Wednesday, May 10, 2017

Nature Communications - 10 May 2017

Nature Communications

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10 May 2017 
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Nature Reviews Microbiology: Collection on Antimicrobial Resistance 

This collection of articles from several Nature journals describes how antimicrobial resistance emerges and details discovery strategies for urgently needed new antimicrobials. 

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AGRICULTURAL GENOMICS 2017 - Functional Genomics toward Green Crops for Sustainable Agriculture 

Hosting Organizations: National Key Laboratory of Crop Genetic Improvement | Huazhong Agricultural University | Nature Genetics | Nature Plants | Nature Communications

October 25-27, 2017
Conference Hall, National Key Laboratory of Crop Genetic Improvement | Wuhan, China
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  Latest Review View all Reviews  
Neuronal control of peripheral insulin sensitivity and glucose metabolism OPEN
Johan Ruud, Sophie M. Steculorum and Jens C. Brüning
The brain controls peripheral glucose metabolism, for example by modulating hepatic gluconeogenesis or by regulating glucose uptake into brown adipose tissue. Here, the authors review the brain regions, neurons and molecular mechanisms involved in these processes, and discuss their relevance to disease.
04 May 2017 | doi: 10.1038/ncomms15259
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Earliest signs of life on land preserved in ca. 3.5 Ga hot spring deposits OPEN
Tara Djokic, Martin J. Van Kranendonk, Kathleen A. Campbell, Malcolm R. Walter and Colin R. Ward
Some of the earliest life on Earth flourished in terrestrial hot springs. Here, the authors present evidence for ca. 3.5 Ga hot spring deposits from the Dresser Formation, Pilbara Craton, Australia, that host some of the earliest known life in the form of stromatolites and other microbial biosignatures.
09 May 2017 | doi: 10.1038/ncomms15263

Perinate and eggs of a giant caenagnathid dinosaur from the Late Cretaceous of central China OPEN
Hanyong Pu, Darla K. Zelenitsky, Junchang Lü, Philip J. Currie, Kenneth Carpenter, Li Xu, Eva B. Koppelhus, Songhai Jia, Le Xiao, Huali Chuang, Tianran Li, Martin Kundrát and Caizhi Shen
The fossil dinosaur embryo ‘Baby Louie’ and associated clutch of eggs were first discovered in the early 1990s, but were not formally described. Here, the authors identify the specimen as an embryo and eggs of the new large caenagnathid oviraptorosaur, Beibeilong sinensis, from the Late Cretaceous of China.
09 May 2017 | doi: 10.1038/ncomms14952

Remote detection of radioactive material using high-power pulsed electromagnetic radiation OPEN
Dongsung Kim, Dongho Yu, Ashwini Sawant, Mun Seok Choe, Ingeun Lee, Sung Gug Kim and EunMi Choi
Detection of hazardous radioactive material far from its source is challenging. Here the authors demonstrate a method with higher sensitivity by utilizing high-power pulsed electromagnetic-wave-induced plasma breakdown, which has potential uses in security and defence.
09 May 2017 | doi: 10.1038/ncomms15394

Amorphous nickel-cobalt complexes hybridized with 1T-phase molybdenum disulfide via hydrazine-induced phase transformation for water splitting OPEN
Haoyi Li, Shuangming Chen, Xiaofan Jia, Biao Xu, Haifeng Lin, Haozhou Yang, Li Song and Xun Wang
Electrocatalysts based on earth-abundant elements have emerged as promising candidates to replace noble metal materials. Here, the authors develop porous hybrid nanostructures combining amorphous Ni-Co complexes with 1T phase MoS2 for enhanced electrocatalytic activity for overall water splitting.
09 May 2017 | doi: 10.1038/ncomms15377

Regulation of cardiomyocyte behavior in zebrafish trabeculation by Neuregulin 2a signaling OPEN
S. Javad Rasouli and Didier Y. R. Stainier
Cardiac trabeculae (which are sponge-like muscular structures) form mostly as a result of cardiomyocyte (CM) delamination in zebrafish. Here, the authors identify Nrg2a in zebrafish as a key regulator of trabeculation, and atrial and non-contractile CMs also respond to Nrg2a despite not forming trabeculae.
09 May 2017 | doi: 10.1038/ncomms15281

Charting organellar importomes by quantitative mass spectrometry OPEN
Christian D. Peikert, Jan Mani, Marcel Morgenstern, Sandro Käser, Bettina Knapp, Christoph Wenger, Anke Harsman, Silke Oeljeklaus, André Schneider and Bettina Warscheid
Knowing the specific protein content of individual organelles is necessary for an integrated understanding of cellular physiology. Here the authors describe a mass spectrometry-based approach to identify the substrates of distinct protein import pathways and define organellar proteomes.
09 May 2017 | doi: 10.1038/ncomms15272

Ultra-large supramolecular coordination cages composed of endohedral Archimedean and Platonic bodies OPEN
Kevin Byrne, Muhammad Zubair, Nianyong Zhu, Xiao-Ping Zhou, Daniel S. Fox, Hongzhou Zhang, Brendan Twamley, Matthew J. Lennox, Tina Düren and Wolfgang Schmitt
Host–guest chemistry in hollow coordination cages can be exploited for a range of applications, but is often limited by inner cavity dimensions. Here, Schmitt and co-workers fabricate supramolecular keplerates that possess ultra-large cross-sectional diameters and are composed of multiple sub-cages.
09 May 2017 | doi: 10.1038/ncomms15268

