Wednesday, May 23, 2018

Nature Communications - 23 May 2018

 
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Label-Free Digital Pathology is Here.

By combining high-speed Mid-IR imaging with advanced machine learning, label-free digital pathology has finally become a reality. Infrared imaging offers a reliable and precise solution for tissue classification on clinically relevant time-scales. 

Learn more about this groundbreaking study that is revolutionizing classical histopathology and omics workflows.
 
 
 
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23 May 2018 
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Al-Sumait Prize Call for Nominations 

Nominations are now open for the $1Million 2018 Health Category of Al-Sumait Prize for African Development. Nominations are accepted for Institutions or Individuals advancing Health in Africa. The nominations period closes on June 30 2018. Conditions, requirements and a link to the nomination form can be found below. 

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Building better yeast OPEN

The Sc2.0 project has set out to synthesise the Saccharomyces cerevisiae genome, with each chromosome redesigned along agreed principles. In this collection of papers, the researchers involved show how SCRaMbLE—Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution—can be used to rapidly reorganise the genome.

22 May 2018 | doi: 10.1038/s41467-018-04159-y
 
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SCRaMbLEing to understand and exploit structural variation in genomes OPEN
Jan Steensels, Anton Gorkovskiy & Kevin J. Verstrepen
22 May 2018 | doi: 10.1038/s41467-018-04308-3
Genomic engineering  Metabolic engineering  Synthetic biology 
 
  Latest Review View all Articles  
 
   
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  Latest Articles View all Articles  
 
A20 critically controls microglia activation and inhibits inflammasome-dependent neuroinflammation OPEN
Sofie Voet , Conor Mc Guire, Nora Hagemeyer, Arne Martens, Anna Schroeder, Peter Wieghofer, Carmen Daems, Ori Staszewski, Lieselotte Vande Walle, Marta Joana Costa Jordao, Mozes Sze, Hanna-Kaisa Vikkula, Delphine Demeestere, Griet Van Imschoot, Charlotte L. Scott, Esther Hoste, Amanda Gonçalves, Martin Guilliams, Saskia Lippens, Claude Libert et al.

As resident macrophages of the brain, microglia are important for neuroinflammatory responses. This work shows that nuclear factor kappa B regulatory protein A20 is important for microglia activation and regulation during inflammation of the central nervous system.

23 May 2018 | doi: 10.1038/s41467-018-04376-5
Interleukins  Multiple sclerosis  Neuroimmunology 

Silicon-oriented regio- and enantioselective rhodium-catalyzed hydroformylation OPEN
Cai You, Xiuxiu Li, Yuhong Yang, Yu-Sheng Yang, Xuefeng Tan, Shuailong Li, Biao Wei, Hui Lv, Lung-Wa Chung & Xumu Zhang

Hydroformylation of 1,2-disubstituted alkenes usually occurs at the α position of the directing heteroatom. Here, the authors report the asymmetric rhodium-catalyzed hydroformylation of 1,2-disubstituted alkenylsilanes with excellent regioselectivity at the β position (relative to the silicon heteroatom) and enantioselectivity.

23 May 2018 | doi: 10.1038/s41467-018-04277-7
Asymmetric catalysis  Asymmetric synthesis  Stereochemistry 

Distinct roles of XPF-ERCC1 and Rad1-Rad10-Saw1 in replication-coupled and uncoupled inter-strand crosslink repair OPEN
Ja-Hwan Seol, Cory Holland, Xiaolei Li, Christopher Kim, Fuyang Li, Melisa Medina-Rivera, Robin Eichmiller, Ignacio F. Gallardo, Ilya J. Finkelstein, Paul Hasty, Eun Yong Shim, Jennifer A. Surtees & Sang Eun Lee

The yeast Rad1–Rad10 complex has multiple roles in DNA damage repair. Here the authors uncover mutants that uncouple the roles in UV excision repair and non-NER functions.

23 May 2018 | doi: 10.1038/s41467-018-04327-0
DNA damage and repair  Genomic instability 

Protein polarization driven by nucleoid exclusion of DnaK(HSP70)–substrate complexes OPEN
Clémence Collet, Jenny-Lee Thomassin, Olivera Francetic, Pierre Genevaux & Guy Tran Van Nhieu

Many bacterial proteins exhibit spatially defined localization important for function. Here the authors show that the polar localization of Shigella IpaC type III secretion substrate is mediated by its interaction with the DnaK chaperone and occlusion by the bacterial nucleoid.

23 May 2018 | doi: 10.1038/s41467-018-04414-2
Chaperones  Microbiology 

Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity OPEN
Quy H. Nguyen, Nicholas Pervolarakis, Kerrigan Blake, Dennis Ma, Ryan Tevia Davis, Nathan James, Anh T. Phung, Elizabeth Willey, Raj Kumar, Eric Jabart, Ian Driver, Jason Rock, Andrei Goga, Seema A. Khan, Devon A. Lawson, Zena Werb & Kai Kessenbrock

Epithelial subpopulations are present in the human breast but how these differentiate or form is unclear. Here, the authors use single-cell RNA sequencing of primary human breast epithelial cells to define previously undescribed luminal, basal epithelial subpopulations and ZEB1-positive basal cells.

23 May 2018 | doi: 10.1038/s41467-018-04334-1
Breast cancer  Cells  High-throughput screening  RNA sequencing 

Probing the pathways of free charge generation in organic bulk heterojunction solar cells OPEN
Jona Kurpiers, Thomas Ferron, Steffen Roland, Marius Jakoby, Tobias Thiede, Frank Jaiser, Steve Albrecht, Silvia Janietz, Brian A. Collins, Ian A. Howard & Dieter Neher

Contradictory models are being debated on the dominant pathways of charge generation in organic solar cells. Here Kurpiers et al. determine the activation energy for this fundamental process and reveal that the main channel is via thermalized charge transfer states instead of hot exciton dissociation.

23 May 2018 | doi: 10.1038/s41467-018-04386-3
Devices for energy harvesting  Electronic devices  Optical techniques 

Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes OPEN
Amparo Garcia-Lopez , Francesca Tessaro, Hendrik R. A. Jonker, Anna Wacker, Christian Richter, Arnaud Comte, Nikolaos Berntenis, Roland Schmucki, Klas Hatje, Olivier Petermann, Gianpaolo Chiriano, Remo Perozzo, Daniel Sciarra, Piotr Konieczny, Ignacio Faustino, Guy Fournet, Modesto Orozco, Ruben Artero, Friedrich Metzger, Martin Ebeling et al.

Spinal muscular atrophy (SMA) is an autosomal recessive disorder with no present cure. Here the authors perform an in vitro screening leading to the identification of a small molecule that alters the conformational dynamics of the TSL2 RNA structure and acts as a modulator of SMN exon 7 splicing.

23 May 2018 | doi: 10.1038/s41467-018-04110-1
High-throughput screening  Molecular modelling  RNA  Solution-state NMR  Target validation 

Synthetic cytokine receptors transmit biological signals using artificial ligands OPEN
Erika Engelowski, Artur Schneider, Manuel Franke, Haifeng Xu, Ramona Clemen, Alexander Lang, Paul Baran, Christian Binsch, Birgit Knebel, Hadi Al-Hasani, Jens M. Moll, Doreen M. Floß, Philipp A. Lang & Jürgen Scheller

Cytokine-induced signaling acts as an ON/OFF switch dependent on the presence of ligands. Here the authors construct synthetic cytokine receptors responsive to synthetic ligands able to activate canonical signaling pathways.

23 May 2018 | doi: 10.1038/s41467-018-04454-8
Interleukins  Molecular engineering  Signal transduction  Synthetic biology 

Combining laser capture microdissection and proteomics reveals an active translation machinery controlling invadosome formation OPEN
Zakaria Ezzoukhry, Elodie Henriet, Fabrice P. Cordelières, Jean-William Dupuy, Marlène Maître, Nathan Gay, Sylvaine Di-Tommaso, Luc Mercier, Jacky G. Goetz, Marion Peter, Frédéric Bard, Violaine Moreau, Anne-Aurélie Raymond & Frédéric Saltel

Invadosomes degrade extracellular matrix and facilitate cell invasion but their molecular composition is not fully understood. Here, the authors combine laser capture and mass spectrometry to map the proteome of invadosomes, showing that they rely on internal translational activity to maintain their structure.

