the authors show that stable nano-oxides can form easily inside severely deformed Cu-Fe grains during heating.

05 March 2018 | doi: 10.1038/s41467-018-03288-8
Metals and alloys  Structural properties 

A diminutive perinate European Enantiornithes reveals an asynchronous ossification pattern in early birds OPEN
Fabien Knoll, Luis M. Chiappe, Sophie Sanchez, Russell J. Garwood, Nicholas P. Edwards, Roy A. Wogelius, William I. Sellers, Phillip L. Manning, Francisco Ortega, Francisco J. Serrano, Jesús Marugán-Lobón, Elena Cuesta, Fernando Escaso & Jose Luis Sanz

Fossil juvenile Mesozoic birds are exceedingly rare and can provide important insight into the early evolution of avian development. Here, Knoll et al. describe one of the smallest known Mesozoic avians, which indicates a clade-wide asynchronous pattern of osteogenesis and great variation in basal bird hatchling size and skeletal maturation tempo.

05 March 2018 | doi: 10.1038/s41467-018-03295-9
Evolutionary developmental biology  Palaeontology 

Dissecting super-enhancer hierarchy based on chromatin interactions OPEN
Jialiang Huang, Kailong Li, Wenqing Cai, Xin Liu, Yuannyu Zhang, Stuart H. Orkin, Jian Xu & Guo-Cheng Yuan

Super-enhancers (SEs) are important regulatory elements for gene expression, but their intrinsic properties remain poorly understood. Here the authors analyse Hi-C and ChIP-seq data and find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers.

05 March 2018 | doi: 10.1038/s41467-018-03279-9
Chromatin structure  Epigenomics  Gene regulatory networks  Transcription 

Robust singlet fission in pentacene thin films with tuned charge transfer interactions OPEN
K. Broch, J. Dieterle, F. Branchi, N. J. Hestand, Y. Olivier, H. Tamura, C. Cruz, V. M. Nichols, A. Hinderhofer, D. Beljonne, F. C. Spano, G. Cerullo, C. J. Bardeen & F. Schreiber

Singlet fission is desirable for highly efficient solar cells, yet the details of the process remain elusive. Here, Broch et al. show that the changes in bulk intermolecular interactions can have little effect on the singlet fission rate in a mixture of pentacene and weakly interacting spacer molecules.

05 March 2018 | doi: 10.1038/s41467-018-03300-1
Excited states  Organic molecules in materials science 

Sea ice dynamics across the Mid-Pleistocene transition in the Bering Sea OPEN
H. Detlef, S. T. Belt, S. M. Sosdian, L. Smik, C. H. Lear, I. R. Hall, P. Cabedo-Sanz, K. Husum & S. Kender

Modelling studies propose sea ice to be one of the underlying mechanisms for the Mid-Pleistocene transition. Here, the authors show Mid-Pleistocene subarctic North Pacific sea ice dynamics based on biomarkers and biogenic opal accumulation rates, supporting the importance of sea ice for climate change.

05 March 2018 | doi: 10.1038/s41467-018-02845-5
Biogeochemistry  Marine chemistry  Palaeoceanography 

MAP4K3 mediates amino acid-dependent regulation of autophagy via phosphorylation of TFEB OPEN
Cynthia L. Hsu, Elian X. Lee, Kara L. Gordon, Edwin A. Paz, Wen-Chuan Shen, Kohta Ohnishi, Jill Meisenhelder, Tony Hunter & Albert R. La Spada

Amino acids stimulate cell growth and depletion in a cell activates autophagy, yet how this is regulated is unclear. Here, the authors show that MAP4K3 (also known as germinal-center kinase-like kinase) acts as an amino acid-dependent regulator of autophagy, via phosphorylation of the transcription factor EB.

05 March 2018 | doi: 10.1038/s41467-018-03340-7
Macroautophagy  Nutrient signalling 

Marine spatial planning makes room for offshore aquaculture in crowded coastal waters OPEN
S. E. Lester, J. M. Stevens, R. R. Gentry, C. V. Kappel, T. W. Bell, C. J. Costello, S. D. Gaines, D. A. Kiefer, C. C. Maue, J. E. Rensel, R. D. Simons, L. Washburn & C. White

Marine spatial planning is used to co-ordinate multiple ocean uses, and is frequently informed by tradeoffs and composite metrics. Here, Lester et al. introduce an approach that plans for multiple uses simultaneously whilst balancing individual objectives, using a case study of aquaculture development in California.

05 March 2018 | doi: 10.1038/s41467-018-03249-1
Ecosystem services  Environmental impact  Ocean sciences  Socioeconomic scenarios 

Operando spectroscopy study of the carbon dioxide electro-reduction by iron species on nitrogen-doped carbon OPEN
Chiara Genovese, Manfred E. Schuster, Emma K. Gibson, Diego Gianolio, Victor Posligua, Ricardo Grau-Crespo, Giannantonio Cibin, Peter P. Wells, Debi Garai, Vladyslav Solokha, Sandra Krick Calderon, Juan J. Velasco-Velez, Claudio Ampelli, Siglinda Perathoner, Georg Held, Gabriele Centi & Rosa Arrigo

Trapping carbon dioxide within usable chemicals is a promising means to mitigate climate change, yet electrochemical C–C couplings are challenging to perform. Here, the authors prepared iron oxyhydroxides on nitrogen-doped carbon that efficiently convert carbon dioxide to acetic acid.