Actively evolving subglacial conduits and eskers initiate ice shelf channels at an Antarctic grounding line OPEN
R. Drews, F. Pattyn, I. J. Hewitt, F. S. L. Ng, S. Berger, K. Matsuoka, V. Helm, N. Bergeot, L. Favier and N. Neckel
The formation mechanisms of ice-shelf channels remain poorly understood. Here, using ice-penetrating radar data, the authors propose that ice-shelf channel morphology in the Roi Baudouin Ice Shelf, East Antarctica, is seeded by esker ridges, indenting the ice from below.
09 May 2017 | doi: 10.1038/ncomms15228

Scalable and efficient separation of hydrogen isotopes using graphene-based electrochemical pumping OPEN
M. Lozada-Hidalgo, S. Zhang, S. Hu, A. Esfandiar, I. V. Grigorieva and A. K. Geim
Thousands of tons of water are processed every year for hydrogen isotope separation, using extremely costly technology. Here the authors demonstrate a fully-scalable graphene electrochemical pump, which promises to dramatically reduce the energy and capital costs.
09 May 2017 | doi: 10.1038/ncomms15215

The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota OPEN
Heiko Vogel, Shantanu P. Shukla, Tobias Engl, Benjamin Weiss, Rainer Fischer, Sandra Steiger, David G. Heckel, Martin Kaltenpoth and Andreas Vilcinskas
Burying beetles feed their offspring on the carrion of vertebrate animals. Here, the authors study gene expression in the insect’s gut, as well as the composition of the microbiota in the gut and in carcasses, providing evidence for metabolic cooperation between host and specific microbes.
09 May 2017 | doi: 10.1038/ncomms15186

Differences between germline and somatic mutation rates in humans and mice OPEN
Brandon Milholland, Xiao Dong, Lei Zhang, Xiaoxiao Hao, Yousin Suh and Jan Vijg
Germline mutation rates are known to vary between species but somatic mutation rates are less well understood. Here the authors compare mice and humans, observing that somatic mutation rates were nearly two orders of magnitude higher in both species, with both mutation rates significantly higher in mice.
09 May 2017 | doi: 10.1038/ncomms15183

Quantum-coherent mixtures of causal relations OPEN
Jean-Philippe W. MacLean, Katja Ried, Robert W. Spekkens and Kevin J. Resch
The set of causal relations that can connect two systems is much richer in the quantum world. Here the authors show that it is possible to have a coherent mixture of a cause-effect and a common-cause mechanism between two systems, realizing this in a quantum optics experiment.
09 May 2017 | doi: 10.1038/ncomms15149

Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice OPEN
Ryan M. Walsh, Erica Y. Shen, Rosemary C. Bagot, Anthony Anselmo, Yan Jiang, Behnam Javidfar, Gregory J. Wojtkiewicz, Jennifer Cloutier, John W. Chen, Ruslan Sadreyev, Eric J. Nestler, Schahram Akbarian and Konrad Hochedlinger
Mutation of the human gene PHF8, encoding a histone demethylase, is linked to cognitive defects but its role in development is unclear. Here, the authors show that Phf8 deletion in mice causes no overt developmental defects but confers resilience to depression, likely through increased serotonin signalling.
09 May 2017 | doi: 10.1038/ncomms15142

Optically levitated nanoparticle as a model system for stochastic bistable dynamics OPEN
F. Ricci, R. A. Rica, M. Spasenović, J. Gieseler, L. Rondin, L. Novotny and R. Quidant
Nano-mechanical resonators improve with high-Q factor and light mass, but this leads to the onset of nonlinear behaviour. Here the authors demonstrate precise control of the non-linear and bistable dynamics of a levitated nanoparticle in vacuum, using it as model system to study stochastic bistable phenomena.
09 May 2017 | doi: 10.1038/ncomms15141

EGFR-dependent TOR-independent endocycles support Drosophila gut epithelial regeneration OPEN
Jinyi Xiang, Jennifer Bandura, Peng Zhang, Yinhua Jin, Hanna Reuter and Bruce A. Edgar
In response to gut epithelial damage, Drosophila stem cells proliferate to produce large polyploid enterocytes (EC), which comprise the bulk of the epithelium. Here, the authors show that stress-dependent EGFR/MAP kinase signalling drives both endoreplication and cell growth in newborn ECs.
09 May 2017 | doi: 10.1038/ncomms15125

Foxp3+ regulatory T cells maintain the bone marrow microenvironment for B cell lymphopoiesis OPEN
Antonio Pierini, Hidekazu Nishikii, Jeanette Baker, Takaharu Kimura, Hye-Sook Kwon, Yuqiong Pan, Yan Chen, Maite Alvarez, William Strober, Andrea Velardi, Judith A. Shizuru, Joy Y. Wu, Shigeru Chiba and Robert S. Negrin
Treg cells suppress peripheral immune responses, but their function in haematopoiesis is unclear. Here the authors show they modulate the bone marrow microenvironment to sustain haematopoietic stem cell-driven generation of mature B cells.
09 May 2017 | doi: 10.1038/ncomms15068

Unconventional double-bended saturation of carrier occupation in optically excited graphene due to many-particle interactions OPEN
Torben Winzer, Martin Mittendorff, Stephan Winnerl, Henry Mittenzwey, Roland Jago, Manfred Helm, Ermin Malic and Andreas Knorr
Saturable absorption, a technologically relevant property of graphene, is usually explained with Pauli blocking of optically driven carriers in the strong-excitation regime. Here, Winzer et al. reveal a new saturation regime at low excitations, resulting in a double-bended saturation behaviour.
09 May 2017 | doi: 10.1038/ncomms15042

Control of type III protein secretion using a minimal genetic system OPEN
Miryoung Song, David J. Sukovich, Luciano Ciccarelli, Julia Mayr, Jesus Fernandez-Rodriguez, Ethan A. Mirsky, Alex C. Tucker, D. Benjamin Gordon, Thomas C. Marlovits and Christopher A. Voigt
The type III secretion system is a needle-like molecular machine under tight regulatory control. Here the authors construct a synthetic type III secretion system gene cluster by deconstructing and rebuilding the wild-type Salmonella pathogenicity island 1.
09 May 2017 | doi: 10.1038/ncomms14737