23 May 2018 | doi: 10.1038/s41467-018-04461-9
Invadopodia  Isolation, separation and purification  Podosomes  Proteomics 

Probing the gating mechanism of the mechanosensitive channel Piezo1 with the small molecule Yoda1 OPEN
Jerome J. Lacroix, Wesley M. Botello-Smith & Yun Luo

Piezo ion channels transduce mechanical stimuli into biological signals but the underlying mechanism has remained elusive. Here, the authors use the selective agonist Yoda1 to identify molecular determinants of Piezo activation, providing mechanistic insights into Piezo-mediated mechanotransduction.

23 May 2018 | doi: 10.1038/s41467-018-04405-3
Ca2+ imaging  Ion channels  Mechanotransduction  Patch clamp 

Separation of current density and electric field domains caused by nonlinear electronic instabilities OPEN
Suhas Kumar & R. Stanley Williams

The usefulness of metal-oxide memristors for memory and brain-inspired computing applications arises from their electronic instabilities, whose details remain limited. In this work, the authors analyze electronic decompositions in several metal oxides, providing new insights for device modeling.

23 May 2018 | doi: 10.1038/s41467-018-04452-w
Electrical and electronic engineering  Nonlinear phenomena 

Deep 2-photon imaging and artifact-free optogenetics through transparent graphene microelectrode arrays OPEN
Martin Thunemann, Yichen Lu, Xin Liu, Kıvılcım Kılıç, Michèle Desjardins, Matthieu Vandenberghe, Sanaz Sadegh, Payam A. Saisan, Qun Cheng, Kimberly L. Weldy, Hongming Lyu, Srdjan Djurovic, Ole A. Andreassen, Anders M. Dale, Anna Devor & Duygu Kuzum

Optical imaging and manipulation technologies cannot be easily integrated with electrical recordings due to generation of light-induced artifacts. Here the authors report the optimization of transparent graphene microelectrode fabrication to achieve artifact-free electrical recordings along with deep 2-photon imaging in vivo.

23 May 2018 | doi: 10.1038/s41467-018-04457-5
Biomedical engineering  Neuroscience 

Dlx1/2 and Otp coordinate the production of hypothalamic GHRH- and AgRP-neurons OPEN
Bora Lee, Janghyun Kim, Taekyeong An, Sangsoo Kim, Esha M. Patel, Jacob Raber, Soo-Kyung Lee, Seunghee Lee & Jae W. Lee

In the hypothalamus, the arcuate nucleus (ARC) contains AgRP-neurons that regulate energy balance as well as GHRH-neurons that regulate linear growth. Here, the authors looked at how the transcription factors Dlx1/2 and Otp link development of AgRP- and GHRH-neurons.

23 May 2018 | doi: 10.1038/s41467-018-04377-4
Cell fate and cell lineage  Developmental neurogenesis 

Structural resolution of inorganic nanotubes with complex stoichiometry OPEN
Geoffrey Monet, Mohamed S. Amara, Stéphan Rouzière, Erwan Paineau, Ziwei Chai, Joshua D. Elliott, Emiliano Poli, Li-Min Liu, Gilberto Teobaldi & Pascale Launois

Structural determination of inorganic nanotubes has lagged far behind that of their carbon-based counterparts. Here, the authors present a transferable methodology, combining wide angle X-ray scattering and computation, to quantitatively resolve the atomic structure of inorganic nanotubes with complex stoichiometry.

23 May 2018 | doi: 10.1038/s41467-018-04360-z
Characterization and analytical techniques  Inorganic chemistry  Organic–inorganic nanostructures 

Self-selection of dissipative assemblies driven by primitive chemical reaction networks OPEN
Marta Tena-Solsona, Caren Wanzke, Benedikt Riess, Andreas R. Bausch & Job Boekhoven

Selection and persistence of chemical non-equilibrium species is crucial for the emergence of life and the exact mechanisms remain elusive. Here the authors show that phase separation is an efficient way to control selection of chemical species when primitive carboxylic acids are brought out-of-equilibrium by high-energy condensing agents.

23 May 2018 | doi: 10.1038/s41467-018-04488-y
Dynamic combinatorial chemistry  Self-assembly 

Trait paranoia shapes inter-subject synchrony in brain activity during an ambiguous social narrative OPEN
Emily S. Finn, Philip R. Corlett, Gang Chen, Peter A. Bandettini & R. Todd Constable

Reactions to the same event can vary vastly based on multiple factors. Here the authors show that people with high trait-level paranoia process ambiguous information in a narrative differently and this can be attributed to greater activity in mentalizing brain regions during the moments of ambiguity.

23 May 2018 | doi: 10.1038/s41467-018-04387-2
Human behaviour  Language  Personality 

Complete microtubule–kinetochore occupancy favours the segregation of merotelic attachments OPEN
Damian Dudka, Anna Noatynska, Chris A. Smith, Nicolas Liaudet, Andrew D. McAinsh & Patrick Meraldi

Single microtubules (MTs) can move chromosomes, but it is unclear why kinetochores bind up to 20 MTs. Here, the authors decrease the number of kinetochore MTs with BAL27862 and see lagging chromosomes, suggesting that numerous kinetochore MTs provide force ensuring robust chromosomal segregation.

23 May 2018 | doi: 10.1038/s41467-018-04427-x
Chromosome segregation  Kinetochores  Mitotic spindle 

Extremely stable graphene electrodes doped with macromolecular acid OPEN
Sung-Joo Kwon, Tae-Hee Han, Taeg Yeoung Ko, Nannan Li, Youngsoo Kim, Dong Jin Kim, Sang-Hoon Bae, Yang Yang, Byung Hee Hong, Kwang S. Kim, Sunmin Ryu & Tae-Woo Lee

Chemical doping is a viable strategy to tune the electrical properties of pristine graphene, but suffers from stability issues. Here, the authors develop a macromolecular chemical doping approach that makes use of polymeric acid and provides high stability.

23 May 2018 | doi: 10.1038/s41467-018-04385-4
Electronic devices  Electronic properties and devices 

The rice blast resistance gene Ptr encodes an atypical protein required for broad-spectrum disease resistance OPEN
Haijun Zhao, Xueyan Wang, Yulin Jia, Bastian Minkenberg, Matthew Wheatley, Jiangbo Fan, Melissa H. Jia, Adam Famoso, Jeremy D. Edwards, Yeshi Wamishe, Barbara Valent, Guo-Liang Wang & Yinong Yang

Genes that confer resistance to plant pathogens such as rice blast disease typically encode NLR-type receptor proteins. Here, Zhao et al. describe a new resistance locus that encodes a non-NLR Armadillo repeat protein required for broad-spectrum resistance in rice.

23 May 2018 | doi: 10.1038/s41467-018-04369-4
Agricultural genetics  Biotic  Plant genetics  Plant immunity 

Large-scale forward genetics screening identifies Trpa1 as a chemosensor for predator odor-evoked innate fear behaviors OPEN
Yibing Wang , Liqin Cao, Chia-Ying Lee, Tomohiko Matsuo, Kejia Wu, Greg Asher, Lijun Tang, Tsuyoshi Saitoh, Jamie Russell, Daniela Klewe-Nebenius, Li Wang, Shingo Soya, Emi Hasegawa, Yoan Chérasse, Jiamin Zhou, Yuwenbin Li, Tao Wang, Xiaowei Zhan, Chika Miyoshi, Yoko Irukayama et al.

TMT is a chemical that evokes innate defensive behaviors yet the molecular mechanisms are not well understood. Here the authors perform a large-scale forward genetics screen in mice and identify Trpa1, a pungency/irritancy receptor, as a chemosensor for predator odor-evoked innate fear and defensive behaviors.

23 May 2018 | doi: 10.1038/s41467-018-04324-3
Genetics of the nervous system  Molecular neuroscience 

Postnatal DNA demethylation and its role in tissue maturation OPEN
Yitzhak Reizel, Ofra Sabag, Yael Skversky, Adam Spiro, Benjamin Steinberg, Diana Bernstein, Amber Wang, Julia Kieckhaefer, Catherine Li, Eli Pikarsky, Rena Levin-Klein, Alon Goren, Klaus Rajewsky, Klaus H. Kaestner & Howard Cedar

Here the authors show that. large fraction of the tissue-specific methylation pattern is generated postnatally. These changes, which occur in response to hormone signaling, appear to play. major role in the regulation of gene expression and tissue maturation in the liver.

23 May 2018 | doi: 10.1038/s41467-018-04456-6
Epigenetics  Transcriptional regulatory elements 

Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome OPEN
B. A. Blount, G-O. F. Gowers, J. C. H. Ho, R. Ledesma-Amaro, D. Jovicevic, R. M. McKiernan, Z. X. Xie, B. Z. Li, Y. J. Yuan & T. Ellis

The Sc2.0 project has built the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system into their synthetic chromosomes. Here the authors use SCRaMbLE to rapidly develop, diversify and screen strains for diverse production and growth characteristics.

