Wednesday, July 18, 2018

Nature Communications - 18 July 2018

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18 July 2018 
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Professor Mark Ferguson, Director-General of Science Foundation Ireland explains why he's looking to attract researchers to work in Ireland.

With access to funding from the Irish Government and industry, it's a great time to think about moving. 

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  Latest Comments    
The prescience of paleoclimatology and the future of the Antarctic ice sheet OPEN
Eric J. Steig & Peter D. Neff
16 July 2018 | doi: 10.1038/s41467-018-05001-1
Cryospheric science  Palaeoclimate 

Hydrology and the future of the Greenland Ice Sheet OPEN
Gwenn E. Flowers
16 July 2018 | doi: 10.1038/s41467-018-05002-0
Climate change  Cryospheric science  Hydrology 

The paradigm shift in Antarctic ice sheet modelling OPEN
Frank Pattyn
16 July 2018 | doi: 10.1038/s41467-018-05003-z
Cryospheric science  Palaeoclimate 
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Task-induced brain state manipulation improves prediction of individual traits OPEN
Abigail S. Greene, Siyuan Gao, Dustin Scheinost & R. Todd Constable

Decoding or predicting cognitive traits from brain activity is an exciting prospect. Here, the authors show that task-based functional connectivity better predicts intelligence-related measures than rest-based connectivity, suggesting that cognitive tasks amplify individual differences in trait-relevant circuitry.

18 July 2018 | doi: 10.1038/s41467-018-04920-3
Intelligence  Network models  Neural circuits 

The solute carrier SLC9C1 is a Na+/H+-exchanger gated by an S4-type voltage-sensor and cyclic-nucleotide binding OPEN
F. Windler, W. Bönigk, H. G. Körschen, E. Grahn, T. Strünker, R. Seifert & U. B. Kaupp

The sperm-specific solute carrier SLC9C1 is a phylogenetic chimaera that carries a voltage-sensing (VSD) and a cyclic nucleotide-binding domain (CNBD). Here authors show by electrophysiology and fluorimetry that SLC9C1 is a genuine Na+/H+ exchanger gated by voltage and cAMP.

18 July 2018 | doi: 10.1038/s41467-018-05253-x
Ion channels  Membrane biophysics  Molecular biophysics 

Slow thermal equilibration in methylammonium lead iodide revealed by transient mid-infrared spectroscopy OPEN
Peijun Guo, Jue Gong, Sridhar Sadasivam, Yi Xia, Tze-Bin Song, Benjamin T. Diroll, Constantinos C. Stoumpos, John B. Ketterson, Mercouri G. Kanatzidis, Maria K. Y. Chan, Pierre Darancet, Tao Xu & Richard D. Schaller

Hybrid organic-inorganic perovskites are emerging materials for efficient photovoltaics; however understanding how charge/heat dissipates inside the material remains a challenge. Here, the authors use a spectroscopic approach to observe unusually slow thermal equilibration between the organic and inorganic components.

18 July 2018 | doi: 10.1038/s41467-018-05015-9
Atomistic models  Condensed-matter physics  Materials for energy and catalysis  Optical spectroscopy 

Bistable and photoswitchable states of matter OPEN
Brady T. Worrell, Matthew K. McBride, Gayla B. Lyon, Lewis M. Cox, Chen Wang, Sudheendran Mavila, Chern-Hooi Lim, Hannah M. Coley, Charles B. Musgrave, Yifu Ding & Christopher N. Bowman

Polymers cross-linked with dynamic bonds can switch the phase from solid to fluid upon stimulus but return quickly to the solid state once the stimulus is removed. Here the authors report a light triggered permanent solid to fluid transition at room temperature with inherent spatiotemporal control in either direction

18 July 2018 | doi: 10.1038/s41467-018-05300-7
Mechanical properties  Organic molecules in materials science  Polymers 

Attosecond time-resolved photoelectron holography OPEN
G. Porat, G. Alon, S. Rozen, O. Pedatzur, M. Krüger, D. Azoury, A. Natan, G. Orenstein, B. D. Bruner, M. J. J. Vrakking & N. Dudovich

Field induced tunneling is one of the fundamental processes of light-matter interaction. Here the authors reconstruct the  temporal properties of tunneling using two-color electron holography with attosecond time resolution using argon atoms.

18 July 2018 | doi: 10.1038/s41467-018-05185-6
Atom optics  Nonlinear optics 

Bilophila wadsworthia aggravates high fat diet induced metabolic dysfunctions in mice OPEN
Jane M. Natividad, Bruno Lamas, Hang Phuong Pham, Marie-Laure Michel, Dominique Rainteau, Chantal Bridonneau, Gregory da Costa, Johan van Hylckama Vlieg, Bruno Sovran, Celia Chamignon, Julien Planchais, Mathias L. Richard, Philippe Langella, Patrick Veiga & Harry Sokol

Lipid intake is known to promote Bilophila wadsworthia growth. Here the authors show that B. wadsworthia aggravates high fat diet induced metabolic dysfunctions and its suppression, both pharmacologically or mediated by Lactobacillus rhamnosus, limits the severity of metabolic impairment.

18 July 2018 | doi: 10.1038/s41467-018-05249-7
Metabolic syndrome  Microbiome 

Caspases maintain tissue integrity by an apoptosis-independent inhibition of cell migration and invasion OPEN
Anna Gorelick-Ashkenazi, Ron Weiss, Lena Sapozhnikov, Anat Florentin, Lama Tarayrah-Ibraheim, Dima Dweik, Keren Yacobi-Sharon & Eli Arama

In addition to regulating programmed cell death, caspases also have non-apoptotic roles. Here, the authors show that low level caspase activity prevents cell migration to maintain tissue integrity.