05 March 2018 | doi: 10.1038/s41467-018-03138-7
Catalytic mechanisms  Electrocatalysis 

Convergent shifts in host-associated microbial communities across environmentally elicited phenotypes OPEN
Tyler J. Carrier & Adam M. Reitzel

Symbiotic microbial communities aid their hosts through developmental and environmental transitions. Here, the authors show that host morphological plasticity is associated with predictable changes in a phenotype-specific microbiome in three species of sea urchin larvae.

05 March 2018 | doi: 10.1038/s41467-018-03383-w
Developmental biology  Evolutionary ecology  Marine biology  Microbiome 

Reactivity of He with ionic compounds under high pressure OPEN
Zhen Liu, Jorge Botana, Andreas Hermann, Steven Valdez, Eva Zurek, Dadong Yan, Hai-qing Lin & Mao-sheng Miao

Helium was long thought to be unable to form stable solid compounds, until a recent discovery that helium reacts with sodium at high pressure. Here, the authors demonstrate the driving force for helium reactivity, showing that it can form new compounds under pressure without forming any local chemical bonds.

05 March 2018 | doi: 10.1038/s41467-018-03284-y
Chemical bonding  Electronic structure  Structure of solids and liquids  Structure prediction 

Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export OPEN
Karine Leblanc, Bernard Quéguiner, Frédéric Diaz, Véronique Cornet, Mónica Michel-Rodriguez, Xavier Durrieu de Madron, Chris Bowler, Shruti Malviya, Melilotus Thyssen, Gérald Grégori, Mathieu Rembauville, Olivier Grosso, Julie Poulain, Colomban de Vargas, Mireille Pujo-Pay & Pascal Conan

Diatoms are major oceanic primary producers, but some species belonging to the nano- and even picoplankton size are poorly characterized. Here the authors describe a massive spring bloom of the smallest known diatom in the Mediterranean Sea and reveal their general oversight at the global scale.

05 March 2018 | doi: 10.1038/s41467-018-03376-9
Carbon cycle  DNA sequencing  Marine biology 

Genomic evidence of speciation reversal in ravens OPEN
Anna M. Kearns, Marco Restani, Ildiko Szabo, Audun Schrøder-Nielsen, Jin Ah Kim, Hayley M. Richardson, John M. Marzluff, Robert C. Fleischer, Arild Johnsen & Kevin E. Omland

Speciation reversal is known mainly from recently diverged lineages that have come into secondary contact following anthropogenic disturbance. Here, Kearns et al. use genomic and phylogenomic analyses to show that the Common Raven (Corvus corax) was formed by the ancient fusion of two non-sister lineages of ravens.

02 March 2018 | doi: 10.1038/s41467-018-03294-w
Evolutionary genetics  Speciation 

Protecting tropical forests from the rapid expansion of rubber using carbon payments OPEN
Eleanor M. Warren-Thomas, David P. Edwards, Daniel P. Bebber, Phourin Chhang, Alex N. Diment, Tom D. Evans, Frances H. Lambrick, James F. Maxwell, Menghor Nut, Hannah J. O’Kelly, Ida Theilade & Paul M. Dolman

Expansion of rubber plantations threatens tropical forest carbon stocks and biodiversity, but may be dis-incentivised using carbon finance. Here, Warren-Thomas et al. use forest and agricultural data for Cambodia to show that carbon prices of $30–$51 per tCO2 are needed to match forest protection costs.

02 March 2018 | doi: 10.1038/s41467-018-03287-9
Climate-change mitigation  Environmental social sciences  Forestry 

Atomic visualization of a non-equilibrium sodiation pathway in copper sulfide OPEN
Jae Yeol Park, Sung Joo Kim, Joon Ha Chang, Hyeon Kook Seo, Jeong Yong Lee & Jong Min Yuk

Copper sulfide allows for high-performance sodium ion storage, yet its sodiation mechanism is poorly understood. Here, the authors examine the atomic structures of sodiated phases via in situ transmission electron microscopy, showing a non-equilibrium reaction pathway.

02 March 2018 | doi: 10.1038/s41467-018-03322-9
Batteries  Transmission electron microscopy 

Carboxylic acid-modified metal oxide catalyst for selectivity-tunable aerobic ammoxidation OPEN
Xiuquan Jia, Jiping Ma, Fei Xia, Yongming Xu, Jin Gao & Jie Xu

Precisely controlling the surface properties of base-metal oxide catalysts to tune the reaction selectivity remains a challenge. Here, the authors show that a green modification of manganese oxide surface with carboxylates can be used to tune the ammoxidation selectivity toward the desired products.

02 March 2018 | doi: 10.1038/s41467-018-03358-x
Heterogeneous catalysis  Materials for energy and catalysis  Sustainability 

Item-level analyses reveal genetic heterogeneity in neuroticism OPEN
Mats Nagel, Kyoko Watanabe, Sven Stringer, Danielle Posthuma & Sophie van der Sluis

Neuroticism can be assessed as a composite score of individual items. Here, Nagel et al. perform genetic association studies for 12 neuroticism items and the sum-score and demonstrate genetic heterogeneity at the item-level.