Preserved cognitive functions with age are determined by domain-dependent shifts in network responsivity OPEN
Dávid Samu, Karen L. Campbell, Kamen A. Tsvetanov, Meredith A. Shafto, Cam-CAN consortium, Carol Brayne, Edward T. Bullmore, Andrew C. Calder, Rhodri Cusack, Tim Dalgleish, John Duncan, Richard N. Henson, Fiona E. Matthews, William D. Marslen-Wilson, James B. Rowe, Teresa Cheung, Simon Davis, Linda Geerligs, Rogier Kievit, Anna McCarrey et al.
Cognitive abilities change with age, but why some decline and some do not is not clear. Here, the authors use data from the Cam-CAN cohort to show that distributed, multi-component brain responsivity and default-mode deactivation supports and characterizes preserved cognition across the adult lifespan.
08 May 2017 | doi: 10.1038/ncomms14743

Highly selective covalent organic functionalization of epitaxial graphene OPEN
Rebeca A. Bueno, José I. Martínez, Roberto F. Luccas, Nerea Ruiz del Árbol, Carmen Munuera, Irene Palacio, Francisco J. Palomares, Koen Lauwaet, Sangeeta Thakur, Jacek M. Baranowski, Wlodek Strupinski, María F. López, Federico Mompean, Mar García-Hernández and José A. Martín-Gago
Organic functionalization is key to the development of graphene-based functional composites, yet selective covalent functionalization is hindered by graphene chemical inertness. Here, the authors demonstrate a versatile route to graphene covalent bonding with amino-terminated organic molecules.
08 May 2017 | doi: 10.1038/ncomms15306

Experimental realization of a multiplexed quantum memory with 225 individually accessible memory cells OPEN
Y-F Pu, N. Jiang, W. Chang, H-X Yang, C. Li and L-M Duan
To realize long-distance quantum communication it is required to have individually addressable quantum memories with programmable access to many cells. Here the authors report DLCZ-type quantum memories with 225 individually accessible memory cells in a macroscopic atomic ensemble
08 May 2017 | doi: 10.1038/ncomms15359

A general method for controlling and resolving rotational orientation of molecules in molecule-surface collisions OPEN
Oded Godsi, Gefen Corem, Yosef Alkoby, Joshua T. Cantin, Roman V. Krems, Mark F. Somers, Jörg Meyer, Geert-Jan Kroes, Tsofar Maniv and Gil Alexandrowicz
The rotational orientation of a molecule plays a fundamental role in molecule-surface collisions, yet is difficult to study. Here, the authors present a general approach for controlling and resolving molecular rotational orientation and apply it to study H2 scattering from flat and stepped copper surfaces.
08 May 2017 | doi: 10.1038/ncomms15357

Activity-based protein profiling as a robust method for enzyme identification and screening in extremophilic Archaea OPEN
Susanne Zweerink, Verena Kallnik, Sabrina Ninck, Sabrina Nickel, Julia Verheyen, Marcel Blum, Alexander Wagner, Ingo Feldmann, Albert Sickmann, Sonja-Verena Albers, Christopher Bräsen, Farnusch Kaschani, Bettina Siebers and Markus Kaiser
Activity-based protein profiling (ABPP) is a chemical proteomics method to profile activity states of enzymes under physiological conditions. Here the authors show that ABPP can be applied to archaeal serine hydrolases in the model organism Sulfolobus acidocaldarius and can be used to identify novel putative serine hydrolases.
08 May 2017 | doi: 10.1038/ncomms15352

Live cell imaging of single genomic loci with quantum dot-labeled TALEs OPEN
Yingxin Ma, Mingxiu Wang, Wei Li, Zhiping Zhang, Xiaowei Zhang, Tianwei Tan, Xian-En Zhang and Zongqiang Cui
Visualizing single genomic loci in living cells remains technically challenging. Here the authors adopt a strategy of labelling a pair of transcription activator-like effectors (TALEs) with differently coloured quantum dots and use them to identify integrated HIV-1 proviral DNA sequences in living cells.
08 May 2017 | doi: 10.1038/ncomms15318

Dynamic molecular oxygen production in cometary comae OPEN
Yunxi Yao and Konstantinos P. Giapis
Abundant molecular oxygen was discovered recently in the coma of comet 67P, thought to be of primordial origin. Here, the authors propose a dynamic reaction mechanism for cometary comae, which produces O2 directly in single collisions of energetic water ions with oxidized cometary surface analogues.
08 May 2017 | doi: 10.1038/ncomms15298

Magnetoelectrical control of nonreciprocal microwave response in a multiferroic helimagnet OPEN
Y. Iguchi, Y. Nii and Y. Onose
Control of microwave propagation is important for future communication technology. Here, Iguchi et al. report the reversal of microwave nonreciprocity by an external electric field in a multiferroic helimagnet Ba2Mg2Fe12O22.
08 May 2017 | doi: 10.1038/ncomms15252

Atomic-level energy storage mechanism of cobalt hydroxide electrode for pseudocapacitors OPEN
Ting Deng, Wei Zhang, Oier Arcelus, Jin-Gyu Kim, Javier Carrasco, Seung Jo Yoo, Weitao Zheng, Jiafu Wang, Hongwei Tian, Hengbin Zhang, Xiaoqiang Cui and Teófilo Rojo
Developing high-performance hybrid energy storage devices requires improved understanding of the mechanism that governs the electrochemical reactions. Here, the authors show the atomic-level working process of cobalt hydroxide electrode for pseudocapacitors.
08 May 2017 | doi: 10.1038/ncomms15194