18 July 2018 | doi: 10.1038/s41467-018-05204-6
Apoptosis  Cell invasion 

Nano-photosensitizer based on layered double hydroxide and isophthalic acid for singlet oxygenation and photodynamic therapy OPEN
Rui Gao, Xuan Mei, Dongpeng Yan, Ruizheng Liang & Min Wei

Usually, several components are needed for efficient 2-photon photodynamic therapy (PDT). Here, the authors sandwiched carboxylic acids between layered double hydroxide nanosheets to obtain a single-handed biocompatible photosensitizer that generates singlet oxygen in high quantum yield.

18 July 2018 | doi: 10.1038/s41467-018-05223-3
Biomedical materials  Nanotechnology in cancer  Targeted therapies 

Thermal sensitivity of CO2 and CH4 emissions varies with streambed sediment properties OPEN
Sophie A. Comer-Warner, Paul Romeijn, Daren C. Gooddy, Sami Ullah, Nicholas Kettridge, Benjamin Marchant, David M. Hannah & Stefan Krause

Rivers and streams are important sources of carbon dioxide and methane; however, the drivers of these streambed gas fluxes are poorly understood. Here, the authors show that temperature sensitivity of streambed greenhouse gas emissions varies with substrate, organic matter content and geological origin.

18 July 2018 | doi: 10.1038/s41467-018-04756-x
Carbon cycle  Geochemistry  Hydrology 

High climate model dependency of Pliocene Antarctic ice-sheet predictions OPEN
Aisling M. Dolan, Bas de Boer, Jorge Bernales, Daniel J. Hill & Alan M. Haywood

Ice sheet models forced by climate model output indicate ice-sheet retreat during the Pliocene, yet concerns remain regarding potential model bias. Here, the authors present results from the Pliocene Ice-sheet Modelling Intercomparison Project, and show that results are highly dependent on the model forcing used.

18 July 2018 | doi: 10.1038/s41467-018-05179-4
Cryospheric science  Palaeoclimate 

Using controlled disorder to probe the interplay between charge order and superconductivity in NbSe2 OPEN
Kyuil Cho, M. Kończykowski, S. Teknowijoyo, M. A. Tanatar, J. Guss, P. B. Gartin, J. M. Wilde, A. Kreyssig, R. J. McQueeney, A. I. Goldman, V. Mishra, P. J. Hirschfeld & R. Prozorov

The interplay between superconductivity and charge density wave (CDW) in 2H-NbSe2 is still not fully understood. Here, Cho et al. use controlled disorder to probe the interplay between these two phases in 2H-NbSe2 and find that superconductivity initially competes with CDW but eventually long-range CDW order assists superconductivity.

18 July 2018 | doi: 10.1038/s41467-018-05153-0
Electronic properties and materials  Superconducting properties and materials 

MreB polymers and curvature localization are enhanced by RodZ and predict E. coli's cylindrical uniformity OPEN
Benjamin P. Bratton, Joshua W. Shaevitz, Zemer Gitai & Randy M. Morgenstein

The actin-like protein MreB coordinates the synthesis of the cell wall, which determines cell shape in bacteria. Here, Bratton et al. show that the transmembrane protein RodZ modulates MreB polymer number and curvature preference, contributing to the cylindrical uniform shape of E. coli cells.

18 July 2018 | doi: 10.1038/s41467-018-05186-5
Cell growth  Cellular microbiology 

A complex of C9ORF72 and p62 uses arginine methylation to eliminate stress granules by autophagy OPEN
Maneka Chitiprolu, Chantal Jagow, Veronique Tremblay, Emma Bondy-Chorney, Geneviève Paris, Alexandre Savard, Gareth Palidwor, Francesca A. Barry, Lorne Zinman, Julia Keith, Ekaterina Rogaeva, Janice Robertson, Mathieu Lavallée-Adam, John Woulfe, Jean-François Couture, Jocelyn Côté & Derrick Gibbings

Many Amyotrophic Lateral Sclerosis (ALS)-linked mutations cause accumulation of stress granules, and most ALS cases are caused by repeat expansions in C9ORF72. Here the authors show that C9ORF72 and the autophagy receptor p62 interact to associate with proteins symmetrically dimethylated on arginines such as FUS, to eliminate stress granules by autophagy.

18 July 2018 | doi: 10.1038/s41467-018-05273-7
Amyotrophic lateral sclerosis  Macroautophagy  Methylation 

Remote C−H functionalization using radical translocating arylating groups OPEN
Florian W. Friese, Christian Mück-Lichtenfeld & Armido Studer

Selective remote functionalization of aliphatic C(sp3)−H bonds is highly challenging and often requires transition metals and/or directing groups. Here, the authors show the γ-arylation of aliphatic alcohols via a two-step radical translocation and subsequent radical aryl migration.

18 July 2018 | doi: 10.1038/s41467-018-05193-6
Synthetic chemistry methodology  Stereochemistry 

The concerted roles of FANCM and Rad52 in the protection of common fragile sites OPEN
Hailong Wang, Shibo Li, Joshua Oaks, Jianping Ren, Lei Li & Xiaohua Wu

Fanconi anemia core proteins have been linked to common fragile site stability. Here the authors shed light into the role of FANCM in common fragile site protection by suppressing double-strand break formation and mitotic recombination.

18 July 2018 | doi: 10.1038/s41467-018-05066-y
DNA recombination  Double-strand DNA breaks 

Propagation topography of redox phase transformations in heterogeneous layered oxide cathode materials OPEN
Linqin Mu, Qingxi Yuan, Chixia Tian, Chenxi Wei, Kai Zhang, Jin Liu, Piero Pianetta, Marca M. Doeff, Yijin Liu & Feng Lin

Here the authors demonstrate a spectroscopic and imaging approach to study redox solid-state phase transformation in lithium ion cathode materials under thermal abuse conditions. The valence curvature of the propagation front alternates as a result of local chemical and structural heterogeneities.