02 March 2018 | doi: 10.1038/s41467-018-03242-8
Behavioural genetics  Genome-wide association studies  Quantitative trait 

DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex OPEN
Philip Ketterer, Adithya N. Ananth, Diederik S. Laman Trip, Ankur Mishra, Eva Bertosin, Mahipal Ganji, Jaco van der Torre, Patrick Onck, Hendrik Dietz & Cees Dekker

FG-Nups are disordered proteins in the nuclear pore complex (NPC) where they selectively control nuclear transport. Here authors build NPC-mimics based on DNA origami rings which attach a certain numbers of Nups to analyse those nanopores by cryoEM and conductance measurements.

02 March 2018 | doi: 10.1038/s41467-018-03313-w
DNA nanostructures  Intrinsically disordered proteins  Nanopores 

Thickness-modulated metal-to-semiconductor transformation in a transition metal dichalcogenide OPEN
Alberto Ciarrocchi, Ahmet Avsar, Dmitry Ovchinnikov & Andras Kis

The electronic band structure of van der Waals crystals is strongly sensitive to the number of layers. Here, the authors observe a thickness-dependent metal-to-semiconductor transition in layered PtSe2 by means of electrical transport measurements.

02 March 2018 | doi: 10.1038/s41467-018-03436-0
Electronic and spintronic devices  Nanoscale devices  Two-dimensional materials 

Resource acquisition and reproductive strategies of tropical forest in response to the El Niño–Southern Oscillation OPEN
Matteo Detto, S. Joseph Wright, Osvaldo Calderón & Helene C. Muller-Landau

It has been suggested that tree phenology may be regulated by climatic oscillations. Here, Detto et al. present a 30 year tropical forest dataset that suggests leaf and fruit production is coordinated with ENSO cycles, with greater leaf fall observed prior to El Niño followed by greater seed production.

02 March 2018 | doi: 10.1038/s41467-018-03306-9
Abiotic  Plant ecology 

A macromolecular approach to eradicate multidrug resistant bacterial infections while mitigating drug resistance onset OPEN
Willy Chin, Guansheng Zhong, Qinqin Pu, Chuan Yang, Weiyang Lou, Paola Florez De Sessions, Balamurugan Periaswamy, Ashlynn Lee, Zhen Chang Liang, Xin Ding, Shujun Gao, Collins Wenhan Chu, Simone Bianco, Chang Bao, Yen Wah Tong, Weimin Fan, Min Wu, James L. Hedrick & Yi Yan Yang

Antibiotic resistance is a major threat across the whole healthcare spectrum. Here, the authors report on the development of biodegradable guanidinium functionalized polycarbonates and demonstrate antimicrobial activity against drug resistant infections.

02 March 2018 | doi: 10.1038/s41467-018-03325-6
Antimicrobial resistance  Biomedical materials  Biopolymers 

Ambient nitrate switches the ammonium consumption pathway in the euphotic ocean OPEN
Xianhui Sean Wan, Hua-Xia Sheng, Minhan Dai, Yao Zhang, Dalin Shi, Thomas W. Trull, Yifan Zhu, Michael W. Lomas & Shuh-Ji Kao

The underlying regulatory mechanisms of phytoplankton assimilation and microbial oxidation of ammonium in the surface ocean are unclear. Here, using isotope labeling experiments, the authors show that ambient nitrate is a key variable bifurcating ammonium flow through assimilation or oxidation.

02 March 2018 | doi: 10.1038/s41467-018-03363-0
Element cycles  Marine chemistry 

Nitrogen-doped tungsten carbide nanoarray as an efficient bifunctional electrocatalyst for water splitting in acid OPEN
Nana Han, Ke R. Yang, Zhiyi Lu, Yingjie Li, Wenwen Xu, Tengfei Gao, Zhao Cai, Ying Zhang, Victor S. Batista, Wen Liu & Xiaoming Sun

Water electrolysis can generate carbon-neutral hydrogen gas from water, yet the required catalysts are often expensive, scarce, and poor at gas release. Here, the authors prepared nitrogen-doped carbon tungstide nanoarrays with high water-splitting activities and bubble-releasing surfaces.

02 March 2018 | doi: 10.1038/s41467-018-03429-z
Electrocatalysis  Nanoscale materials 

MT4-MMP deficiency increases patrolling monocyte recruitment to early lesions and accelerates atherosclerosis OPEN
Cristina Clemente, Cristina Rius, Laura Alonso-Herranz, Mara Martín-Alonso, Ángela Pollán, Emilio Camafeita, Fernando Martínez, Rubén A. Mota, Vanessa Núñez, Cristina Rodríguez, Motoharu Seiki, José Martínez-González, Vicente Andrés, Mercedes Ricote & Alicia G. Arroyo

Matrix metalloproteinases (MMP) are involved in vascular remodeling associated with plaque progression. Little is known about their immune regulatory role in vascular disorders. Here, the authors report that MT4-MMP-deficiency increases the recruitment of patrolling monocytes to early atherosclerotic lesions, which accelerates atherosclerosis.