22 May 2018 | doi: 10.1038/s41467-018-03143-w
Genomic engineering  Metabolic engineering  Synthetic biology 

Revealing missing charges with generalised quantum fluctuation relations OPEN
J. Mur-Petit, A. Relaño, R. A. Molina & D. Jaksch

Conservation laws are a key ingredient in the non-equilibrium dynamics of quantum many-body systems. Here, the authors develop generalised quantum fluctuation relations in order to identify the presence of conserved quantities relevant for a generalised Gibbs ensemble.

22 May 2018 | doi: 10.1038/s41467-018-04407-1
Quantum physics  Statistical physics, thermodynamics and nonlinear dynamics 

Hygroscopic compounds in spider aggregate glue remove interfacial water to maintain adhesion in humid conditions OPEN
Saranshu Singla, Gaurav Amarpuri, Nishad Dhopatkar, Todd A. Blackledge & Ali Dhinojwala

Spider aggregate glue avoids failure in humid environments but the fundamental mechanism behind it is still unknown. Here, the authors demonstrate that humidity-dependent structural changes of glycoproteins and sequestering of liquid water by low molecular mass compounds prevents adhesion failure of the glue in humid environments.

22 May 2018 | doi: 10.1038/s41467-018-04263-z
Biological physics  Biomechanics  Organic molecules in materials science 

Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods OPEN
Wei Liu, Zhouqing Luo, Yun Wang, Nhan T. Pham, Laura Tuck, Irene Pérez-Pi, Longying Liu, Yue Shen, Chris French, Manfred Auer, Jon Marles-Wright, Junbiao Dai & Yizhi Cai

Pathway optimization and chassis engineering are usually carried out in a step-wise and trial-and-error manner. Here the authors present ’SCRaMbLE-in’ that combines in-vitro pathway rapid prototyping with in-vivo genome integration and optimization.

22 May 2018 | doi: 10.1038/s41467-018-04254-0
Genomic engineering  Metabolic engineering  Synthetic biology 

Coupling bimolecular PARylation biosensors with genetic screens to identify PARylation targets OPEN
Dragomir B. Krastev, Stephen J. Pettitt, James Campbell, Feifei Song, Barbara E. Tanos, Stoyno S. Stoynov, Alan Ashworth & Christopher J. Lord

Poly ADP-ribosylation (PARylation) is a highly dynamic post-translation protein modification, but most methods only detect stable PARylation events. Here the authors develop a split-GFP-based sensor for PARylation detection in live cells and use it to identify a new centrosomal PARylation target.

22 May 2018 | doi: 10.1038/s41467-018-04466-4
Fluorescent proteins  PolyADP-ribosylation 

Plasma membrane LAT activation precedes vesicular recruitment defining two phases of early T-cell activation OPEN
Lakshmi Balagopalan, Jason Yi, Tiffany Nguyen, Katherine M. McIntire, Adam S. Harned, Kedar Narayan & Lawrence E. Samelson

Controversy exists over the function of plasma membrane versus intracellular vesicular LAT in T-cell receptor signaling. Here the authors use high resolution imaging of the temporal dynamics of LAT involvement to show that both sources of LAT are required, but at distinct stages.

22 May 2018 | doi: 10.1038/s41467-018-04419-x
Imaging the immune system  Signal transduction  T cells 

Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES OPEN
Zhouqing Luo, Lihui Wang, Yun Wang, Weimin Zhang, Yakun Guo, Yue Shen, Linghuo Jiang, Qingyu Wu, Chong Zhang, Yizhi Cai & Junbiao Dai

The use of synthetic chromosomes and the recombinase-based SCRaMbLE system could enable rapid strain evolution through massive chromosome rearrangements. Here the authors present ReSCuES, which uses auxotrophic markers to rapidly identify yeast with rearrangements for strain engineering.

22 May 2018 | doi: 10.1038/s41467-017-00806-y
Genome evolution  Synthetic biology 

Super-resolution architecture of mammalian centriole distal appendages reveals distinct blade and matrix functional components OPEN
T. Tony Yang, Weng Man Chong, Won-Jing Wang, Gregory Mazo, Barbara Tanos, Zhengmin Chen, Thi Minh Nguyet Tran, Yi-De Chen, Rueyhung Roc Weng, Chia-En Huang, Wann-Neng Jane, Meng-Fu Bryan Tsou & Jung-Chi Liao

Distal appendages (DAPs) at the cilia base mediate membrane docking during ciliogenesis. Here the authors use super-resolution microscopy to map 16 centriole distal end components, revealing the structure of the backbone of the DAP, as well as a previously undescribed distal appendage matrix.

22 May 2018 | doi: 10.1038/s41467-018-04469-1
Centrosome  Cilia  Ciliogenesis 

Autophagy promotes the survival of dormant breast cancer cells and metastatic tumour recurrence OPEN
Laura Vera-Ramirez, Suman K. Vodnala, Ryan Nini, Kent W. Hunter & Jeffrey E. Green

Highly metastatic dormant cancer cells contribute to breast cancer recurrence, but the underlying mechanism is less understood. Here, the authors show that dormant breast cancer cells depend on autophagy to ensure their long term survival and distant recurrence

22 May 2018 | doi: 10.1038/s41467-018-04070-6
Breast cancer  Mitophagy 

Similar temperature scale for valence changes in Kondo lattices with different Kondo temperatures OPEN
K. Kummer, C. Geibel, C. Krellner, G. Zwicknagl, C. Laubschat, N. B. Brookes & D. V. Vyalikh

The competition between interactions promoting magnetic order and those suppressing magnetism causes unusual electronic behaviour in Kondo lattice materials. Here, the authors show the energy scale for valence fluctuations is not controlled by the Kondo scale, contrary to expectations from single-site models.

22 May 2018 | doi: 10.1038/s41467-018-04438-8
Electronic properties and materials  Magnetic properties and materials  Phase transitions and critical phenomena 

Value added transformation of ubiquitous substrates into highly efficient and flexible electrodes for water splitting OPEN
Atharva Sahasrabudhe, Harsha Dixit, Rahul Majee & Sayan Bhattacharyya

Water electrolysis provides a means to convert water into carbon-neutral fuels, but current devices are typically heavy, inflexible, or require costly substrates. Here, the authors transform paper and cotton fabrics into efficient, durable, and flexible supports for water-splitting electrocatalysts.

22 May 2018 | doi: 10.1038/s41467-018-04358-7
Electrocatalysis  Nanoparticles 

Augmenting the Calvin–Benson–Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway OPEN
Hong Yu, Xiaoqian Li, Fabienne Duchoud, Derrick S. Chuang & James C. Liao

Improving carbon fixation efficiency and reducing carbon loss have been long term goals for people working on photosynthetic organism improvement. Here, the authors design a synthetic malyl-CoA-glycerate pathway for efficient acetyl-CoA synthesis and verify its function in vitro, in E. coli and in cyanobacterium.

22 May 2018 | doi: 10.1038/s41467-018-04417-z
C3 photosynthesis  Metabolic engineering  Synthetic biology 

Cross-plane coherent acoustic phonons in two-dimensional organic-inorganic hybrid perovskites OPEN
Peijun Guo, Constantinos C. Stoumpos, Lingling Mao, Sridhar Sadasivam, John B. Ketterson, Pierre Darancet, Mercouri G. Kanatzidis & Richard D. Schaller

Two-dimensional, organic-inorganic hybrid perovskites have sustained research interest due to attractive optoelectronic and excitonic properties. Here, Guo et al. systematically investigate coherent acoustic phonon transport versus layer thickness in these materials with strong acoustic impedance mismatch

22 May 2018 | doi: 10.1038/s41467-018-04429-9
Acoustics  Electronic materials  Organic–inorganic nanostructures  Solar cells  Two-dimensional materials 

Hox and Wnt pattern the primary body axis of an anthozoan cnidarian before gastrulation OPEN
Timothy Q. DuBuc, Thomas B. Stephenson, Amber Q. Rock & Mark Q. Martindale

Hox genes regulate anterior–posterior axis formation but their role in cnidarians is unclear. Here, the authors disrupt Hox genes NvAx1 and NvAx6 in the starlet sea anemone, Nematostella vectensis, showing antagonist function in patterning the oral–aboral axis and a link to Wnt signaling.

22 May 2018 | doi: 10.1038/s41467-018-04184-x
Embryology  Evolution  Evolutionary developmental biology 

rbFOX1/MBNL1 competition for CCUG RNA repeats binding contributes to myotonic dystrophy type 1/type 2 differences OPEN

Myotonic dystrophy (DM) type 2 is a neuromuscular pathology caused by large expansions of CCTG repeats. Here the authors find that rbFOX1 RNA binding protein binds to CCUG RNA repeats and competes with MBNL1 for the binding to CCUG repeats, releasing MBNL1 from sequestration in DM2 muscle cells.