18 July 2018 | doi: 10.1038/s41467-018-05172-x
Batteries  Microscopy 

p38-mediated phosphorylation at T367 induces EZH2 cytoplasmic localization to promote breast cancer metastasis OPEN
Talha Anwar, Caroline Arellano-Garcia, James Ropa, Yu-Chih Chen, Hong Sun Kim, Euisik Yoon, Sierrah Grigsby, Venkatesha Basrur, Alexey I. Nesvizhskii, Andrew Muntean, Maria E. Gonzalez, Kelley M. Kidwell, Zaneta Nikolovska-Coleska & Celina G. Kleer

Polycomb group protein EZH2 is overexpressed in ER- breast cancer, promoting metastasis. Here, the authors show that independent of the polycomb group, phosphorylation of EZH2 at T367 by p38 promotes cytoplasmic localization of EZH2, binding to vinculin and other regulators of cell migration and invasion.

18 July 2018 | doi: 10.1038/s41467-018-05078-8
Metastasis  Oncogenes  Phosphorylation 

TBK-binding protein 1 regulates IL-15-induced autophagy and NKT cell survival OPEN
Lele Zhu, Xiaoping Xie, Lingyun Zhang, Hui Wang, Zuliang Jie, Xiaofei Zhou, Jianhong Shi, Shuli Zhao, Boxiang Zhang, Xuhong Cheng & Shao-Cong Sun

Interleukin-15 (IL-15) regulates the homeostasis of many immune cell types, including natural killer T (NKT) cells, but the underlying mechanism is not completely clear. Here the authors analyse Tbkbp1-deficient mice and show that IL-15 induces Tbkbp1-dependent autophagy to modulate NKT survival.

18 July 2018 | doi: 10.1038/s41467-018-05097-5
Autophagy  Interleukins  NKT cells  Signal transduction 

Nucleoporin 107, 62 and 153 mediate Kcnq1ot1 imprinted domain regulation in extraembryonic endoderm stem cells OPEN
Saqib S. Sachani, Lauren S. Landschoot, Liyue Zhang, Carlee R. White, William A. MacDonald, Michael C. Golding & Mellissa R. W. Mann

Genomic imprinting restricts transcription to predominantly one parental allele. Here the authors perform a screen for epigenetic factors involved in paternal allelic silencing at the Kcnq1ot1 imprinted domain in mouse extraembryonic endoderm stem cells and characterize a role for specific nucleoporins in mediating Kcnq1ot1 imprinted regulation.

18 July 2018 | doi: 10.1038/s41467-018-05208-2
Embryonic stem cells  Imprinting 

Manipulation of facet orientation in hybrid perovskite polycrystalline films by cation cascade OPEN
Guanhaojie Zheng, Cheng Zhu, Jingyuan Ma, Xiaonan Zhang, Gang Tang, Runguang Li, Yihua Chen, Liang Li, Jinsong Hu, Jiawang Hong, Qi Chen, Xingyu Gao & Huanping Zhou

Crystal facet orientations of the polycrystalline hybrid lead halide perovskite thin films play a crucial role in determining the device performance. Here Zheng et al. demonstrate effective control of the crystal stacking mode by cation cascade doping, which promotes the charge transport in the photovoltaic device.

18 July 2018 | doi: 10.1038/s41467-018-05076-w
Devices for energy harvesting  Solar cells 

Unveiling the bosonic nature of an ultrashort few-electron pulse OPEN
Gregoire Roussely, Everton Arrighi, Giorgos Georgiou, Shintaro Takada, Martin Schalk, Matias Urdampilleta, Arne Ludwig, Andreas D. Wieck, Pacome Armagnat, Thomas Kloss, Xavier Waintal, Tristan Meunier & Christopher Bäuerle

Electronic excitations in low-dimensional quantum nanoelectronic devices are collective waves that are strongly affected by the Coulomb interaction. Here, the authors demonstrate that they are able to prepare these collective excitations down to the single electron level and control their propagation.

18 July 2018 | doi: 10.1038/s41467-018-05203-7
Electronic devices  Electronic properties and materials  Semiconductors 

Large ice loss variability at Nioghalvfjerdsfjorden Glacier, Northeast-Greenland OPEN
Christoph Mayer, Janin Schaffer, Tore Hattermann, Dana Floricioiu, Lukas Krieger, Paul A. Dodd, Torsten Kanzow, Carlo Licciulli & Clemens Schannwell

The Greenland Ice Sheet has increasingly lost mass over the past few decades, yet the contribution from glaciers in Northeast Greenland is difficult to quantify. Here, the authors show that the floating part of 79 North Glacier has continuously lost mass since at least 2001, with a very high annual variability.

17 July 2018 | doi: 10.1038/s41467-018-05180-x
Climate-change impacts  Cryospheric science  Physical oceanography 

Exchange-biasing topological charges by antiferromagnetism OPEN
Qing Lin He, Gen Yin, Alexander J. Grutter, Lei Pan, Xiaoyu Che, Guoqiang Yu, Dustin A. Gilbert, Steven M. Disseler, Yizhou Liu, Padraic Shafer, Bin Zhang, Yingying Wu, Brian J. Kirby, Elke Arenholz, Roger K. Lake, Xiaodong Han & Kang L. Wang

Spin-polarized carriers could show an extra Hall component when moving through certain real-space topological spin textures. Here, He et al. report an exchange bias experienced by the topological spin textures living at the interface between a topological insulator and an adjacent antiferromagnet, suggesting a chiral spin texture is induced.

17 July 2018 | doi: 10.1038/s41467-018-05166-9
Magnetic properties and materials  Topological insulators 

Cold deep subduction recorded by remnants of a Paleoproterozoic carbonated slab OPEN
Cheng Xu, Jindřich Kynický, Wenlei Song, Renbiao Tao, Zeng Lü, Yunxiu Li, Yueheng Yang, Miroslav Pohanka, Michaela V. Galiova, Lifei Zhang & Yingwei Fei

The onset of modern-style plate tectonics remains under debate. Here, Xu et al. report a cold thermal-gradient recorded in an eclogite xenolith in Paleoproterozoic carbonatite from orogen, and propose that modern-style subduction has operated since at least the Paleoproterozoic.