02 March 2018 | doi: 10.1038/s41467-018-03351-4
Atherosclerosis  Integrins  Mechanisms of disease  Peritoneal macrophages 

CryoEM structure of the human SLC4A4 sodium-coupled acid-base transporter NBCe1 OPEN
Kevin W. Huynh, Jiansen Jiang, Natalia Abuladze, Kirill Tsirulnikov, Liyo Kao, Xuesi Shao, Debra Newman, Rustam Azimov, Alexander Pushkin, Z. Hong Zhou & Ira Kurtz

Na+-coupled acid-base membrane transport proteins regulate blood pressure, ion homeostasis and acid-base chemistry. Here the authors present the 3.9 Å resolution cryoEM structure of the sodium-bicarbonate cotransporter NBCe1 and characterize its ion coordination site and ion accessibility pathway with mutagenesis experiments.

02 March 2018 | doi: 10.1038/s41467-018-03271-3
Cryoelectron microscopy  Transporters 

A peptide tag-specific nanobody enables high-quality labeling for dSTORM imaging OPEN
David Virant, Bjoern Traenkle, Julia Maier, Philipp D. Kaiser, Mona Bodenhöfer, Christian Schmees, Ilijana Vojnovic, Borbála Pisak-Lukáts, Ulrike Endesfelder & Ulrich Rothbauer

Nanobodies (Nbs) coupled to organic dyes are increasingly used for super-resolution cell imaging, but producing gene-specific Nbs is time-consuming. Here the authors present a peptide-tag/Nb combination for dSTORM imaging which can be easily adapted to different targets in fixed and live cells.

02 March 2018 | doi: 10.1038/s41467-018-03191-2
Cytoskeleton  Fluorescence imaging  Super-resolution microscopy 

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow OPEN
Yafeng Zhu, Lukas M. Orre, Henrik J. Johansson, Mikael Huss, Jorrit Boekel, Mattias Vesterlund, Alejandro Fernandez-Woodbridge, Rui M. M. Branca & Janne Lehtiö

Proteogenomics enables the discovery of protein coding regions and disease-relevant mutations but their verification remains challenging. Here, the authors combine peptide discovery, curation and validation in an integrated proteogenomics workflow, robustly identifying unknown coding regions and mutations.

02 March 2018 | doi: 10.1038/s41467-018-03311-y
Genome  Mass spectrometry  Proteome informatics  Proteomics 

Germinal center entry not selection of B cells is controlled by peptide-MHCII complex density OPEN
Chen-Hao Yeh, Takuya Nojima, Masayuki Kuraoka & Garnett Kelsoe

It has been thought that germinal center (GC) B cells with the highest density of peptide-MHCII molecules receive the most T cell help. Here the authors use heterozygous MHCII inactivation to instead show that after recruitment into the GCs, BCR affinity increases over time independent of the MHC density.

02 March 2018 | doi: 10.1038/s41467-018-03382-x
Clonal selection  Germinal centres 

Strong selection during the last millennium for African ancestry in the admixed population of Madagascar OPEN
Denis Pierron, Margit Heiske, Harilanto Razafindrazaka, Veronica Pereda-loth, Jazmin Sanchez, Omar Alva, Amal Arachiche, Anne Boland, Robert Olaso, Jean-Francois Deleuze, Francois-Xavier Ricaut, Jean-Aimé Rakotoarisoa, Chantal Radimilahy, Mark Stoneking & Thierry Letellier

The population of Madagascar arose from admixture of Austronesian and Bantu genetic backgrounds. Analyzing local ancestry in genomes of 700 Malagasy, Pierron et al. identify signals of recent positive selection for African ancestry in a region on chromosome 1 with implications for physiology and disease risk.

02 March 2018 | doi: 10.1038/s41467-018-03342-5
Evolutionary genetics  Genome evolution  Malaria  Population genetics 

Replica molding-based nanopatterning of tribocharge on elastomer with application to electrohydrodynamic nanolithography OPEN
Qiang Li, Akshit Peer, In Ho Cho, Rana Biswas & Jaeyoun Kim

Tribocharging, or the buildup of charge on surfaces after they are rubbed together, can play unusual roles in material behavior, yet it is unclear how nanostructuring impacts charge buildup and distribution. Here, authors use replica molding to localize and pattern charges around nanocup rims.

02 March 2018 | doi: 10.1038/s41467-018-03319-4
Polymers  Surface patterning 

Visible light reduces C. elegans longevity OPEN
C. Daniel De Magalhaes Filho, Brian Henriquez, Nicole E. Seah, Ronald M. Evans, Louis R. Lapierre & Andrew Dillin

The nematode C. elegans is known to alter its behavior in response to UV light. Here, the authors show that visible light triggers photo-oxidative stress and a wider stress response in C. elegans, suggesting that light exposure during routine laboratory handling may influence the outcome of lifespan experiments.