Precise determination of graphene functionalization by in situ Raman spectroscopy OPEN
Philipp Vecera, Julio C. Chacón-Torres, Thomas Pichler, Stephanie Reich, Himadri R. Soni, Andreas Görling, Konstantin Edelthalhammer, Herwig Peterlik, Frank Hauke and Andreas Hirsch
Raman spectroscopy is a versatile tool to gain insight into the functionalization of graphene-based materials, yet unequivocal assignment of the vibrational modes associated with covalent binding has so far remained elusive. Here, the authors succeed in an experimental and theoretical identification of this molecular fingerprint.
08 May 2017 | doi: 10.1038/ncomms15192

Quantum-circuit refrigerator OPEN
Kuan Yen Tan, Matti Partanen, Russell E. Lake, Joonas Govenius, Shumpei Masuda and Mikko Möttönen
Efficient on-demand cooling of the functional degrees of freedom in solid-state implementations of quantum information processing devices remains a challenge. Here the authors demonstrate direct cooling of a photonic mode of a superconducting resonator using voltage-controllable electron tunnelling.
08 May 2017 | doi: 10.1038/ncomms15189

Mapping the orbital structure of impurity bound states in a superconductor OPEN
Deung-Jang Choi, Carmen Rubio-Verdú, Joeri de Bruijckere, Miguel M. Ugeda, Nicolás Lorente and Jose Ignacio Pascual
The complex internal structure of magnetic impurities, which locally distort superconductivity, is usually neglected. Here, Choi et al. report that the number and shape of Shiba states are correlated to the spin-polarized atomic orbitals of the impurity, valuable to design atomic-scale superconducting devices.
08 May 2017 | doi: 10.1038/ncomms15175

Signalome-wide assessment of host cell response to hepatitis C virus OPEN
Gholamreza Haqshenas, Jianmin Wu, Kaylene J. Simpson, Roger J. Daly, Hans J. Netter, Thomas F. Baumert and Christian Doerig
Development of antiviral strategies depends on an understanding of virus–host interactions. Here, using HCV, Haqshenas et al. show that antibody microarray combined with a targeted siRNA screen can be a powerful tool to identify cellular signalling pathways that are important for virus replication.
08 May 2017 | doi: 10.1038/ncomms15158

Antibody-powered nucleic acid release using a DNA-based nanomachine OPEN
Simona Ranallo, Carl Prévost-Tremblay, Andrea Idili, Alexis Vallée-Bélisle and Francesco Ricci
Responsive molecular machines can perform specific tasks triggered by environmental or chemical stimuli. Here, the authors show that antibodies can be used as inputs to modulate the binding of a molecular cargo to a designed DNA-based nanomachine, with potential applications in diagnostics and drug delivery.
08 May 2017 | doi: 10.1038/ncomms15150

Intron retention is regulated by altered MeCP2-mediated splicing factor recruitment OPEN
Justin J. -L. Wong, Dadi Gao, Trung V. Nguyen, Chau-To Kwok, Michelle van Geldermalsen, Rob Middleton, Natalia Pinello, Annora Thoeng, Rajini Nagarajah, Jeff Holst, William Ritchie and John E. J. Rasko
Intron retention is a conserved mechanism that controls gene expression but its regulation is poorly understood. Here, the authors provide evidence that DNA methylation regulates intron retention and find reduced MeCP2 occupancy and splicing factor recruitment near affected splice junctions.
08 May 2017 | doi: 10.1038/ncomms15134

Hepatic p63 regulates steatosis via IKKβ/ER stress OPEN
Begoña Porteiro, Marcos F. Fondevila, Teresa C. Delgado, Cristina Iglesias, Monica Imbernon, Paula Iruzubieta, Javier Crespo, Amaia Zabala-Letona, Johan Fernø, Bárbara González-Terán, Nuria Matesanz, Lourdes Hernández-Cosido, Miguel Marcos, Sulay Tovar, Anxo Vidal, Julia Sánchez-Ceinos, Maria M. Malagon, Celia Pombo, Juan Zalvide, Arkaitz Carracedo et al.
p53 regulates lipid metabolism and fatty acid oxidation, and its inactivation promotes diet-induced liver steatosis. Here Porteiro et al. show that p53 deficiency leads to compensatory p63 upregulation, which, in turn, triggers endoplasmic reticulum stress through IKKβ activation, fatty acid synthesis and lipid accumulation.
08 May 2017 | doi: 10.1038/ncomms15111

Field induced spontaneous quasiparticle decay and renormalization of quasiparticle dispersion in a quantum antiferromagnet OPEN
Tao Hong, Y. Qiu, M. Matsumoto, D. A. Tennant, K. Coester, K. P. Schmidt, F. F. Awwadi, M. M. Turnbull, H. Agrawal and A. L. Chernyshev
Spontaneous magnon decay in canted antiferromagnets has been theoretically investigated extensively, but experimental evidence is limited. Here the authors study the spin ½ antiferromagnet DLCB via neutron scattering, revealing field-induced spontaneous magnon decay associated with three-magnon interactions.
05 May 2017 | doi: 10.1038/ncomms15148

A dynamic eco-evolutionary model predicts slow response of alpine plants to climate warming OPEN
Olivier Cotto, Johannes Wessely, Damien Georges, Günther Klonner, Max Schmid, Stefan Dullinger, Wilfried Thuiller and Frédéric Guillaume
Environmental niche models are often used to predict species responses to climate change but they neglect the potential for evolutionary responses. Here, Cotto et al. develop a model incorporating demographic processes and evolutionary dynamics and show that perennial alpine plants persist in unsuitable habitats but produce maladapted offspring.
05 May 2017 | doi: 10.1038/ncomms15399

Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes OPEN
Surojit Biswas, Konstantin Kerner, Paulo José Pereira Lima Teixeira, Jeffery L. Dangl, Vladimir Jojic and Philip A. Wigge
Global patterns of gene transcription can be represented with reduced dimensionality. Here, the authors devise a method called Tradict that learns and uses 100 marker genes to predict transcriptome-wide pathway expression levels and patterns that reflect cell activity and state.
05 May 2017 | doi: 10.1038/ncomms15309

Stat3 regulates centrosome clustering in cancer cells via Stathmin/PLK1 OPEN
Edward J. Morris, Eiko Kawamura, Jordan A. Gillespie, Aruna Balgi, Nagarajan Kannan, William J. Muller, Michel Roberge and Shoukat Dedhar
Cancer cells have amplified centrosomes and deal with this abnormality by clustering them together so that they can be segregated in daughter cells. Here the authors perform a screening looking for inhibitors of this clustering process and find that STAT3 regulates this process independently of its transcriptional function.
05 May 2017 | doi: 10.1038/ncomms15289

The essential role of YAP O-GlcNAcylation in high-glucose-stimulated liver tumorigenesis OPEN
Xiao Zhang, Yongxia Qiao, Qi Wu, Yan Chen, Shaowu Zou, Xiangfan Liu, Guoqing Zhu, Yinghui Zhao, Yuxin Chen, Yongchun Yu, Qiuhui Pan, Jiayi Wang and Fenyong Sun
Yap is a transcriptional factor involved in tumorigenesis. Here the authors show that a previously unknown post-translational modification of Yap, O-GlcNAcylation, increases its transcriptional activity and is required for high glucose-induced liver cancer development.
05 May 2017 | doi: 10.1038/ncomms15280

Menin enhances c-Myc-mediated transcription to promote cancer progression OPEN
Gongwei Wu, Mengqiu Yuan, Shengqi Shen, Xiaoyu Ma, Jingwen Fang, Lianbang Zhu, Linchong Sun, Zhaoji Liu, Xiaoping He, De Huang, Tingting Li, Chenchen Li, Jun Wu, Xin Hu, Zhaoyong Li, Libing Song, Kun Qu, Huafeng Zhang and Ping Gao
Menin is a protein with context-dependent oncogenic or oncosuppressive roles; the oncogenic activity is mainly due to its function as a cofactor of the MLL1 histone methyltransferase complex. Here the authors show that Menin regulates c-Myc-dependent transformation independently of the MLL complex.
05 May 2017 | doi: 10.1038/ncomms15278

Quantification of differential gene expression by multiplexed targeted resequencing of cDNA OPEN
Peer Arts, Jori van der Raadt, Sebastianus H.C. van Gestel, Marloes Steehouwer, Jay Shendure, Alexander Hoischen and Cornelis A. Albers
Transcriptome sequencing is a powerful tool for functional analysis of different types of RNA molecules in a wide range of applications. Here the authors use targeted resequencing of cDNA with single-molecule molecular inversion probes as a cost-effective, high-throughput tool for mRNA quantification.
05 May 2017 | doi: 10.1038/ncomms15190

Protein kinase C-alpha suppresses autophagy and induces neural tube defects via miR-129-2 in diabetic pregnancy OPEN
Fang Wang, Cheng Xu, E. Albert Reece, Xuezheng Li, Yanqing Wu, Christopher Harman, Jingwen Yu, Daoyin Dong, Cheng Wang, Penghua Yang, Jianxiang Zhong and Peixin Yang
Maternal diabetes can induce neural tube defects (NTD). Here, the authors show that in mice, deletion of Prkca (encoding protein kinase C-alpha) restores autophagy, via suppression of miR-129-2 and reversal of reduced peroxisome proliferator-activated receptor c coactivator 1alpha, so reducing NTDs.
05 May 2017 | doi: 10.1038/ncomms15182

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens OPEN
David W. Morgens, Michael Wainberg, Evan A. Boyle, Oana Ursu, Carlos L. Araya, C. Kimberly Tsui, Michael S. Haney, Gaelen T. Hess, Kyuho Han, Edwin E. Jeng, Amy Li, Michael P. Snyder, William J. Greenleaf, Anshul Kundaje and Michael C. Bassik
CRISPR-Cas9 screens are powerful high-throughput tools but can be confounded by nuclease toxicity. Here the authors design a library of variable length gRNAs with thousands of negative controls, including the targeting of ‘safe’ loci to account for on-target site DNA damage toxicity.
05 May 2017 | doi: 10.1038/ncomms15178

Hallmarks of Hunds coupling in the Mott insulator Ca2RuO4 OPEN
D. Sutter, C. G. Fatuzzo, S. Moser, M. Kim, R. Fittipaldi, A. Vecchione, V. Granata, Y. Sassa, F. Cossalter, G. Gatti, M. Grioni, H. M. Rønnow, N. C. Plumb, C. E. Matt, M. Shi, M. Hoesch, T. K. Kim, T-R Chang, H-T Jeng, C. Jozwiak et al.
Detailed knowledge of the low-energy electronic structure is required to understand the Mott insulating phase of Ca2RuO4. Here, Sutter et al. provide directly the experimental band structure of the paramagnetic insulating phase of Ca2RuO4 and unveil the electronic origin of its Mott phase.
05 May 2017 | doi: 10.1038/ncomms15176

Wide bandgap BaSnO3 films with room temperature conductivity exceeding 104 S cm−1 OPEN
Abhinav Prakash, Peng Xu, Alireza Faghaninia, Sudhanshu Shukla, Joel W. Ager, Cynthia S. Lo and Bharat Jalan
With impressive electronic transport properties, wide bandgap perovskite oxides are promising transparent conductors. Prakash et al. report n-type BaSnO3 films with room temperature conductivity exceeding 104 S cm−1 and investigate factors limiting carrier mobility.
05 May 2017 | doi: 10.1038/ncomms15167