17 July 2018 | doi: 10.1038/s41467-018-05140-5
Geology  Petrology 

Observation of nuclear quantum effects and hydrogen bond symmetrisation in high pressure ice OPEN
Thomas Meier, Sylvain Petitgirard, Saiana Khandarkhaeva & Leonid Dubrovinsky

Hydrogen atoms in water ices, under pressures at which they might exist in ocean exoplanets and icy moons, exhibit dynamics that are still poorly understood. Here, 1H-NMR experiments approaching the Mbar range shed light on the symmetrisation of hydrogen bonds preceding and accompanying the transformation of ice VII into ice X.

17 July 2018 | doi: 10.1038/s41467-018-05164-x
Phase transitions and critical phenomena  Planetary science  Solid-state NMR  Structure of solids and liquids 

Insightful classification of crystal structures using deep learning OPEN
Angelo Ziletti, Devinder Kumar, Matthias Scheffler & Luca M. Ghiringhelli

Classifying crystal structures using their space group is important to understand material properties, but the process currently requires user input. Here, the authors use machine learning to automatically classify more than 100,000 simulated perfect and defective crystal structures.

17 July 2018 | doi: 10.1038/s41467-018-05169-6
Applied mathematics  Structural materials  Theory and computation 

APC2 controls dendrite development by promoting microtubule dynamics OPEN
Olga I. Kahn, Philipp Schätzle, Dieudonnée van de Willige, Roderick P. Tas, Feline W. Lindhout, Sybren Portegies, Lukas C. Kapitein & Casper C. Hoogenraad

Microtubules in dendrites are characterized by mixed polarity orientation. Here, the authors show a role for adenomatous polyposis coli 2 (APC2) in regulating dendrite microtubule dynamics and dendrite development.

17 July 2018 | doi: 10.1038/s41467-018-05124-5
Cellular neuroscience  Microtubules  Molecular neuroscience 

Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides OPEN
Rathi Saravanan, Daniel A Holdbrook, Jitka Petrlova, Shalini Singh, Nils A Berglund, Yeu Khai Choong, Sven Kjellström, Peter J Bond, Martin Malmsten & Artur Schmidtchen

Thrombin-derived C-terminal peptides (TCPs) have anti-endotoxic functions in wounds by binding to bacterial lipopolysaccharide (LPS) and Gram-negative bacteria. Here authors use a spectrum of biophysical techniques to determine the conformation of a TCP in complex with LPS and define the interaction between TCPs and CD14.

17 July 2018 | doi: 10.1038/s41467-018-05242-0
Biophysics  Computational biology and bioinformatics  Inflammation  Innate immunity  Molecular biophysics 

Downregulated NDR1 protein kinase inhibits innate immune response by initiating an miR146a-STAT1 feedback loop OPEN
Zhiyong Liu, Qiang Qin, Cheng Wu, Hui Li, Jia’nan Shou, Yuting Yang, Meidi Gu, Chunmei Ma, Wenlong Lin, Yan Zou, Yuanyuan Zhang, Feng Ma, Jihong Sun & Xiaojian Wang

The authors show that NDR1 promotion of STAT1 translation is an important event for IFN-dependent antiviral immune response. These data suggest that NDR1 has an important role in controlling viral infections.

17 July 2018 | doi: 10.1038/s41467-018-05176-7
Antimicrobial responses  Innate immunity  Signal transduction 

Role of disordered bipolar complexions on the sulfur embrittlement of nickel general grain boundaries OPEN
Tao Hu, Shengfeng Yang, Naixie Zhou, Yuanyao Zhang & Jian Luo

Sulfur at nickel grain boundaries can cause catastrophic failure, but the mechanisms behind that embrittlement remain poorly understood. Here, the authors image and model bipolar sulfur–nickel structures at amorphous-like and bilayer-like facets of general grain boundaries that cause embrittlement.

17 July 2018 | doi: 10.1038/s41467-018-05070-2
Atomistic models  Metals and alloys  Phase transitions and critical phenomena 

Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes OPEN
Bruce A. Rheaume, Amyeo Jereen, Mohan Bolisetty, Muhammad S. Sajid, Yue Yang, Kathleen Renna, Lili Sun, Paul Robson & Ephraim F. Trakhtenberg

Retinal ganglion cells (RGCs) are diverse in cellular function and physiology. This study demonstrates additional RGC heterogeneity using single cell transcriptomic analyses to classify 40 classes of RGCs in early postnatal mice before eye opening.

17 July 2018 | doi: 10.1038/s41467-018-05134-3
Cellular neuroscience  Retina  Transcriptomics 

Stromal PTEN determines mammary epithelial response to radiotherapy OPEN
Gina M. Sizemore, Subhasree Balakrishnan, Katie A. Thies, Anisha M. Hammer, Steven T. Sizemore, Anthony J. Trimboli, Maria C. Cuitiño, Sarah A. Steck, Gary Tozbikian, Raleigh D. Kladney, Neelam Shinde, Manjusri Das, Dongju Park, Sarmila Majumder, Shiva Krishnan, Lianbo Yu, Soledad A. Fernandez, Arnab Chakravarti, Peter G. Shields, Julia R. White et al.

The tumor microenvironment influences tumor progression. Here the authors show that lack of stromal PTEN phosphatase induces DNA repair defects in the neighboring mammary gland epithelial cells via hyperactivation of EGF-receptor signaling, resulting in higher radiation-induced DNA damage and hyperplasia.

17 July 2018 | doi: 10.1038/s41467-018-05266-6
Breast cancer  Cancer microenvironment  DNA damage and repair  Radiotherapy 

Self-healing and superstretchable conductors from hierarchical nanowire assemblies OPEN
Pin Song, Haili Qin, Huai-Ling Gao, Huai-Ping Cong & Shu-Hong Yu

Stretchable conductors are important for further developments in the electronics industry, but improving the deformability when maintaining the high-level conductivity is still challenging. Here the authors demonstrate a ternary self-healing silver nanowire/polymer network as high-performance stretchable conductor.