02 March 2018 | doi: 10.1038/s41467-018-02934-5
Ageing  Caenorhabditis elegans 

Far-field probing of leaky topological states in all-dielectric metasurfaces OPEN
Maxim A. Gorlach, Xiang Ni, Daria A. Smirnova, Dmitry Korobkin, Dmitry Zhirihin, Alexey P. Slobozhanyuk, Pavel A. Belov, Andrea Alù & Alexander B. Khanikaev

Topological modes in photonics systems are not completely confined to the structure but can leak into free space. Here, Gorlach et al. exploit these leaky modes to probe the topological properties of a dielectric metasurface from far-field scattering measurements.

02 March 2018 | doi: 10.1038/s41467-018-03330-9
Metamaterials  Nanophotonics and plasmonics  Topological matter 

Decomposing the Bragg glass and the peak effect in a Type-II superconductor OPEN
Rasmus Toft-Petersen, Asger B. Abrahamsen, Sandor Balog, Lionel Porcar & Mark Laver

The disordering of the vortex lattice in a type-II superconductor is widely perceived to underpin unusual peaks in the temperature and field dependence of critical current. By contrast, here Toft-Petersen et al. find an order-disorder transition in a superconducting vanadium sample that is unconnected with peaks observed in critical current.

02 March 2018 | doi: 10.1038/s41467-018-03267-z
Electrical and electronic engineering  Structure of solids and liquids  Superconducting properties and materials 

Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography OPEN
Young-Sang Yu, Maryam Farmand, Chunjoong Kim, Yijin Liu, Clare P. Grey, Fiona C. Strobridge, Tolek Tyliszczak, Rich Celestre, Peter Denes, John Joseph, Harinarayan Krishnan, Filipe R. N. C. Maia, A. L. David Kilcoyne, Stefano Marchesini, Talita Perciano Costa Leite, Tony Warwick, Howard Padmore, Jordi Cabana & David A. Shapiro

Here the authors show the development of soft X-ray ptychographic tomography to quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nano-particles from a composite battery electrode.

02 March 2018 | doi: 10.1038/s41467-018-03401-x
Batteries  Imaging techniques 

The effects of currents and potentials on the selectivities of copper toward carbon dioxide electroreduction OPEN
Dan Ren, Jinhuan Fong & Boon Siang Yeo

Electrochemical reduction of carbon dioxide provides a means to convert environmental carbon into utile products. Product selectivity factors are disputed. Here, authors examine 24 copper catalysts and show that mass transport plus the electrochemical potential window drive selectivity.

02 March 2018 | doi: 10.1038/s41467-018-03286-w
Electrocatalysis  Heterogeneous catalysis 

Sipa1 deficiency unleashes a host-immune mechanism eradicating chronic myelogenous leukemia-initiating cells OPEN
Yan Xu, Satoshi Ikeda, Kentaro Sumida, Ryusuke Yamamoto, Hiroki Tanaka & Nagahiro Minato

Chronic myelogenous leukemia (CML)-initiating cells are resistant to kinase inhibitors. Here the authors show that deficiency of the Rap1 GTPase-activating protein Sipa1 in the tumor microenvironment releases an immune response that eradicates CML-initiating cells via interplay between stromal and T cells.

02 March 2018 | doi: 10.1038/s41467-018-03307-8
Cancer microenvironment  Chronic myeloid leukaemia  Tumour immunology 

Spin-controlled atom–ion chemistry OPEN
Tomas Sikorsky, Ziv Meir, Ruti Ben-shlomi, Nitzan Akerman & Roee Ozeri

Chemical reactions with ultracold atoms and ions are explored so far with the atom–ion interactions. Here the authors discuss spin-exchange process and show that the spin state of an ensemble of neutral Rb atoms can be used to control the final spin of an imbedded Sr+ ion in the collisions.

02 March 2018 | doi: 10.1038/s41467-018-03373-y
Atomic and molecular collision processes  Reaction kinetics and dynamics  Physics  Ultracold gases 

Measurement of the Berry curvature of solids using high-harmonic spectroscopy OPEN
Tran Trung Luu & Hans Jakob Wörner

The Berry phase and curvature have become important concepts in many different fields of physics. Here, Luu and Wörner directly retrieve the Berry phase using polarimetry of extreme ultraviolet high harmonic generation in α-quartz.

02 March 2018 | doi: 10.1038/s41467-018-03397-4
High-harmonic generation  Nonlinear optics 

Rotating robots move collectively and self-organize OPEN
Christian Scholz, Michael Engel & Thorsten Pöschel

Active rotating particles were shown to undergo a phase separation through numerical simulations. Here the authors provide an experimental realization of this phenomenon by presenting an ensemble of 3D-printed robots that rotate in different directions and interact with each other.

02 March 2018 | doi: 10.1038/s41467-018-03154-7
Phase transitions and critical phenomena  Statistical physics 

Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits OPEN
Yang Wu, Jian Zeng, Futao Zhang, Zhihong Zhu, Ting Qi, Zhili Zheng, Luke R. Lloyd-Jones, Riccardo E. Marioni, Nicholas G. Martin, Grant W. Montgomery, Ian J. Deary, Naomi R. Wray, Peter M. Visscher, Allan F. McRae & Jian Yang

The identification of the causal gene at a GWAS locus remains to be a challenging task. Here, using the SMR & HEIDI method to integrate GWAS, eQTL and mQTL data, Wu et al. map DNA methylation sites to the transcriptome and thereby prioritize functionally relevant genes for 12 human complex traits.