22 May 2018 | doi: 10.1038/s41467-018-04370-x
Alternative splicing  Neuromuscular disease 

Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models OPEN
Samuel Y. Ng , Noriaki Yoshida, Amanda L. Christie, Mahmoud Ghandi, Neekesh V. Dharia, Joshua Dempster, Mark Murakami, Kay Shigemori, Sara N. Morrow, Alexandria Van Scoyk, Nicolas A. Cordero, Kristen E. Stevenson, Maneka Puligandla, Brian Haas, Christopher Lo, Robin Meyers, Galen Gao, Andrew Cherniack, Abner Louissaint Jr, Valentina Nardi et al.

T- and NK-cell lymphomas (TCL) are a group of lymphoid malignancies characterized by poor prognosis, but the absence of appropriate pre-clinical models has hampered the development of effective therapies. Here the authors establish several pre-clinical models and identify vulnerabilities that could be further exploited to treat patients afflicted by these diseases.

22 May 2018 | doi: 10.1038/s41467-018-04356-9
Cancer genomics  Molecular medicine  Preclinical research 

L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast OPEN
Lena Hochrein, Leslie A. Mitchell, Karina Schulz, Katrin Messerschmidt & Bernd Mueller-Roeber

The International Synthetic Yeast Sc2.0 project has built Cre recombinase sites into synthetic chromosomes, enabling rapid genome evolution. Here the authors demonstrate L-SCRaMbLE, a light-controlled recombinase tool with improved control over recombination events.

22 May 2018 | doi: 10.1038/s41467-017-02208-6
Biotechnology  DNA recombination  Genetic engineering  Optogenetics 

In vitro DNA SCRaMbLE OPEN
Yi Wu, Rui-Ying Zhu, Leslie A. Mitchell, Lu Ma, Rui Liu, Meng Zhao, Bin Jia, Hui Xu, Yun-Xiang Li, Zu-Ming Yang, Yuan Ma, Xia Li, Hong Liu, Duo Liu, Wen-Hai Xiao, Xiao Zhou, Bing-Zhi Li, Ying-Jin Yuan & Jef D. Boeke

SCRaMbLE allows for the rapid and large scale rearrangement of genetic data in yeast carrying synthetic chromosomes. Here the authors demonstrate an in vitro use of the method to generate DNA libraries for optimization of biochemical reactions.

22 May 2018 | doi: 10.1038/s41467-018-03743-6
Metabolic engineering  Synthetic biology 

Kin discrimination allows plants to modify investment towards pollinator attraction OPEN
Rubén Torices, José M. Gómez & John R. Pannell

Plants can recognize nearby kin and alter their growth in response. Here, Torices et al. demonstrate that flower production can also be sensitive to social context, with plants producing larger floral displays in the presence of relatives, which may increase attraction of pollinators to the group.

22 May 2018 | doi: 10.1038/s41467-018-04378-3
Flowering  Social evolution 

Controlling the coherence of a diamond spin qubit through its strain environment OPEN
Young-Ik Sohn, Srujan Meesala, Benjamin Pingault, Haig A. Atikian, Jeffrey Holzgrafe, Mustafa Gündoğan, Camille Stavrakas, Megan J. Stanley, Alp Sipahigil, Joonhee Choi, Mian Zhang, Jose L. Pacheco, John Abraham, Edward Bielejec, Mikhail D. Lukin, Mete Atatüre & Marko Lončar

Silicon-vacancy centres in diamond are promising candidates as emitters in photonic quantum networks, but their coherence is degraded by large electron-phonon interactions. Sohn et al. demonstrate the use of strain to tune a silicon vacancy’s electronic structure and suppress phonon-mediated decoherence.

22 May 2018 | doi: 10.1038/s41467-018-04340-3
Optical properties of diamond  Mechanical engineering  Quantum information  Qubits 

Hypoxia induces senescence of bone marrow mesenchymal stem cells via altered gut microbiota OPEN
Junyue Xing, Yongquan Ying, Chenxi Mao, Yiwei Liu, Tingting Wang, Qian Zhao, Xiaoling Zhang, Fuxia Yan & Hao Zhang

Systemic chronic hypoxia is a feature of many diseases and may influence the communication between bone marrow and gut microbiota. Here, the authors show that chronic hypoxia predisposes bone marrow stem cells to premature senescence, which may be due to gut dysbiosis and gut microbiota-derived d-galactose accumulation.

22 May 2018 | doi: 10.1038/s41467-018-04453-9
Hypoxia  Medical research  Mesenchymal stem cells  Microbiome 

Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS OPEN
Raphaelle Luisier, Giulia E. Tyzack, Claire E. Hall, Jamie S. Mitchell, Helen Devine, Doaa M. Taha, Bilal Malik, Ione Meyer, Linda Greensmith, Jia Newcombe, Jernej Ule, Nicholas M. Luscombe & Rickie Patani

Intron retention (IR) can increase protein diversity and function, and yet unregulated IR may be detrimental to cellular health. This study shows that aberrant IR occurs in ALS and finds nuclear loss of an RNA-binding protein called SFPQ as a new molecular hallmark in this devastating condition.

22 May 2018 | doi: 10.1038/s41467-018-04373-8
Alternative splicing  Induced pluripotent stem cells  Neural stem cells  Neurology  Pathogenesis 

Heterozygous diploid and interspecies SCRaMbLEing OPEN
Michael J. Shen, Yi Wu, Kun Yang, Yunxiang Li, Hui Xu, Haoran Zhang, Bing-Zhi Li, Xia Li, Wen-Hai Xiao, Xiao Zhou, Leslie A. Mitchell, Joel S. Bader, Yingjin Yuan & Jef D. Boeke

SCRaMbLE has been used to rearrange synthetic chromosomes that have been introduced into host yeast. Here the authors produce semi-synthetic heterozygous diploid strains for rapid selection of phenotypes and map the rearrangements underlying selected phenotypes such as thermoresistance and caffeine resistance.

22 May 2018 | doi: 10.1038/s41467-018-04157-0
Experimental evolution  Genome evolution  Genomic engineering  Synthetic biology 

High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing OPEN
Peng Zhang, Ji-Han Xia, Jing Zhu, Ping Gao, Yi-Jun Tian, Meijun Du, Yong-Chen Guo, Sufyan Suleman, Qin Zhang, Manish Kohli, Lori S. Tillmans, Stephen N. Thibodeau, Amy J. French, James R. Cerhan, Li-Dong Wang, Gong-Hong Wei & Liang Wang

Functional characterization of disease-causing variants at risk loci in cancer is challenging. Here, in prostate cancer the authors report a pipeline for high-throughput single-nucleotide polymorphisms sequencing (SNPs-seq) for large scale screening of functional SNPs at disease risk loci.

22 May 2018 | doi: 10.1038/s41467-018-04451-x
Genetic variation  Genetics research  Genomic analysis  Genomics  Sequencing 

Deficiency of PRKD2 triggers hyperinsulinemia and metabolic disorders OPEN
Yao Xiao , Can Wang, Jia-Yu Chen, Fujian Lu, Jue Wang, Ning Hou, Xiaomin Hu, Fanxin Zeng, Dongwei Ma, Xueting Sun, Yi Ding, Yan Zhang, Wen Zheng, Yuli Liu, Haibao Shang, Wenzhen Zhu, Chensheng Han, Yulin Zhang, Kunfu Ouyang, Liangyi Chen et al.

Hyperinsulinemia can precede the development of insulin resistance. Here the authors identify a PKD2 mutation that leads to hyperinsulinemia and insulin resistance in Rhesus monkey and show that PKD2 deficiency promotes beta cell insulin secretion by activating L-type Ca2+ channels.

22 May 2018 | doi: 10.1038/s41467-018-04352-z
Islets of Langerhans  Metabolic syndrome  Type 2 diabetes 

Precise control of SCRaMbLE in synthetic haploid and diploid yeast OPEN
Bin Jia, Yi Wu, Bing-Zhi Li, Leslie A. Mitchell, Hong Liu, Shuo Pan, Juan Wang, Hao-Ran Zhang, Nan Jia, Bo Li, Michael Shen, Ze-Xiong Xie, Duo Liu, Ying-Xiu Cao, Xia Li, Xiao Zhou, Hao Qi, Jef D. Boeke & Ying-Jin Yuan

The SCRaMbLE system integrated into Sc2.0’s synthetic yeast chromosome project allows rapid strain evolution. Here the authors use a genetic logic gate to control induction of recombination in a haploid and diploid yeast carrying synthetic chromosomes.