17 July 2018 | doi: 10.1038/s41467-018-05238-w
Composites  Electronic devices  Polymers 

A radical S-adenosyl-L-methionine enzyme and a methyltransferase catalyze cyclopropane formation in natural product biosynthesis OPEN
Wen-Bing Jin, Sheng Wu, Xiao-Hong Jian, Hua Yuan & Gong-Li Tang

The biosynthesis of the antitumour antibiotic CC-1065 includes formation of a cyclopropane. Here, the authors identify the two enzymes that work together to catalyze this reaction, a radical S-adenosyl-l-methionine enzyme and a methyltransferase, and propose a mechanism for the cyclopropanation.

17 July 2018 | doi: 10.1038/s41467-018-05217-1
Biosynthesis  Enzyme mechanisms 

Unconventional fractional quantum Hall states and Wigner crystallization in suspended Corbino graphene OPEN
Manohar Kumar, Antti Laitinen & Pertti Hakonen

Understanding of ordered phases of interacting electrons in 2D systems is a fundamental many-body physics problem. Here, the authors report unconventional fractional quantum Hall phases in graphene Corbino devices originating from residual interactions of composite fermions in partially filled higher Landau levels. They also demonstrate the exceptional strength of the Coulomb interactions in suspended graphene by reaching the field-induced Wigner crystal state.

17 July 2018 | doi: 10.1038/s41467-018-05094-8
Electronic properties and devices  Graphene  Quantum Hall 

Direct observation of DNA target searching and cleavage by CRISPR-Cas12a OPEN
Yongmoon Jeon, You Hee Choi, Yunsu Jang, Jihyeon Yu, Jiyoung Goo, Gyejun Lee, You Kyeong Jeong, Seung Hwan Lee, In-San Kim, Jin-Soo Kim, Cherlhyun Jeong, Sanghwa Lee & Sangsu Bae

Cas12a is a RNA-guided DNA endonuclease whose detailed mechanisms of target searching and DNA cleavage remained unclear. Here authors use single-molecule fluorescence assays to show that Cas12a searches for their on-target site.

17 July 2018 | doi: 10.1038/s41467-018-05245-x
Biophysical chemistry  CRISPR-Cas9 genome editing  Single-molecule biophysics 

Persistent spin texture enforced by symmetry OPEN
L. L. Tao & Evgeny Y. Tsymbal

Persistent spin texture (PST) can generate fascinating physics that is promising for spintronics applications but requires non-trivial sample design. Here the authors alternatively propose that a class of materials has intrinsic PST enforced by the nonsymmorphic space group symmetry of the crystal.

17 July 2018 | doi: 10.1038/s41467-018-05137-0
Electronic properties and materials  Spintronics 

Highly active enzymes by automated combinatorial backbone assembly and sequence design OPEN
Gideon Lapidoth, Olga Khersonsky, Rosalie Lipsh, Orly Dym, Shira Albeck, Shelly Rogotner & Sarel J. Fleishman

Computationally designed enzymes often show lower activity or stability than their natural counterparts. Here, the authors present an evolution-inspired method for automated enzyme design, creating stable enzymes with accurate active site architectures and wild-type-like activities.

17 July 2018 | doi: 10.1038/s41467-018-05205-5
Enzymes  Molecular modelling  Protein design  X-ray crystallography 

Integrated genetic and epigenetic analysis of myxofibrosarcoma OPEN
Koichi Ogura, Fumie Hosoda, Yasuhito Arai, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Momoko Nagai, Mamoru Kato, Erika Arakawa, Wakako Mukai, Hirofumi Rokutan, Akira Kawai, Sakae Tanaka & Tatsuhiro Shibata

Myxofibrosarcoma occurs in adults and is associated with high local relapse. Here, based on exome/transcriptome sequencing and DNA methylation analysis, the authors identify driver genes and methylation clusters associated with unique combinations of mutations, outcomes, and immune cell compositions.

17 July 2018 | doi: 10.1038/s41467-018-03891-9
Cancer genomics  Sarcoma 

Mie-coupled bound guided states in nanowire geometric superlattices OPEN
Seokhyoung Kim, Kyoung-Ho Kim, David J. Hill, Hong-Gyu Park & James F. Cahoon

The utility of nanowires for all-optical operation has been limited by a lack of coupling scheme with band selectivity. Here, the authors introduce a nanowire geometric superlattice that allows controlled, narrow-band guiding in silicon nanowires through direct coupling of a Mie resonance with a bound guided state.

17 July 2018 | doi: 10.1038/s41467-018-05224-2
Integrated optics  Nanowires  Optical physics  Optoelectronic devices and components 

The replication initiation determinant protein (RepID) modulates replication by recruiting CUL4 to chromatin OPEN
Sang-Min Jang, Ya Zhang, Koichi Utani, Haiqing Fu, Christophe E. Redon, Anna B. Marks, Owen K. Smith, Catherine J. Redmond, Adrian M. Baris, Danielle A. Tulchinsky & Mirit I. Aladjem

RepID has previously been shown to promote origin firing. Here the authors reveal that RepID regulates replication origins via the recruitment of the CRL4 complex, and prevents re-initiation and unscheduled DNA replication.

17 July 2018 | doi: 10.1038/s41467-018-05177-6
Cancer therapy  DNA replication  Origin firing  Protein–protein interaction networks  Ubiquitylation 

An intercross population study reveals genes associated with body size and plumage color in ducks OPEN
Zhengkui Zhou, Ming Li, Hong Cheng, Wenlei Fan, Zhengrong Yuan, Qiang Gao, Yaxi Xu, Zhanbao Guo, Yunsheng Zhang, Jian Hu, Hehe Liu, Dapeng Liu, Weihuang Chen, Zhuqing Zheng, Yong Jiang, Zhiguo Wen, Yongming Liu, Hua Chen, Ming Xie, Qi Zhang et al.

Ducks, one of the most common domestic fowls, originated from mallards. Here, the authors perform whole-genome sequencing of mallards, indigenous-breed ducks, and Pekin ducks, as well as 1026 ducks from a population generated by wild × domestic crosses to identify selection signals and map variants associated with body size and plumage color.