Cataract-associated P23T γD-crystallin retains a native-like fold in amorphous-looking aggregates formed at physiological pH OPEN
Jennifer C. Boatz, Matthew J. Whitley, Mingyue Li, Angela M. Gronenborn and Patrick C. A. van der Wel
Aggregation of eye lens proteins leads to cataracts, a major cause of blindness. Here the authors use solid state NMR to probe the structure of γD-crystallin eye lens proteins aggregates, which are found to retain a native-like conformation.
05 May 2017 | doi: 10.1038/ncomms15137

The molecular mechanism of the type IVa pilus motors OPEN
Matthew McCallum, Stephanie Tammam, Ahmad Khan, Lori L. Burrows and P. Lynne Howell
Bacterial type IVa pili are protein filaments used for motility and protein secretion. Here the authors present crystal structures of the Geobacter metallireducens PilB ATPase in two nucleotide states, and suggest a clockwise rotation of the central sub-pores of PilB that would support the assembly of a right-handed helical pilus.
05 May 2017 | doi: 10.1038/ncomms15091

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer OPEN
Woosung Chung, Hye Hyeon Eum, Hae-Ock Lee, Kyung-Min Lee, Han-Byoel Lee, Kyu-Tae Kim, Han Suk Ryu, Sangmin Kim, Jeong Eon Lee, Yeon Hee Park, Zhengyan Kan, Wonshik Han and Woong-Yang Park
Genetic heterogeneity in breast cancer has been demonstrated at a single-cell resolution with high levels of genome coverage. Here, the authors perform transcriptome analysis of 515 single cells from 11 patients and define core gene expression signatures for subtype-specific single breast cancer cells and tumour-infiltrating immune cells.
05 May 2017 | doi: 10.1038/ncomms15081

Nickel-catalysed retro-hydroamidocarbonylation of aliphatic amides to olefins OPEN
Jiefeng Hu, Minyan Wang, Xinghui Pu and Zhuangzhi Shi
Converting the normally highly stable amide bond into different functionalities is a challenging task. Here the authors report a nickel-catalysed retro-hydroamidocarbonylation procedure, allowing the conversion of aliphatic amides into alkenes across a range of substrates.
05 May 2017 | doi: 10.1038/ncomms14993

Magnetotransport on the nano scale OPEN
Philip Willke, Thomas Kotzott, Thomas Pruschke and Martin Wenderoth
Macroscopic magneto-transport measurements enable investigation of the transport properties of materials in the presence of magnetic fields, yet they do not allow access to atomic scale details. Here, the authors combine scanning tunneling potentiometry with magnetic fields to demonstrate nanoscale magneto-transport.
04 May 2017 | doi: 10.1038/ncomms15283

Sequencing and de novo assembly of a near complete indica rice genome OPEN
Huilong Du, Ying Yu, Yanfei Ma, Qiang Gao, Yinghao Cao, Zhuo Chen, Bin Ma, Ming Qi, Yan Li, Xianfeng Zhao, Jing Wang, Kunfan Liu, Peng Qin, Xin Yang, Lihuang Zhu, Shigui Li and Chengzhi Liang
High-quality reference genomes facilitate analysis of genome structure and variation. Here Du et al. create a near-complete assembly of the indica rice genome by combining single molecule sequencing with mapping data and fosmid sequences and identify genetic variants by comparison with other rice genomes.
04 May 2017 | doi: 10.1038/ncomms15324

Observation of dynamic atom-atom correlation in liquid helium in real space OPEN
W. Dmowski, S. O. Diallo, K. Lokshin, G. Ehlers, G. Ferré, J. Boronat and T. Egami
Liquid helium can be treated as an ideal gas or a condensed liquid and displays intriguing features like Bose–Einstein condensation. Here the authors show that roton excitation reveals information on real space dynamic atom-atom correlations in superfluid helium, which could be used to benchmark models.
04 May 2017 | doi: 10.1038/ncomms15294

Probing nanoscale oxygen ion motion in memristive systems OPEN
Yuchao Yang, Xiaoxian Zhang, Liang Qin, Qibin Zeng, Xiaohui Qiu and Ru Huang
Ion transport in solid-state materials is a fundamental process for many modern technologies. Utilizing electrostatic force microscopy, Yang et al. directly visualize ion motion and verify the oxygen ion dynamics within HfO2—a common metal-oxide based memristive material.
04 May 2017 | doi: 10.1038/ncomms15173

Coulomb engineering of the bandgap and excitons in two-dimensional materials OPEN
Archana Raja, Andrey Chaves, Jaeeun Yu, Ghidewon Arefe, Heather M. Hill, Albert F. Rigosi, Timothy C. Berkelbach, Philipp Nagler, Christian Schüller, Tobias Korn, Colin Nuckolls, James Hone, Louis E. Brus, Tony F. Heinz, David R. Reichman and Alexey Chernikov
Electronic bandgap tuning in semiconductors enables key functionalities in solid-state devices. Here, the authors present a strategy to control the bandgap of atomically thin WS2 and WSe2 semiconductors via manipulation of the surrounding dielectric environment rather than by modifications of the materials themselves.
04 May 2017 | doi: 10.1038/ncomms15251

Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker’s yeast OPEN
Ali R. Awan, Benjamin A. Blount, David J. Bell, William M. Shaw, Jack C.H. Ho, Robert M. McKiernan and Tom Ellis
Filamentous fungi are a valuable source of natural therapeutic products such as antibiotics. Here the authors engineer monocellular S. cerevisiae to perform complex secondary metabolism typical of multicellular fungi in order to demonstrate biosynthesis and secretion of bioactive penicillin.
04 May 2017 | doi: 10.1038/ncomms15202