22 May 2018 | doi: 10.1038/s41467-018-03084-4
Genome evolution  Mutagenesis  Synthetic biology 

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm OPEN
Jennifer M. Michaud, Luke R. Thompson, Drishti Kaul, Josh L. Espinoza, R. Alexander Richter, Zhenjiang Zech Xu, Christopher Lee, Kevin M. Pham, Charlotte M. Beall, Francesca Malfatti, Farooq Azam, Rob Knight, Michael D. Burkart, Christopher L. Dupont & Kimberly A. Prather

Factors controlling the transfer of microbes from the ocean to the atmosphere are unclear. Here, Michaud et al. study this process in an enclosed ocean-atmosphere facility, and show that the degree of aerosolization of bacteria and viruses is taxon-specific.

22 May 2018 | doi: 10.1038/s41467-018-04409-z
Air microbiology  Atmospheric chemistry 

Large quantum-spin-Hall gap in single-layer 1T′ WSe2 OPEN
P. Chen, Woei Wu Pai, Y.-H. Chan, W.-L. Sun, C.-Z. Xu, D.-S. Lin, M. Y. Chou, A.-V. Fedorov & T.-C. Chiang

The current known two-dimensional topological insulators with small band gaps limit the potential for room temperature applications. Here, Chen et al. observe a sizable gap of 129 meV in a 1T'-WSe2 single layer grown on bilayer graphene with in-gap edge state near the layer boundary.

21 May 2018 | doi: 10.1038/s41467-018-04395-2
Electronic properties and materials  Quantum Hall  Surfaces, interfaces and thin films 

Continuous addition of progenitors forms the cardiac ventricle in zebrafish OPEN
Anastasia Felker, Karin D. Prummel, Anne M. Merks, Michaela Mickoleit, Eline C. Brombacher, Jan Huisken, Daniela Panáková & Christian Mosimann

Late-differentiating second heart field progenitors contribute to atrium, ventricle, and outflow tract in the zebrafish heart but how remains unclear. Here, the authors image heart formation in transgenics based on the cardiopharyngeal gene tbx1 and show that progenitors are continuously added.

21 May 2018 | doi: 10.1038/s41467-018-04402-6
Cell lineage  Heart development  Organogenesis 

High-fidelity entanglement between a trapped ion and a telecom photon via quantum frequency conversion OPEN
Matthias Bock, Pascal Eich, Stephan Kucera, Matthias Kreis, Andreas Lenhard, Christoph Becher & Jürgen Eschner

Entanglement between photons and stationary quantum nodes is a fundamental resource for quantum communication, but typical transition wavelengths are far from the telecom band. Here, the authors deal with the problem using polarisation-independent, entanglement-preserving frequency conversion.

21 May 2018 | doi: 10.1038/s41467-018-04341-2
Atomic and molecular interactions with photons  Quantum information  Quantum optics  Single photons and quantum effects 

Special temperatures in frustrated ferromagnets OPEN
L. Bovo, M. Twengström, O. A. Petrenko, T. Fennell, M. J. P. Gingras, S. T. Bramwell & P. Henelius

Competing interactions in frustrated magnets give rise to complex emergent phenomena, which challenge a full microscopic understanding but invite comparison to other systems. Bovo et al. find an analogy to classical gases and identify special temperatures that reveal fine details of the microscopic Hamiltonian.

21 May 2018 | doi: 10.1038/s41467-018-04297-3
Ferromagnetism  Magnetic properties and materials  Thermodynamics 

Nanoparticle-templated nanofiltration membranes for ultrahigh performance desalination OPEN
Zhenyi Wang, Zhangxin Wang, Shihong Lin, Huile Jin, Shoujian Gao, Yuzhang Zhu & Jian Jin

Nanofiltration membranes are important for water desalination technologies, but designing membranes that achieve both high permeance and high salt rejection remains challenging. Here, the authors use sacrificial nanoparticles in the membrane fabrication process, leading to crumpled structures with ultrahigh permeance.

21 May 2018 | doi: 10.1038/s41467-018-04467-3
Chemical engineering  Environmental chemistry  Metal–organic frameworks  Polymers 

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models OPEN
Jiarui Ding, Anne Condon & Sohrab P. Shah

Although single-cell transcriptome data are increasingly available, their interpretation remains a challenge. Here, the authors present a dimensionality reduction approach that preserves both the local and global neighbourhood structures in the data thus enhancing its interpretability.

21 May 2018 | doi: 10.1038/s41467-018-04368-5
Bioinformatics  Computational models  Machine learning 

Tomographic and multimodal scattering-type scanning near-field optical microscopy with peak force tapping mode OPEN
Haomin Wang, Le Wang, Devon S. Jakob & Xiaoji G. Xu

Scanning near-field optical microscopy (SNOM) offers nanometer-scale spatial resolution, but generally does not retain tomographic information. Here, Wang et al. develop peak-force SNOM to section scattered fields and improve imaging resolution.

21 May 2018 | doi: 10.1038/s41467-018-04403-5
Characterization and analytical techniques  Imaging studies  Imaging techniques  Infrared spectroscopy 

Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs OPEN
Rebecca E. O’Connor, Michael N. Romanov, Lucas G. Kiazim, Paul M. Barrett, Marta Farré, Joana Damas, Malcolm Ferguson-Smith, Nicole Valenzuela, Denis M. Larkin & Darren K. Griffin

Ancient diapsids diverged into the lineages leading to turtles and birds over 250 million years ago. Here, the authors use genomic and molecular cytogenetic analyses of modern species to infer the genome structure of the diapsid common ancestor (DCA) and the changes occurring along the lineage to birds through theropod dinosaurs.

21 May 2018 | doi: 10.1038/s41467-018-04267-9
Comparative genomics  Evolutionary biology  Evolutionary genetics 

Polarization insensitive frequency conversion for an atom-photon entanglement distribution via a telecom network OPEN
Rikizo Ikuta, Toshiki Kobayashi, Tetsuo Kawakami, Shigehito Miki, Masahiro Yabuno, Taro Yamashita, Hirotaka Terai, Masato Koashi, Tetsuya Mukai, Takashi Yamamoto & Nobuyuki Imoto

Quantum repeater-based communication requires the ability to interface good quantum memories to telecom photons. Here, the authors report polarization-insensitive frequency conversion to telecom wavelength of a photon entangled with a Rb ensemble, preserving the entanglement in the process.

21 May 2018 | doi: 10.1038/s41467-018-04338-x
Atomic and molecular interactions with photons  Quantum information  Quantum optics  Single photons and quantum effects 

Multiple convergent supergene evolution events in mating-type chromosomes OPEN
Sara Branco, Fantin Carpentier, Ricardo C. Rodríguez de la Vega, Hélène Badouin, Alodie Snirc, Stéphanie Le Prieur, Marco A. Coelho, Damien M. de Vienne, Fanny E. Hartmann, Dominik Begerow, Michael E. Hood & Tatiana Giraud

Supergenes result from beneficial linkage and recombination suppression between two or more genes. Giraud and colleagues use whole genome sequencing data to show convergent evolution of supergenes on mating-type chromosomes in multiple closely-related fungal lineages.

21 May 2018 | doi: 10.1038/s41467-018-04380-9
Evolutionary biology  Evolutionary genetics 

MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity OPEN

In leukemia, diverse fusion proteins involving the MLL gene can drive oncogenic activity. Here, the authors describe a dependency of MLL-leukemia cells on the methyltransferase SETD2 to maintain genomic integrity during leukemia initiation and maintenance.

18 May 2018 | doi: 10.1038/s41467-018-04329-y
Acute myeloid leukaemia 

Supramolecularly directed rotary motion in a photoresponsive receptor OPEN
Sander J. Wezenberg & Ben L. Feringa

Unidirectional rotation in a synthetic molecular motor is typically driven by intrinsic asymmetry or sequences of chemical transformations. Here, the authors control the direction of a molecule’s rotation through supramolecular binding of a chiral guest and subsequent transfer of its chiral information.

18 May 2018 | doi: 10.1038/s41467-018-04249-x
Organic chemistry  Photochemistry  Supramolecular chemistry 

Factor XIIIA—expressing inflammatory monocytes promote lung squamous cancer through fibrin cross-linking OPEN
Alessandro Porrello , Patrick L. Leslie, Emily B. Harrison, Balachandra K. Gorentla, Sravya Kattula, Subrata K. Ghosh, Salma H. Azam, Alisha Holtzhausen, Yvonne L. Chao, Michele C. Hayward, Trent A. Waugh, Sanggyu Bae, Virginia Godfrey, Scott H. Randell, Cecilia Oderup, Liza Makowski, Jared Weiss, Matthew D. Wilkerson, D. Neil Hayes, H. Shelton Earp et al.