17 July 2018 | doi: 10.1038/s41467-018-04868-4
Animal breeding  Genome evolution  Population genetics 

Cell fate potentials and switching kinetics uncovered in a classic bistable genetic switch OPEN
Xiaona Fang, Qiong Liu, Christopher Bohrer, Zach Hensel, Wei Han, Jin Wang & Jie Xiao

Bistable switches are a common regulatory motif in cell fate decision-making circuits with two mutually exclusive expression states. Here the authors develop a bistable reporter system and report two additional expression states.

17 July 2018 | doi: 10.1038/s41467-018-05071-1
Gene regulatory networks  Genetic circuit engineering  Single-molecule biophysics 

Thresholds of lake and reservoir connectivity in river networks control nitrogen removal OPEN
Noah M. Schmadel, Judson W. Harvey, Richard B. Alexander, Gregory E. Schwarz, Richard B. Moore, Ken Eng, Jesus D. Gomez-Velez, Elizabeth W. Boyer & Durelle Scott

Lakes, reservoirs, and other ponded waters are common in large river basins yet their influence on nitrogen budgets is often indistinct. Here, the authors show how a ponded waters’ relative size, shape, and degree of connectivity to the river network control nitrogen removal.

17 July 2018 | doi: 10.1038/s41467-018-05156-x
Element cycles  Environmental sciences  Hydrology 

Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals OPEN
Giulia I. M. Pasquesi, Richard H. Adams, Daren C. Card, Drew R. Schield, Andrew B. Corbin, Blair W. Perry, Jacobo Reyes-Velasco, Robert P. Ruggiero, Michael W. Vandewege, Jonathan A. Shortt & Todd A. Castoe

Large-scale patterns of genomic repeat element evolution have been studied mainly in birds and mammals. Here, the authors analyze the genomes of over 60 squamate reptiles and show high variation in repeat elements compared to mammals and birds, and particularly high microsatellite seeding in snakes.

17 July 2018 | doi: 10.1038/s41467-018-05279-1
Comparative genomics  Genome evolution  Mobile elements  Molecular evolution 

Water-dispersible PEG-curcumin/amine-functionalized covalent organic framework nanocomposites as smart carriers for in vivo drug delivery OPEN
Guiyang Zhang, Xinle Li, Qiaobo Liao, Yanfeng Liu, Kai Xi, Wenyu Huang & Xudong Jia

Despite their potential application as drug-delivery carriers, covalent organic frameworks (COF) have been only evaluated in vitro. Here the authors show by real time tracking in vivo the cell uptake of anticancer-drug loaded and water dispersible COFs.

17 July 2018 | doi: 10.1038/s41467-018-04910-5
Biosurfaces  Chemical modification  Drug delivery 

A potentially abundant junctional RNA motif stabilized by m6A and Mg2+ OPEN
Bei Liu, Dawn K. Merriman, Seung H. Choi, Maria A. Schumacher, Raphael Plangger, Christoph Kreutz, Stacy M. Horner, Kate D. Meyer & Hashim M. Al-Hashimi

N6-Methyladenosine (m6A) is a post-transcriptional RNA modification that modulates RNA structure through a destabilization of m6A base pairing. Here the authors use NMR and UV melting experiments and show that m6A can also stabilize m6A–U base pairs and global RNA structure when positioned adjacent to a 5ʹ bulge.

17 July 2018 | doi: 10.1038/s41467-018-05243-z
RNA  Solution-state NMR 

Adding chemically selective subtraction to multi-material 3D additive manufacturing OPEN
David Gräfe, Andreas Wickberg, Markus Michael Zieger, Martin Wegener, Eva Blasco & Christopher Barner-Kowollik

Subtractive manufacturing of microstructures is important for many applications, yet photoresists for 3D laser lithography allow only removal after development under harsh cleavage conditions. Here, the authors introduce a set of chemoselective cleavable photoresists allowing the orthogonal cleavage of microstructures under mild conditions.

17 July 2018 | doi: 10.1038/s41467-018-05234-0
Organic–inorganic nanostructures  Polymer synthesis  Synthesis and processing 

A TRAF3-NIK module differentially regulates DNA vs RNA pathways in innate immune signaling OPEN
Kislay Parvatiyar, Jose Pindado, Anurupa Dev, Saba Roghiyh Aliyari, Shivam A. Zaver, Hoda Gerami, Maxime Chapon, Amir A. Ghaffari, Anant Dhingra & Genhong Cheng

The innate immunity system detects viral pathogens by sensing viral DNA or RNA via distinct pathways, but whether these pathways cross-regulate is unclear. Here the authors show that TRAF3, a known regulator of the RNA-sensing pathway, modulates an NF-κB activator NIK to control DNA-sensing by the adaptor STING in immune cells.

17 July 2018 | doi: 10.1038/s41467-018-05168-7
Infection  NF-kappaB  Pattern recognition receptors  RIG-I-like receptors 

Dynamic and programmable morphology and size evolution via a living hierarchical self-assembly strategy OPEN
Xing Wang, Peiyuan Gao, Yanyu Yang, Hongxia Guo & Decheng Wu

Controlling shape-shift and size-growth in nanostructures are important developments in nanoscience but controlling morphology change with an instant on/off function remains challenging. Here the authors demonstrate control over morphology and size transformation of POSS molecules based on living thiol-disulfide exchange reactions.

17 July 2018 | doi: 10.1038/s41467-018-05142-3
Self-assembly  Supramolecular polymers 

Creating two self-assembly micro-environments to achieve supercrystals with dual structures using polyhedral nanoparticles OPEN
Yih Hong Lee, Chee Leng Lay, Wenxiong Shi, Hiang Kwee Lee, Yijie Yang, Shuzhou Li & Xing Yi Ling

Crystals with multiple structures often perform special functions in nature, inspiring the creation of synthetic analogues. Here, the authors subject polyhedral nanoparticles to two self-assembly micro-environments to realize supercrystals with dual structures, in which the order of the surface layer differs from the bulk structure.