Subsampling scaling OPEN
A. Levina and V. Priesemann
We can often observe only a small fraction of a system, which leads to biases in the inference of its global properties. Here, the authors develop a framework that enables overcoming subsampling effects, apply it to recordings from developing neural networks, and find that neural networks become critical as they mature.
04 May 2017 | doi: 10.1038/ncomms15140

Automated multiplex genome-scale engineering in yeast OPEN
Tong Si, Ran Chao, Yuhao Min, Yuying Wu, Wen Ren and Huimin Zhao
Genome-scale engineering is a powerful technique for understanding biology and designing microorganisms but has been limited to bacterial species. Here the authors present an automated platform for genome-scale engineering in Saccharomyces cerevisiae using CRISPR-Cas and RNAi.
04 May 2017 | doi: 10.1038/ncomms15187

CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum OPEN
Yu Jiang, Fenghui Qian, Junjie Yang, Yingmiao Liu, Feng Dong, Chongmao Xu, Bingbing Sun, Biao Chen, Xiaoshu Xu, Yan Li, Renxiao Wang and Sheng Yang
Corynebacterium glutamicum is an important industrial microbe, however it has proven difficult to genetically engineer using Cas9 from Streptococcus pyogenes. Here the authors report effective genome engineering of the bacterium using Cpf1 from Francisella novicida.
04 May 2017 | doi: 10.1038/ncomms15179

Ube2D3 and Ube2N are essential for RIG-I-mediated MAVS aggregation in antiviral innate immunity OPEN
Yuheng Shi, Bofeng Yuan, Wenting Zhu, Rui Zhang, Lin Li, Xiaojing Hao, She Chen and Fajian Hou
The RIG-I-MAVS signalling pathway plays an important role in sensing virus infection. Here the authors identify the ubiquitin-conjugating enzymes Ube2D3 and Ube2N as essential for RIG-I activation and define their roles in mediating MAVS aggregation.
04 May 2017 | doi: 10.1038/ncomms15138

Fabrication of MoSe2 nanoribbons via an unusual morphological phase transition OPEN
Yuxuan Chen, Ping Cui, Xibiao Ren, Chendong Zhang, Chuanhong Jin, Zhenyu Zhang and Chih-Kang Shih
The unique electronic properties of two-dimensional materials are determined not only by their shape, but also the precise atomic arrangement of atoms along edges. Here, Chen et al. have developed a bottom-up epitaxial growth of MoSe2 nanoribbons that controls both geometry and edge states.
04 May 2017 | doi: 10.1038/ncomms15135

Redesigning the QA binding site of Photosystem II allows reduction of exogenous quinones OPEN
Han-Yi Fu, Daniel Picot, Yves Choquet, Guillaume Longatte, Adnan Sayegh, Jérôme Delacotte, Manon Guille-Collignon, Frédéric Lemaître, Fabrice Rappaport and Francis-André Wollman
Devices that harness electron flow from photosynthetic organisms generally compromise host photosynthesis. Here, the authors show that, by redesigning the QA site of Photosystem II, it is possible to reroute electrons to an exogenous quinone while maintaining endogenous photosynthetic electron transfer in a green alga.
03 May 2017 | doi: 10.1038/ncomms15274

Organocatalytic atroposelective synthesis of axially chiral styrenes OPEN
Sheng-Cai Zheng, San Wu, Qinghai Zhou, Lung Wa Chung, Liu Ye and Bin Tan
Many methods exist for the atroposelective synthesis of axially chiral biaryls, but axially chiral styrenes are much less explored. Here the authors report an organocatalytic procedure for the synthesis of configurationally stable, axially chiral styrenes with high enantio- and diastereoselectivities.
03 May 2017 | doi: 10.1038/ncomms15238

A sequential EMT-MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes OPEN
Qiuhong Li, Andrew P. Hutchins, Yong Chen, Shengbiao Li, Yongli Shan, Baojian Liao, Dejin Zheng, Xi Shi, Yinxiong Li, Wai-Yee Chan, Guangjin Pan, Shicheng Wei, Xiaodong Shu and Duanqing Pei
Reprogramming has been shown to involve EMT-MET; however, its role in cell differentiation is unclear. Here the authors show that during in vitro differentiation of hepatocytes, Activin A-induced formation of definitive endoderm requires EMT mediated by TGFβ signalling, followed by a MET process.
03 May 2017 | doi: 10.1038/ncomms15166

The careg element reveals a common regulation of regeneration in the zebrafish myocardium and fin OPEN
Catherine Pfefferli and Anna Jaźwińska
Common mechanisms underlie organ regeneration, but it is unclear if the same regulatory elements are activated in distinct cells, such as cardiomyocytes and fibroblasts. Here, the authors identify a ctgfa upstream sequence, called careg, induced by TGFb/Activin during zebrafish heart and fin regeneration.
03 May 2017 | doi: 10.1038/ncomms15151

Arabidopsis proteins with a transposon-related domain act in gene silencing OPEN
Yoko Ikeda, Thierry Pélissier, Pierre Bourguet, Claude Becker, Marie-Noëlle Pouch-Pélissier, Romain Pogorelcnik, Magdalena Weingartner, Detlef Weigel, Jean-Marc Deragon and Olivier Mathieu
Host genomes have evolved multiple silencing mechanisms to repress transposable element activity. Here Ikeda et al. show that the Arabidopsis MAIL1 and MAIN genes encode a retrotransposon-related plant mobile domain and define an alternative silencing pathway largely independent of DNA methylation and siRNAs.
03 May 2017 | doi: 10.1038/ncomms15122