Lung squamous carcinomas (LUSC) are poorly molecularly characterized, but sub-populations show promising response to immune checkpoint inhibitors. Here, the authors identify a subset of LUSC characterized by infiltration of inflammatory monocytes, where metastasis is linked to Factor XIIIA promoting fibrin cross-linking.

18 May 2018 | doi: 10.1038/s41467-018-04355-w
Monocytes and macrophages  Non-small-cell lung cancer 

Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks OPEN
Nobuhiko Muramoto, Arisa Oda, Hidenori Tanaka, Takahiro Nakamura, Kazuto Kugou, Kazuki Suda, Aki Kobayashi, Shiori Yoneda, Akinori Ikeuchi, Hiroki Sugimoto, Satoshi Kondo, Chikara Ohto, Takehiko Shibata, Norihiro Mitsukawa & Kunihiro Ohta

DNA double-strand break (DSB) leads to genome rearrangements with various genetic and phenotypic effects. Here, the authors develop a tool to induce large-scale genome restructuring by introducing conditional multiple DNA breaks, and produce various traits in yeast and Arabidopsis thaliana.

18 May 2018 | doi: 10.1038/s41467-018-04256-y
DNA recombination  Evolutionary biology  Genetic engineering 

Enhanced efficacy of combined temozolomide and bromodomain inhibitor therapy for gliomas using targeted nanoparticles OPEN
Fred C. Lam, Stephen W. Morton, Jeffrey Wyckoff, Tu-Lan Vu Han, Mun Kyung Hwang, Amanda Maffa, Elena Balkanska-Sinclair, Michael B Yaffe, Scott R Floyd & Paula T Hammond

The blood-brain barrier often limits effective delivery of treatments for glioblastoma . In this study, the authors develop transferrin-functionalized nanoparticles able to traverse the intact blood-brain barrier and deliver combination temozolomide and bromodomain inhibitor therapy to glioma-bearing mice.

18 May 2018 | doi: 10.1038/s41467-018-04315-4
CNS cancer  Nanoparticles  Targeted therapies 

Stepwise control of host–guest interaction using a coordination polymer gel OPEN
Rahul Dev Mukhopadhyay, Gourab Das & Ayyappanpillai Ajayaghosh

Achieving precise control of host–guest interactions in artificial systems is difficult. Here the authors use the thermodynamics of a system in equilibrium to control stepwise release and capture of cyclodextrin (guest) using a coordination polymer as the host and temperature as the stimulus.

18 May 2018 | doi: 10.1038/s41467-018-04303-8
Molecular self-assembly  Self-assembly 

Transient metal-centered states mediate isomerization of a photochromic ruthenium-sulfoxide complex OPEN
Amy A. Cordones, Jae Hyuk Lee, Kiryong Hong, Hana Cho, Komal Garg, Martial Boggio-Pasqua, Jeffrey J. Rack, Nils Huse, Robert W. Schoenlein & Tae Kyu Kim

An essential open question in functional transition metal complexes is the relative roles of charge-transfer and metal-centered excited states. Here the authors identify the important role of metal-centered excited states in the linkage photoisomerization of a photochromic Ru-sulfoxide complex.

18 May 2018 | doi: 10.1038/s41467-018-04351-0
Chemical physics  Ligands 

Optical wireless link between a nanoscale antenna and a transducing rectenna OPEN
Arindam Dasgupta, Marie-Maxime Mennemanteuil, Mickaël Buret, Nicolas Cazier, Gérard Colas-des-Francs & Alexandre Bouhelier

Integrating optical and electrical components for communication systems is challenging due to the differences of scale. The authors have developed an on-chip light-to-electrical wireless link between a nanoantenna and an optical rectifier, envisioned as a solution for future integrated wireless interconnects.

18 May 2018 | doi: 10.1038/s41467-018-04382-7
Nanophotonics and plasmonics  Optoelectronic devices and components  Photonic devices 

Bacterial encapsulins as orthogonal compartments for mammalian cell engineering OPEN
Felix Sigmund, Christoph Massner, Philipp Erdmann, Anja Stelzl, Hannes Rolbieski, Mitul Desai, Sarah Bricault, Tobias P. Wörner, Joost Snijder, Arie Geerlof, Helmut Fuchs, Martin Hrabĕ de Angelis, Albert J. R. Heck, Alan Jasanoff, Vasilis Ntziachristos, Jürgen Plitzko & Gil G. Westmeyer

Artificial compartments have been expressed in prokaryotes and yeast, but similar capabilities have been missing for mammalian cell engineering. Here the authors use bacterial encapsulins to engineer genetically controlled multifunctional orthogonal compartments in mammalian cells.

18 May 2018 | doi: 10.1038/s41467-018-04227-3
Biomaterials – proteins  Biomineralization  Cellular imaging  Metalloproteins  Nanostructures 

Targeting G protein-coupled receptor signaling at the G protein level with a selective nanobody inhibitor OPEN
Sahil Gulati, Hui Jin, Ikuo Masuho, Tivadar Orban, Yuan Cai, Els Pardon, Kirill A. Martemyanov, Philip D. Kiser, Phoebe L. Stewart, Christopher P. Ford, Jan Steyaert & Krzysztof Palczewski

G protein-coupled receptors (GPCRs) activate and dissociate the G protein heterotrimer into Gα-GTP and Gβγ dimer, which facilitate distinct signalling events. Here authors develop a nanobody, Nb5 that modulates Gβγ-mediated signaling without affecting GTP-bound Gαq and Gαs-mediated signaling events.

18 May 2018 | doi: 10.1038/s41467-018-04432-0
Biochemistry  G protein-coupled receptors  Membrane proteins  Structural biology 

TAK1 mediates microenvironment-triggered autocrine signals and promotes triple-negative breast cancer lung metastasis OPEN
Oihana Iriondo, Yarong Liu, Grace Lee, Mostafa Elhodaky, Christian Jimenez, Lin Li, Julie Lang, Pin Wang & Min Yu

Therapeutic options for triple-negative breast cancer (TNBC) metastasis are limited. Here they show nanoparticle-mediated delivery of TAK1 inhibitor 5Z-7-Oxozeaenol to inhibit TNBC lung metastasis in mice, and that TAK1 might promote TNBC cell adaptation in lung microenvironment by positive feedback mediated by P38 signaling.

18 May 2018 | doi: 10.1038/s41467-018-04460-w
Breast cancer  Cancer microenvironment  Metastasis 

Activity of acetyltransferase toxins involved in Salmonella persister formation during macrophage infection OPEN
Julian A. Rycroft, Bridget Gollan, Grzegorz J. Grabe, Alexander Hall, Angela M. Cheverton, Gerald Larrouy-Maumus, Stephen A. Hare & Sophie Helaine

The recalcitrance of many infections to antibiotic treatment may be due to the presence of ‘persisters’, or non-growing, antibiotic-tolerant bacteria. Here, the authors study the structures and functions of aminoacyl-tRNA acetyltransferase toxins, and their roles in persister formation in Salmonella.

18 May 2018 | doi: 10.1038/s41467-018-04472-6
Antibiotics  Bacteriology 

Iodine-catalyzed diazo activation to access radical reactivity OPEN
Pan Li, Jingjing Zhao, Lijun Shi, Jin Wang, Xiaodong Shi & Fuwei Li

Radical reactivity of diazo compounds, useful organic building blocks, is yet underexplored. Here, the authors report an iodine-catalyzed radical activation of diazo compounds affording a variety of substituted cyclopropanes, pyrroles and epoxides under either thermal- or photo-initiated conditions.

17 May 2018 | doi: 10.1038/s41467-018-04331-4
Homogeneous catalysis  Synthetic chemistry methodology  Reaction mechanisms 

Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A OPEN
Raissa Schor, Carsten Schotte, Daniel Wibberg, Jörn Kalinowski & Russell J. Cox

Xenovulene A is a fungal compound that has the potential to be used as an antidepressant. Here, the authors unravel the pathway leading to its formation in fungi and discover a new class of enzymes, which accounts for some unusual chemistry in the synthesis of xenovulene.