17 July 2018 | doi: 10.1038/s41467-018-05102-x
Nanoparticles  Self-assembly  SERS 

Injectable antibacterial conductive nanocomposite cryogels with rapid shape recovery for noncompressible hemorrhage and wound healing OPEN
Xin Zhao, Baolin Guo, Hao Wu, Yongping Liang & Peter X. Ma

To improve trauma survival and surgical outcomes, hemostatic agents are needed. Here, the authors report on the development of injectable, biocompatible carbon nanotube reinforced quaternized chitosan cryogels with shape memory, conductivity and antibacterial properties for hemostatic control.

17 July 2018 | doi: 10.1038/s41467-018-04998-9
Biomaterials  Biomedical materials  Tissue engineering 

Mechanical architecture and folding of E. coli type 1 pilus domains OPEN
Alvaro Alonso-Caballero, Jörg Schönfelder, Simon Poly, Fabiano Corsetti, David De Sancho, Emilio Artacho & Raul Perez-Jimenez

The pilus type 1 of uropathogenic E. coli must resist mechanical forces to remain attached to the epithelium. Here the authors use single-molecule force spectroscopy to demonstrate a hierarchy of mechanical stability among the pilus domains and show that the oxidoreductase DsbA also acts as a folding chaperone on the domains.

16 July 2018 | doi: 10.1038/s41467-018-05107-6
Biophysics  Protein folding 

Microscale ecology regulates particulate organic matter turnover in model marine microbial communities OPEN
Tim N. Enke, Gabriel E. Leventhal, Matthew Metzger, José T. Saavedra & Otto X. Cordero

Particle-attached bacteria play a key ecosystem role by degrading complex organic materials in the ocean. Here, the authors use model marine microbial communities to show that community composition and interspecies interactions can significantly slowdown the rates of particle turnover in the environment.

16 July 2018 | doi: 10.1038/s41467-018-05159-8
Carbon cycle  Ecology  Microbiology 

Neutralizing negative epigenetic regulation by HDAC5 enhances human haematopoietic stem cell homing and engraftment OPEN
Xinxin Huang, Bin Guo, Sheng Liu, Jun Wan & Hal E. Broxmeyer

Enhancement of haematopoietic stem cell (HSC) homing and engraftment is critical for haematopoietic cell transplantation. Here, the authors find that HDAC5 inhibition enhances HSC homing and engraftment by increasing p65 acetylation and enhancing NF-kB mediated CXCR4 transcription.

16 July 2018 | doi: 10.1038/s41467-018-05178-5
Cell biology  Chemotaxis  Haematopoietic stem cells 

CD32 expression is associated to T-cell activation and is not a marker of the HIV-1 reservoir OPEN
Roger Badia, Ester Ballana, Marc Castellví, Edurne García-Vidal, Maria Pujantell, Bonaventura Clotet, Julia G. Prado, Jordi Puig, Miguel A. Martínez, Eva Riveira-Muñoz & José A. Esté

CD32 has been previously shown to be expressed preferentially by CD4 T cells latently harbouring HIV-1. Here the authors show that CD32 expression in CD4 T cells is associated with T cell activation, is up-regulated by HIV-1 infection and importantly does not appear to represent an enriched cellular niche for latent HIV-1.

16 July 2018 | doi: 10.1038/s41467-018-05157-w
CD4-positive T cells  HIV infections  Retrovirus 

TMEM106B drives lung cancer metastasis by inducing TFEB-dependent lysosome synthesis and secretion of cathepsins OPEN
Samrat T. Kundu, Caitlin L. Grzeskowiak, Jared J. Fradette, Laura A. Gibson, Leticia B. Rodriguez, Chad J. Creighton, Kenneth L. Scott & Don L. Gibbons

One of the major causes of cancer-related mortality is represented by metastatic lung cancer. Here the authors characterize the role of TMEM106B in driving metastatic lung adenocarcinoma and suggest that TMEM106B-mediated secretion of cathespin impacts cell migration and invasion of lung cancer cells, increasing metastatic spreading.

16 July 2018 | doi: 10.1038/s41467-018-05013-x
Metastasis  Non-small-cell lung cancer 

In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer OPEN
Caitlin L. Grzeskowiak, Samrat T. Kundu, Xiulei Mo, Andrei A. Ivanov, Oksana Zagorodna, Hengyu Lu, Richard H. Chapple, Yiu Huen Tsang, Daniela Moreno, Maribel Mosqueda, Karina Eterovic, Jared J. Fradette, Sumreen Ahmad, Fengju Chen, Zechen Chong, Ken Chen, Chad J. Creighton, Haian Fu, Gordon B. Mills, Don L. Gibbons et al.

KRAS-driven lung cancers represent an aggressive form of NSCLC. In this study the authors perform an in vivo functional screening and identify GATAD2B as a driver of tumor growth and metastasis in KRAS-driven lung cancer.

16 July 2018 | doi: 10.1038/s41467-018-04572-3
Cancer  Cancer genetics 

Fe-N system at high pressure reveals a compound featuring polymeric nitrogen chains OPEN
M. Bykov, E. Bykova, G. Aprilis, K. Glazyrin, E. Koemets, I. Chuvashova, I. Kupenko, C. McCammon, M. Mezouar, V. Prakapenka, H.-P. Liermann, F. Tasnádi, A. V. Ponomareva, I. A. Abrikosov, N. Dubrovinskaia & L. Dubrovinsky

Owing to the energetic nature of N–N bonds, poly-nitrogen compounds are considered promising high energy density materials. Here, the authors synthesize three iron–nitrogen compounds at high pressure, including FeN4, which features polymeric nitrogen chains of [N42−]n units.