Pointwise error estimates in localization microscopy OPEN
Martin Lindén, Vladimir Ćurić, Elias Amselem and Johan Elf
Super-resolution localization microscopy produces biophysical information in the form of estimated positions of single molecules. Here, Lindén et al. estimate the uncertainty of single localizations, and show that this additional information can improve data analysis and localization precision.
03 May 2017 | doi: 10.1038/ncomms15115

Genetic variation and RNA structure regulate microRNA biogenesis OPEN
Noemi Fernandez, Ross A. Cordiner, Robert S. Young, Nele Hug, Sara Macias and Javier F. Cáceres
A single variant in mir-30c-1 found in breast and gastric cancer patients leads to increased levels of mature miRNA. Here the authors show that this variant alters the RNA structure of this pri-miRNA leading to enhanced binding of SRSF3 and increased Drosha-mediated processing.
03 May 2017 | doi: 10.1038/ncomms15114

TCF1+ hepatitis C virus-specific CD8+ T cells are maintained after cessation of chronic antigen stimulation OPEN
Dominik Wieland, Janine Kemming, Anita Schuch, Florian Emmerich, Percy Knolle, Christoph Neumann-Haefelin, Werner Held, Dietmar Zehn, Maike Hofmann and Robert Thimme
Virus-specific CD8+ T cells lose effector function over the course of chronic infection, a process called ‘exhaustion’, but the fate of these cells after treatment-induced antigen elimination is unknown. Here the authors show that exhausted cells persist in patients even after direct-acting antiviral therapy removes antigen exposure, and that these cells are responsive on re-exposure to antigen.
03 May 2017 | doi: 10.1038/ncomms15050

A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease OPEN
Michal R. Szymanski, Wangsheng Yu, Aleksandra M. Gmyrek, Mark A. White, Ian J. Molineux, J. Ching Lee and Y. Whitney Yin
Human EXOG is crucial for mitochondrial DNA repair. Here the authors present the crystal structures of hEXOG in apo form and as DNA complex and suggest a `tape-measure' activity to generate optimal substrates for mitochondrial base excision repair.
03 May 2017 | doi: 10.1038/ncomms14959

The comparative immunology of wild and laboratory mice, Mus musculus domesticus OPEN
Stephen Abolins, Elizabeth C. King, Luke Lazarou, Laura Weldon, Louise Hughes, Paul Drescher, John G. Raynes, Julius C. R. Hafalla, Mark E. Viney and Eleanor M. Riley
Laboratory mice are the cornerstone of immunology but how well they represent wild mice is not clear. Here the authors compare and contrast various immune parameters between wild-caught mice and laboratory (C57BL/6) mice and identify a previously unknown myeloid cell population specific to wild mice.
03 May 2017 | doi: 10.1038/ncomms14811

Temporal and tissue-specific requirements for T-lymphocyte IL-6 signalling in obesity-associated inflammation and insulin resistance OPEN
Elaine Xu, Mafalda M. A. Pereira, Ismene Karakasilioti, Sebastian Theurich, Mona Al-Maarri, Gunter Rappl, Ari Waisman, F. Thomas Wunderlich and Jens C. Brüning
Interleukin-6 (IL-6) is increased in obesity and activates T cells to promote inflammation. Here, Xu et al. use mice that lack IL-6 receptors on T cells to uncover the temporal and tissue-specific effects of classic and trans IL-6 signalling on inflammation and insulin resistance on a high-fat diet.
03 May 2017 | doi: 10.1038/ncomms14803

Comprehensive population-wide analysis of Lynch syndrome in Iceland reveals founder mutations in MSH6 and PMS2 OPEN
Sigurdis Haraldsdottir, Thorunn Rafnar, Wendy L. Frankel, Sylvia Einarsdottir, Asgeir Sigurdsson, Heather Hampel, Petur Snaebjornsson, Gisli Masson, Daniel Weng, Reynir Arngrimsson, Birte Kehr, Ahmet Yilmaz, Stefan Haraldsson, Patrick Sulem, Tryggvi Stefansson, Peter G. Shields, Fridbjorn Sigurdsson, Tanios Bekaii-Saab, Pall H. Moller, Margret Steinarsdottir et al.
Lynch syndrome is characterized by predisposition to colorectal cancer and mutations in genes involved in mismatch repair. Here, the authors use whole genome sequencing and immunohistochemistry of mismatch repair proteins to show a high prevalence of Lynch syndrome in the Icelandic population.
03 May 2017 | doi: 10.1038/ncomms14755
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  Latest Corrigendum  
Corrigendum: Regulation of monocyte cell fate by blood vessels mediated by Notch signalling OPEN
Jaba Gamrekelashvili, Roberto Giagnorio, Jasmin Jussofie, Oliver Soehnlein, Johan Duchene, Carlos G. Briseño, Saravana K. Ramasamy, Kashyap Krishnasamy, Anne Limbourg, Christine Häger, Tamar Kapanadze, Chieko Ishifune, Rabea Hinkel, Freddy Radtke, Lothar J. Strobl, Ursula Zimber-Strobl, L. Christian Napp, Johann Bauersachs, Hermann Haller, Koji Yasutomo et al.
03 May 2017 | doi: 10.1038/ncomms15486
  Latest Errata  
Erratum: Origin and structure of polar domains in doped molecular crystals OPEN
E. Meirzadeh, I. Azuri, Y. Qi, D. Ehre, A. M. Rappe, M. Lahav, L. Kronik and I. Lubomirsky
09 May 2017 | doi: 10.1038/ncomms15590

Erratum: Layer-specificity in the effects of attention and working memory on activity in primary visual cortex OPEN
Timo van Kerkoerle, Matthew W. Self and Pieter R. Roelfsema
03 May 2017 | doi: 10.1038/ncomms15555

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