17 May 2018 | doi: 10.1038/s41467-018-04364-9
Biosynthesis  Natural product synthesis 

Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes OPEN
Gwen Lomberk , Yuna Blum, Rémy Nicolle, Asha Nair, Krutika Satish Gaonkar, Laetitia Marisa, Angela Mathison, Zhifu Sun, Huihuang Yan, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Tamas Ordog, Jeong-Heon Lee, Gavin Oliver, Eric Klee, Vincent Moutardier, Odile Gayet, Benjamin Bian, Pauline Duconseil et al.

Pancreatic ductal adenocarcinoma (PDAC) is a complex disease and its underlying epigenomic heterogeneity is not fully understood. Here, the authors utilize patient-derived PDAC xenografts to define the epigenomic landscape of PDAC, highlighting chromatin states linked to differing disease aggressiveness and survival.

17 May 2018 | doi: 10.1038/s41467-018-04383-6
Cancer  Epigenomics 

MxB is an interferon-induced restriction factor of human herpesviruses OPEN
Michel Crameri, Michael Bauer, Nicole Caduff, Raphael Walker, Fiona Steiner, Francesca D. Franzoso, Cornelia Gujer, Karin Boucke, Talissa Kucera, Andrea Zbinden, Christian Münz, Cornel Fraefel, Urs F. Greber & Jovan Pavlovic

MxB is an interferon-induced GTPase that inhibits HIV replication. Here, Crameri et al. show that MxB restricts replication of herpesviruses by inhibiting delivery of incoming viral DNA into the nucleus, and this antiviral activity depends on MxB’s GTPase activity.

17 May 2018 | doi: 10.1038/s41467-018-04379-2
Herpes virus  Interferons  Nuclear transport  Restriction factors 

Immunogene therapy with fusogenic nanoparticles modulates macrophage response to Staphylococcus aureus OPEN
Byungji Kim, Hong-Bo Pang, Jinyoung Kang, Ji-Ho Park, Erkki Ruoslahti & Michael J. Sailor

In the context of increasing bacterial antibiotic-resistance, gene therapy that targets the immune system to clear infection is a major goal. Here the authors show a silicon based nanosystem that modulates the macrophage response in an in vivo model of Staphylococcal pneumonia.

17 May 2018 | doi: 10.1038/s41467-018-04390-7
Bacterial infection  Drug delivery  Nanoparticles  Transfection 

Probing femtosecond lattice displacement upon photo-carrier generation in lead halide perovskite OPEN
Giovanni Batignani, Giuseppe Fumero, Ajay Ram Srimath Kandada, Giulio Cerullo, Marina Gandini, Carino Ferrante, Annamaria Petrozza & Tullio Scopigno

The electron–phonon coupling is the key to understand optoelectronic properties in lead halide perovskites but it is difficult to probe. Here Batignani et al. observe two new phonon modes with impulsive vibrational spectroscopy providing the evidence of the polaronic nature of the photo-excitation.

17 May 2018 | doi: 10.1038/s41467-018-04367-6
Raman spectroscopy  Semiconductors  Solar cells  Ultrafast photonics 

Dynamically induced cascading failures in power grids OPEN
Benjamin Schäfer, Dirk Witthaut, Marc Timme & Vito Latora

Communication networks and power grids may be subject to cascading failures which can lead to outages. Here the authors propose to investigate cascades using dynamical transients of electrical power grids, thereby identifying possible vulnerabilities that might remain undetected with any static approach.

17 May 2018 | doi: 10.1038/s41467-018-04287-5
Complex networks  Energy modelling 

A novel small molecule chaperone of rod opsin and its potential therapy for retinal degeneration OPEN
Yuanyuan Chen, Yu Chen, Beata Jastrzebska, Marcin Golczak, Sahil Gulati, Hong Tang, William Seibel, Xiaoyu Li, Hui Jin, Yong Han, Songqi Gao, Jianye Zhang, Xujie Liu, Hossein Heidari-Torkabadi, Phoebe L. Stewart, William E. Harte, Gregory P. Tochtrop & Krzysztof Palczewski

Mutations that lead to misfolding of rhodopsin can cause retinitis pigmentosa. Here, the authors carry out a high throughput screen to identify a small molecule chaperone of rod opsin, and show that it protects mouse models of retinitis pigmentosa from retinal degeneration.

17 May 2018 | doi: 10.1038/s41467-018-04261-1
Protein transport  Receptor pharmacology  Retinal diseases 

High-resolution AFM structure of DNA G-wires in aqueous solution OPEN
Krishnashish Bose, Christopher J. Lech, Brahim Heddi & Anh Tuân Phan

DNA and RNA G-quadruplexes can stack to form higher-order structures called G-wires. Here the authors report high-resolution AFM images of higher-order DNA G-quadruplexes in aqueous solution that could impact the design of G-wire based nanodevices and the understanding of G-wires in biology.

17 May 2018 | doi: 10.1038/s41467-018-04016-y
Atomic force microscopy  DNA and RNA 

Elucidating the genetic architecture of reproductive ageing in the Japanese population OPEN
Momoko Horikoshi, Felix R. Day, Masato Akiyama, Makoto Hirata, Yoichiro Kamatani, Koichi Matsuda, Kazuyoshi Ishigaki, Masahiro Kanai, Hollis Wright, Carlos A. Toro, Sergio R. Ojeda, Alejandro Lomniczi, Michiaki Kubo, Ken K. Ong & John. R. B. Perry

The timing of female reproductive capacity is influenced by genetic and environmental factors. Here, in genome-wide association studies, the authors identify genetic loci for age at menarche and onset of menopause in Japanese women, and highlight differences with European populations.

17 May 2018 | doi: 10.1038/s41467-018-04398-z
Endocrine reproductive disorders  Genome-wide association studies 

Light-induced formation of partially reduced oxygen species limits the lifetime of photosystem 1-based biocathodes OPEN
Fangyuan Zhao, Steffen Hardt, Volker Hartmann, Huijie Zhang, Marc M. Nowaczyk, Matthias Rögner, Nicolas Plumeré, Wolfgang Schuhmann & Felipe Conzuelo

Photobiodevices use photosynthetic proteins such as those of the photosystem 1 (PS1) to enable light-induced charge separation, but they suffer from limited long-term stability. Here authors employ scanning photoelectrochemical microscopy on a PS1 biocathode and find that several pathways generate oxygen radicals.

17 May 2018 | doi: 10.1038/s41467-018-04433-z
Bioanalytical chemistry  Biophysics  Energy  Enzymes 

LRRC8/VRAC anion channels enhance β-cell glucose sensing and insulin secretion OPEN
Till Stuhlmann, Rosa Planells-Cases & Thomas J. Jentsch

Insulin secretion by β-cells is stimulated by glucose and is dependent on the induction of β-cell membrane depolarization, mainly driven by the closure of KATP channels, which in turn promotes voltage-gated Ca2+ channel opening. Here the authors show that LRRC8 volume-regulated anion channels (VRACs) modulate glucose-stimulated calcium increase and insulin secretion.

17 May 2018 | doi: 10.1038/s41467-018-04353-y
Homeostasis  Ion channel signalling  Islets of Langerhans 

Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment OPEN
Shazia Ashraf , Hiroki Kudo, Jia Rao, Atsuo Kikuchi, Eugen Widmeier, Jennifer A. Lawson, Weizhen Tan, Tobias Hermle, Jillian K. Warejko, Shirlee Shril, Merlin Airik, Tilman Jobst-Schwan, Svjetlana Lovric, Daniela A. Braun, Heon Yung Gee, David Schapiro, Amar J. Majmundar, Carolin E. Sadowski, Werner L. Pabst, Ankana Daga et al.

Nephrotic syndrome is the second most common chronic kidney disease but there are no targeted treatment strategies available. Here the authors identify mutations of six genes codifying for proteins involved in cytoskeleton remodelling and modulation of small GTPases in 17 families with nephrotic syndrome.

17 May 2018 | doi: 10.1038/s41467-018-04193-w
Genetics  Medical genetics 

Coulombic-enhanced hetero radical pairing interactions OPEN
Xujun Zheng, Yang Zhang, Ning Cao, Xin Li, Shuoqing Zhang, Renfeng Du, Haiying Wang, Zhenni Ye, Yan Wang, Fahe Cao, Haoran Li, Xin Hong, Andrew C.-H. Sue, Chuluo Yang, Wei-Guang Liu & Hao Li

Homo radical spin-pairing interactions between two identical aromatic radicals are common in supramolecular chemistry, but hetero interactions between two different aromatic radicals are seldom observed. Here, the authors find that hetero radical pairing between a radical cation and a radical anion, together with Coulombic attraction, can drive host-guest recognition, representing a new supramolecular recognition motif.