02 March 2018 | doi: 10.1038/s41467-018-03371-0
Data integration  Epigenomics  Genetics 

A light carbon isotope composition for the Sun OPEN
James R. Lyons, Ehsan Gharib-Nezhad & Thomas R. Ayres

The Sun’s light stable isotopes compositions can help us understand how our solar system formed. Here, the authors find that solar C is depleted relative to bulk Earth indicating that the 13C enrichment of the terrestrial planets is from CO self-shielding or inheritance from the parent cloud.

02 March 2018 | doi: 10.1038/s41467-018-03093-3
Geochemistry  Stars 

Studying light-harvesting models with superconducting circuits OPEN
Anton Potočnik, Arno Bargerbos, Florian A. Y. N. Schröder, Saeed A. Khan, Michele C. Collodo, Simone Gasparinetti, Yves Salathé, Celestino Creatore, Christopher Eichler, Hakan E. Türeci, Alex W. Chin & Andreas Wallraff

Investigating photosynthesis processes in biological samples is challenging due to their complex and disordered structure. Based on analog quantum simulations with superconducting quantum circuits, the authors show how the interplay of quantum coherence and environmental interactions affects energy transport.

02 March 2018 | doi: 10.1038/s41467-018-03312-x
Biological physics  Quantum simulation 

K. Saha, V. Chandrasekaran, O. Heber, M. A. Iron, M. L. Rappaport & D. Zajfman

Isomerization is a basic process in nature, with implications for chemical reactivity including in space. Here, the authors observe ultraslow isomerization in an isolated gas-phase carbon chain to its cyclic isomer lasting up to hundreds of microseconds, which may impact the creation of larger carbons in the interstellar medium.

02 March 2018 | doi: 10.1038/s41467-018-03197-w
Atomic and molecular interactions with photons  Macromolecules and clusters 

Nfat/calcineurin signaling promotes oligodendrocyte differentiation and myelination by transcription factor network tuning OPEN
Matthias Weider , Laura Julia Starost, Katharina Groll, Melanie Küspert, Elisabeth Sock, Miriam Wedel, Franziska Fröb, Christian Schmitt, Tina Baroti, Anna C. Hartwig, Simone Hillgärtner, Sandra Piefke, Tanja Fadler, Marc Ehrlich, Corinna Ehlert, Martin Stehling, Stefanie Albrecht, Ammar Jabali, Hans R. Schöler, Jürgen Winkler et al.

Oligodendrocyte differentiation is known to depend on transcription factors Sox10, Nkx2.2, and Olig2. Here, the authors show that Nfat/calcineurin signaling contributes to oligodendrocyte differentiation by relieving mutual repression of Nkx2.2 and Olig2.

02 March 2018 | doi: 10.1038/s41467-018-03336-3
Differentiation  Oligodendrocyte 

Spin-orbit interaction of light induced by transverse spin angular momentum engineering OPEN
Zengkai Shao, Jiangbo Zhu, Yujie Chen, Yanfeng Zhang & Siyuan Yu

Harnessing both orbital and spin angular momentum in light fields enables various applications in bio-sensing and nano-photonics. Here, the authors create engineered spin-orbit coupling between orbital angular momentum and transverse spin angular momentum in light using a vortex-emitting waveguide.

02 March 2018 | doi: 10.1038/s41467-018-03237-5
Nanophotonics and plasmonics  Sub-wavelength optics 

Formation of size-dependent and conductive phase on lithium iron phosphate during carbon coating OPEN
Yulong Liu, Jian Liu, Jiajun Wang, Mohammad Norouzi Banis, Biwei Xiao, Andrew Lushington, Wei Xiao, Ruying Li, Tsun-Kong Sham, Guoxian Liang & Xueliang Sun

Coating the active materials of interest with carbon is a widely employed way to boost the performance of lithium ion batteries. Here the authors show the formation of a conductive phase on LiFePO4 during carbon coating, which is size, annealing temperature and reduction atmosphere dependent.

02 March 2018 | doi: 10.1038/s41467-018-03324-7
Batteries  Mechanical engineering  Nanoscale materials  Solid-state chemistry 

A mechanism for CO regulation of ion channels OPEN
Sofia M. Kapetanaki, Mark J. Burton, Jaswir Basran, Chiasa Uragami, Peter C. E. Moody, John S. Mitcheson, Ralf Schmid, Noel W. Davies, Pierre Dorlet, Marten H. Vos, Nina M. Storey & Emma Raven

Despite being highly toxic, carbon monoxide (CO) is also essential as an intracellular signalling molecule, but CO-dependent signalling is poorly understood. Here, authors employ spectroscopic and electrophysiology methods and find that CO activates KATP channels via SUR2A, a heme-regulated receptor.

02 March 2018 | doi: 10.1038/s41467-018-03291-z
Metalloproteins  Potassium channels 

Reconstruction of complex single-cell trajectories using CellRouter OPEN
Edroaldo Lummertz da Rocha, R. Grant Rowe, Vanessa Lundin, Mohan Malleshaiah, Deepak Kumar Jha, Carlos R. Rambo, Hu Li, Trista E. North, James J. Collins & George Q. Daley

Single cell analysis provides insight into cell states and transitions, but to interpret the data, improved algorithms are needed. Here, the authors present CellRouter as a method to analyse single-cell trajectories from RNA-sequencing data, and provide insight into erythroid, myeloid and lymphoid differentiation.