17 May 2018 | doi: 10.1038/s41467-018-04335-0
Interlocked molecules  Self-assembly 

Revealing isoelectronic size conversion dynamics of metal nanoclusters by a noncrystallization approach OPEN
Qiaofeng Yao, Victor Fung, Cheng Sun, Sida Huang, Tiankai Chen, De-en Jiang, Jim Yang Lee & Jianping Xie

How metal nanoclusters evolve in size is poorly understood, particularly at the atomic level. Here, the authors use mass spectrometry to study the size conversion dynamics between two isoelectronic gold nanoclusters with atomic resolution, revealing that the growth reaction proceeds through a distinct balanced equation.

17 May 2018 | doi: 10.1038/s41467-018-04410-6
Inorganic chemistry  Materials chemistry  Nanoscale materials 

X-ray structure of a carpet-like antimicrobial defensin–phospholipid membrane disruption complex OPEN
Michael Järvå, Fung T. Lay, Thanh Kha Phan, Cassandra Humble, Ivan K. H. Poon, Mark R. Bleackley, Marilyn A. Anderson, Mark D. Hulett & Marc Kvansakul

Defensins are cationic antimicrobial peptides that permeabilize membranes of pathogens presumably via the assembly of defensin–lipid oligomers. Here authors provide evidence for this by solving the crystal structure of a plant defensin in an oligomeric state with phospholipids.

17 May 2018 | doi: 10.1038/s41467-018-04434-y
Antimicrobial responses  X-ray crystallography 

Stereodivergent synthesis of vicinal quaternary-quaternary stereocenters and bioactive hyperolactones OPEN
Haifeng Zheng, Yan Wang, Chaoran Xu, Xi Xu, Lili Lin, Xiaohua Liu & Xiaoming Feng

Stereodivergent construction of adjacent quaternary-quaternary stereocenters remains a formidable synthetic challenge. Here, the authors report a nickel-catalyzed enantioselective dearomatization Claisen rearrangement leading to vicinal all-carbon stereocentres and apply it to the stereodivergent synthesis of bioactive hyperolactones.

17 May 2018 | doi: 10.1038/s41467-018-04123-w
Homogeneous catalysis  Synthetic chemistry methodology  Natural product synthesis 

Single cell analysis of kynurenine and System L amino acid transport in T cells OPEN
Linda V. Sinclair, Damien Neyens, George Ramsay, Peter M. Taylor & Doreen A. Cantrell

Kynurenine is an immunomodulatory aryl hydrocarbon receptor (AHR) ligand. Here the authors show, using a new flow cytometry based method, that kynurenine needs to be transported across the plasma membrane of activated T cells by the transporter protein SLC7A5 to activate the AHR.

17 May 2018 | doi: 10.1038/s41467-018-04366-7
Biochemistry  Cell biology  Flow cytometry  T cells 

CD4+ T cells are activated in regional lymph nodes and migrate to skin to initiate lymphedema OPEN
Gabriela D. García Nores, Catherine L. Ly, Daniel A. Cuzzone, Raghu P. Kataru, Geoffrey E. Hespe, Jeremy S. Torrisi, Jung Ju Huang, Jason C. Gardenier, Ira L. Savetsky, Matthew D. Nitti, Jessie Z. Yu, Sonia Rehal & Babak J. Mehrara

CD4+ T cells are critical for the development of lymphedema. Here the authors show how these cells contribute to lymphedema and identify that the sphingosine-1-phosphate receptor modulator FTY720 can prevent lymphedema in a mouse tail injury model by blocking the release of CD4+ T cells from the lymph nodes to the skin.

17 May 2018 | doi: 10.1038/s41467-018-04418-y
CD4-positive T cells  Skin diseases 

Calreticulin and integrin alpha dissociation induces anti-inflammatory programming in animal models of inflammatory bowel disease OPEN
Masayoshi Ohkuro , Jun-Dal Kim, Yoshikazu Kuboi, Yuki Hayashi, Hayase Mizukami, Hiroko Kobayashi-Kuramochi, Kenzo Muramoto, Manabu Shirato, Fumiko Michikawa-Tanaka, Jun Moriya, Teruya Kozaki, Kazuma Takase, Kenichi Chiba, Kishan Lal Agarwala, Takayuki Kimura, Makoto Kotake, Tetsuya Kawahara, Naoki Yoneda, Shinsuke Hirota, Hiroshi Azuma et al.

Inflammatory bowel disease (IBD) is initiated by integrins-mediated leukocyte adhesion to the activated colonic microvascular endothelium. Here, the authors show that inhibition of the calreticulin binding to integrin α subunits ameliorates the severity of IBD in animal models.

17 May 2018 | doi: 10.1038/s41467-018-04420-4
Inflammatory bowel disease  Target validation 

CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation OPEN
Daisuke Miki, Wenxin Zhang, Wenjie Zeng, Zhengyan Feng & Jian-Kang Zhu

Efficient gene targeting in higher plants remains challenging. Here, the authors develop a sequential transformation method for CRISPR/Cas9-mediated gene targeting in Arabidopsis and demonstrate its functionality at five genomic sites in two endogenous loci.

17 May 2018 | doi: 10.1038/s41467-018-04416-0
CRISPR-Cas9 genome editing  Genetic engineering  Molecular engineering in plants 
 
  Latest Correspondence    
 
Hamiltonian path analysis of viral genomes OPEN
Reidun Twarock, German Leonov & Peter G. Stockley
22 May 2018 | doi: 10.1038/s41467-018-03713-y
Molecular modelling  Virus structures 
 
  Latest Author Corrections    
 
Author Correction: Atomic-resolution three-dimensional hydration structures on a heterogeneously charged surface OPEN
Kenichi Umeda, Lidija Zivanovic, Kei Kobayashi, Juha Ritala, Hiroaki Kominami, Peter Spijker, Adam S. Foster & Hirofumi Yamada
23 May 2018 | doi: 10.1038/s41467-018-04401-7
Atomic force microscopy  Characterization and analytical techniques  Molecular dynamics  Scanning probe microscopy 

Author Correction: A RAB35-p85/PI3K axis controls oscillatory apical protrusions required for efficient chemotactic migration OPEN
Salvatore Corallino, Chiara Malinverno, Beate Neumann, Christian Tischer, Andrea Palamidessi, Emanuela Frittoli, Magdalini Panagiotakopoulou, Andrea Disanza, Gema Malet-Engra, Paulina Nastaly, Camilla Galli, Chiara Luise, Giovanni Bertalot, Salvatore Pece, Pier Paolo Di Fiore, Nils Gauthier, Aldo Ferrari, Paolo Maiuri & Giorgio Scita
22 May 2018 | doi: 10.1038/s41467-018-04515-y
Chemotaxis  Growth factor signalling  Mesenchymal migration 

Author Correction: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development OPEN
Mingtang Xie, Hongyu Chen, Ling Huang, Ryan C. O’Neil, Maxim N. Shokhirev & Joseph R. Ecker
22 May 2018 | doi: 10.1038/s41467-018-04514-z
Cytokinin  Shoot apical meristem 

Author Correction: Biochemical phosphates observed using hyperpolarized 31P in physiological aqueous solutions OPEN
Atara Nardi-Schreiber, Ayelet Gamliel, Talia Harris, Gal Sapir, Jacob Sosna, J. Moshe Gomori & Rachel Katz-Brull
22 May 2018 | doi: 10.1038/s41467-018-04538-5
Biophysics  Diagnostic markers 

Author Correction: Small-molecule TFEB pathway agonists that ameliorate metabolic syndrome in mice and extend C. elegans lifespan OPEN
21 May 2018 | doi: 10.1038/s41467-018-04519-8
Haematological cancer 
 
  Latest Publisher Corrections    
 
Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage OPEN
Marcus J. G. W. Ladds , Ingeborg M. M. van Leeuwen, Catherine J. Drummond, Su Chu, Alan R. Healy, Gergana Popova, Andrés Pastor Fernández, Tanzina Mollick, Suhas Darekar, Saikiran K. Sedimbi, Marta Nekulova, Marijke C. C. Sachweh, Johanna Campbell, Maureen Higgins, Chloe Tuck, Mihaela Popa, Mireia Mayoral Safont, Pascal Gelebart, Zinayida Fandalyuk, Alastair M. Thompson et al.
22 May 2018 | doi: 10.1038/s41467-018-04198-5
Drug development  Mechanism of action  Small molecules  Target identification 

Publisher Correction: Aerodynamic generation of electric fields in turbulence laden with charged inertial particles OPEN
M. Di Renzo & J. Urzay
21 May 2018 | doi: 10.1038/s41467-018-04545-6
Aerospace engineering  Fluid dynamics  Mathematics and computing  Mechanical engineering 
 
 

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