01 March 2018 | doi: 10.1038/s41467-018-03214-y
Haematopoietic stem cells  Regulatory networks  Stem-cell differentiation  Systems analysis 

Elongator and codon bias regulate protein levels in mammalian peripheral neurons OPEN
Joy Goffena, Frances Lefcort, Yongqing Zhang, Elin Lehrmann, Marta Chaverra, Jehremy Felig, Joseph Walters, Richard Buksch, Kevin G. Becker & Lynn George

Familial dysautonomia is linked to mutations in IKBKAP, a scaffolding protein for the Elongator complex, which regulates codon-biased gene translation in yeast. Here the authors show in mammalian neurons that IKBKAP loss alters expression of codon-biased genes, including some involved in DNA damage.

01 March 2018 | doi: 10.1038/s41467-018-03221-z
Cellular neuroscience  Gene expression  Gene ontology  Proteomics 

Electron heating and thermal relaxation of gold nanorods revealed by two-dimensional electronic spectroscopy OPEN
Aude Lietard, Cho-Shuen Hsieh, Hanju Rhee & Minhaeng Cho

Electron dynamics in plasmonic nanoparticles are often studied with transient absorption spectroscopy. Here, Lietard et al. apply two-dimensional electronic spectroscopy, a method generally used for molecular spectroscopy, to study ultrafast nonlinear dynamics of electrons in excited gold nanorods.

01 March 2018 | doi: 10.1038/s41467-018-03002-8
Characterization and analytical techniques  Nanophotonics and plasmonics  Optical spectroscopy 

Whole-exome sequencing reveals the origin and evolution of hepato-cholangiocarcinoma OPEN
Anqiang Wang, Liangcai Wu, Jianzhen Lin, Longzhe Han, Jin Bian, Yan Wu, Simon C. Robson, Lai Xue, Yunxia Ge, Xinting Sang, Wenze Wang & Haitao Zhao

Hepatocellular-cholangiocarcinoma (H-ChC) is a rare subtype of liver cancer with features of hepatocellular carcinoma and intrahepatic cholangiocarcinoma. Here, the authors utilize whole exome sequencing to highlight the monoclonal origin and stemness of H-ChC, as well as substantial intratumoral heterogeneity.

01 March 2018 | doi: 10.1038/s41467-018-03276-y
Cancer genomics  Liver cancer 

De novo adipocyte differentiation from Pdgfrβ+ preadipocytes protects against pathologic visceral adipose expansion in obesity OPEN
Mengle Shao, Lavanya Vishvanath, Napoleon C. Busbuso, Chelsea Hepler, Bo Shan, Ankit X. Sharma, Shiuhwei Chen, Xinxin Yu, Yu A. An, Yi Zhu, William L. Holland & Rana K. Gupta

Adipocyte hyperplasia is thought to have beneficial metabolic effects in obesity, but definitive evidence is lacking. Here, Shao et al. promote de novo formation of adipocytes in visceral white adipose tissue (WAT) of adult mice through inducible overexpression of Pparg in Pdgfrβ+ preadipocytes and show that this protects from pathological WAT remodeling.

01 March 2018 | doi: 10.1038/s41467-018-03196-x
Diabetes  Metabolic disorders  Obesity 

Early circulating tumor DNA dynamics and clonal selection with palbociclib and fulvestrant for breast cancer OPEN
Ben O’Leary, Sarah Hrebien, James P. Morden, Matthew Beaney, Charlotte Fribbens, Xin Huang, Yuan Liu, Cynthia Huang Bartlett, Maria Koehler, Massimo Cristofanilli, Isaac Garcia-Murillas, Judith M. Bliss & Nicholas C. Turner

Circulating tumor DNA (ctDNA) may provide a prediction of treatment response, but could be impacted by tumor heterogeneity. Here, the authors investigate ctDNA in CDK4/6 inhibitor treatment in advanced breast cancer, finding ctDNA levels predict progression-free survival and anticipate clonal selection.

01 March 2018 | doi: 10.1038/s41467-018-03215-x
Breast cancer  Cancer genomics  Tumour biomarkers 

Molecular probes reveal deviations from Amontons’ law in multi-asperity frictional contacts OPEN
B. Weber, T. Suhina, T. Junge, L. Pastewka, A. M. Brouwer & D. Bonn

Amontons’ law assumes that friction and normal forces depend linearly on the contact area. Here, the authors use a new contact detection method to show that the law is broken because asperities interact and deform in the contact area to change it, thereby also changing the friction force.

01 March 2018 | doi: 10.1038/s41467-018-02981-y
Structural properties  Surfaces, interfaces and thin films 

Conserved roles of C. elegans and human MANFs in sulfatide binding and cytoprotection OPEN
Meirong Bai, Roman Vozdek, Aleš Hnízda, Chenxiao Jiang, Bingying Wang, Ladislav Kuchar, Tiejun Li, Yuefan Zhang, Chase Wood, Liang Feng, Yongjun Dang & Dengke K. Ma

MANF is a secreted ER stress-inducible protein that protects neurons, pancreatic β cells and cardiomyocytes from cell death under oxidative stress, hypoxic or ischemic conditions. Here the authors show that MANF confers cytoprotection through direct binding to sulfatide followed by cellular uptake in both C. elegans and mammalian cells.

01 March 2018 | doi: 10.1038/s41467-018-03355-0
Cell signalling  Eukaryote  Lipids 

TET-mediated epimutagenesis of the Arabidopsis thaliana methylome OPEN
Lexiang Ji, William T. Jordan, Xiuling Shi, Lulu Hu, Chuan He & Robert J. Schmitz

In plants, variation in DNA methylation can influence agronomically important traits. Here the authors show that expression of a human Ten-eleven translocation enzyme can generate heritable hypomethylation alleles in Arabidopsis, providing a novel method to manipulate DNA methylation for breeding and research purposes.

01 March 2018 | doi: 10.1038/s41467-018-03289-7
Epigenomics  Plant molecular biology 

Rapid measurement of inhibitor binding kinetics by isothermal titration calorimetry OPEN
Justin M. Di Trani, Stephane De Cesco, Rebecca O’Leary, Jessica Plescia, Claudia Jorge do Nascimento, Nicolas Moitessier & Anthony K. Mittermaier

There is growing evidence that the kinetics of interactions between inhibitors and their targets can strongly impact therapeutic efficacy. Here the authors describe an isothermal titration calorimetry-based method that can rapidly quantify inhibition kinetics and measure sub-nM binding affinities.

01 March 2018 | doi: 10.1038/s41467-018-03263-3
Biophysical methods  Drug discovery  Enzymes  Small molecules 

Genetic study links components of the autonomous nervous system to heart-rate profile during exercise OPEN
Niek Verweij, Yordi J. van de Vegte & Pim van der Harst

Response of the heart rate (HR) to exercise is associated with cardiac fitness and risk of cardiac death. Here, in a genome-wide association study, Verweij et al. identify 23 loci for HR increase during exercise or HR recovery, and highlight pleiotropy with blood pressure by polygenic risk score analysis.

01 March 2018 | doi: 10.1038/s41467-018-03395-6
Cardiovascular genetics  Genetics of the nervous system  Genome-wide association studies 
  Latest Author Corrections    
Author Correction: Glacigenic sedimentation pulses triggered post-glacial gas hydrate dissociation OPEN
Jens Karstens, Haflidi Haflidason, Lukas W. M. Becker, Christian Berndt, Lars Rüpke, Sverre Planke, Volker Liebetrau, Mark Schmidt & Jürgen Mienert
07 March 2018 | doi: 10.1038/s41467-018-03587-0
Geophysics  Sedimentology 

Author Correction: Cancer-associated fibroblasts induce metalloprotease-independent cancer cell invasion of the basement membrane OPEN
Alexandros Glentis, Philipp Oertle, Pascale Mariani, Aleksandra Chikina, Fatima El Marjou, Youmna Attieh, Francois Zaccarini, Marick Lae, Damarys Loew, Florent Dingli, Philemon Sirven, Marie Schoumacher, Basile G. Gurchenkov, Marija Plodinec & Danijela Matic Vignjevic
07 March 2018 | doi: 10.1038/s41467-018-03304-x
Cancer microenvironment  Cell invasion 
  Latest Publisher Corrections    
Publisher Correction: Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology OPEN
James C. Stegen, Tim Johnson, James K. Fredrickson, Michael J. Wilkins, Allan E. Konopka, William C. Nelson, Evan V. Arntzen, William B. Chrisler, Rosalie K. Chu, Sarah J. Fansler, Emily B. Graham, David W. Kennedy, Charles T. Resch, Malak Tfaily & John Zachara
07 March 2018 | doi: 10.1038/s41467-018-03572-7
Carbon cycle  Geochemistry  Hydrology  Microbial ecology 

Publisher Correction: Beyond a phenomenological description of magnetostriction OPEN
A. H. Reid , X. Shen, P. Maldonado, T. Chase, E. Jal, P. W. Granitzka, K. Carva, R. K. Li, J. Li, L. Wu, T. Vecchione, T. Liu, Z. Chen, D. J. Higley, N. Hartmann, R. Coffee, J. Wu, G. L. Dakowski, W. F. Schlotter, H. Ohldag et al.
07 March 2018 | doi: 10.1038/s41467-018-03389-4
Magnetic properties and materials  Nanoparticles  Structure of solids and liquids 

Publisher Correction: IgG1 memory B cells keep the memory of IgE responses OPEN
Jin-Shu He, Sharrada Subramaniam, Vipin Narang, Kandhadayar Srinivasan, Sean P. Saunders, Daniel Carbajo, Tsao Wen-Shan, Nur Hidayah Hamadee, Josephine Lum, Andrea Lee, Jinmiao Chen, Michael Poidinger, Francesca Zolezzi, Juan J. Lafaille & Maria A. Curotto de Lafaille
01 March 2018 | doi: 10.1038/s41467-018-03364-z
Allergy  Immunogenetics  Immunological memory 

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