16 July 2018 | doi: 10.1038/s41467-018-05143-2
Chemical bonding  Solid-phase synthesis  Solid-state chemistry 

Multi-omics monitoring of drug response in rheumatoid arthritis in pursuit of molecular remission OPEN
Shinya Tasaki, Katsuya Suzuki, Yoshiaki Kassai, Masaru Takeshita, Atsuko Murota, Yasushi Kondo, Tatsuya Ando, Yusuke Nakayama, Yuumi Okuzono, Maiko Takiguchi, Rina Kurisu, Takahiro Miyazaki, Keiko Yoshimoto, Hidekata Yasuoka, Kunihiro Yamaoka, Rimpei Morita, Akihiko Yoshimura, Hiroyoshi Toyoshiba & Tsutomu Takeuchi

Little information is available on molecular changes in response to treatment of rheumatoid arthritis (RA). Here the authors report a multi-omics study collecting patients' transcriptome, proteome, and immunophenotype data to help understand the impact of drug treatments on RA molecular phenotypes.

16 July 2018 | doi: 10.1038/s41467-018-05044-4
Biomarkers  Predictive medicine  Rheumatoid arthritis 

TCM visualizes trajectories and cell populations from single cell data OPEN
Wuming Gong, Il-Youp Kwak, Naoko Koyano-Nakagawa, Wei Pan & Daniel J. Garry

Time series single cell expression data has large variance between time points and is challenging for analysis. Here, the authors develop a new dimension reduction and data visualization tool for large scale temporal scRNA-seq data which identifies trajectories and subpopulations.

16 July 2018 | doi: 10.1038/s41467-018-05112-9
Developmental biology  Statistical methods  Systems biology 

Hippocampal projections to the anterior olfactory nucleus differentially convey spatiotemporal information during episodic odour memory OPEN
Afif J. Aqrabawi & Jun Chul Kim

Hippocampus is necessary for integrating the context with sensory cues to retrieve memory for unique episodes. Here, the authors show that inhibiting topographically organized projections from hippocampus to the anterior olfactory nucleus independently impairs spatial and temporal odour memory recall.

16 July 2018 | doi: 10.1038/s41467-018-05131-6
Hippocampus  Neural circuits  Olfactory cortex 

Intrinsically ionic conductive cellulose nanopapers applied as all solid dielectrics for low voltage organic transistors OPEN
Shilei Dai, Yingli Chu, Dapeng Liu, Fei Cao, Xiaohan Wu, Jiachen Zhou, Bilei Zhou, Yantao Chen & Jia Huang

Next-generation organic electronics require flexible organic field effect transistors that show low-voltage operation and are biodegradable. Here, Huang and co-workers demonstrate high-performance transistors that utilize solid-state ionic conductive cellulose nanopaper as the dielectric.

16 July 2018 | doi: 10.1038/s41467-018-05155-y
Electronic devices  Electronic properties and materials 

Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota OPEN
Lingfei Hu, Christelle A. M. Robert, Selma Cadot, Xi Zhang, Meng Ye, Beibei Li, Daniele Manzo, Noemie Chervet, Thomas Steinger, Marcel G. A. van der Heijden, Klaus Schlaeppi & Matthias Erb

Plants can modify soil microbiota through root exudation, but how this process influences plant health in turn is often unclear. Here, Hu et al. show that maize benzoxazinoids released into the soil modify root-associated microbiota and thereby increase leaf defenses of the next plant generation.

16 July 2018 | doi: 10.1038/s41467-018-05122-7
Biotic  Microbiome  Secondary metabolism 

Different population dynamics in the supplementary motor area and motor cortex during reaching OPEN
A. H. Lara, J. P. Cunningham & M. M. Churchland

Population activity dynamics underlie many neural computations. Here the authors develop a novel hypothesis-guided dimensionality reduction approach that reveals very different population dynamics in the SMA and M1, despite superficially similar single-neuron responses.

16 July 2018 | doi: 10.1038/s41467-018-05146-z
Motor cortex  Premotor cortex 

Self-hydrogenated shell promoting photocatalytic H2 evolution on anatase TiO2 OPEN
Yue Lu, Wen-Jin Yin, Kai-Lin Peng, Kuan Wang, Qi Hu, Annabella Selloni, Fu-Rong Chen, Li-Min Liu & Man-Ling Sui

Photocatalytic water splitting on TiO2 is a promising route to H2 fuel production, but the mechanistic pathway at the water–TiO2 interface remains poorly understood. Here, using liquid environmental TEM and first-principles calculations, the authors unveil the formation of a self-hydrogenated shell on the TiO2 surface that further promotes H2 production.

16 July 2018 | doi: 10.1038/s41467-018-05144-1
Characterization and analytical techniques  Nanoparticles  Photocatalysis 

Insulin/Snail1 axis ameliorates fatty liver disease by epigenetically suppressing lipogenesis OPEN
Yan Liu, Lin Jiang, Chengxin Sun, Nicole Ireland, Yatrik M. Shah, Yong Liu & Liangyou Rui

Insulin promotes lipogenesis but, on the other hand, insulin resistance is associated with increased lipogenesis in the liver. Here the authors show that Snail1 is upregulated by insulin and inhibits lipogenesis by repressing Fasn expression but insulin-mediated Snail1 upregulation is impaired during obesity and insulin resistance.

16 July 2018 | doi: 10.1038/s41467-018-05309-y
Fatty acids  Hepatocytes  Insulin signalling  Non-alcoholic fatty liver disease 

Differential cell-intrinsic regulations of germinal center B and T cells by miR-146a and miR-146b OPEN
Sunglim Cho, Hyang-Mi Lee, I-Shing Yu, Youn Soo Choi, Hsi-Yuan Huang, Somaye Sadat Hashemifar, Ling-Li Lin, Mei-Chi Chen, Nikita D. Afanasiev, Aly Azeem Khan, Shu-Wha Lin, Alexander Y. Rudensky, Shane Crotty & Li-Fan Lu

In the germinal center (GC), B and T cells interact to induce the production of protective antibodies against threats. Here the authors show that microRNA miR-146a modulates CD40 signaling in GC B cells, while both miR-146a and miR-146b synergize to control GC T cell responses, thereby implicating intricate controls of GC response by miR-146.

16 July 2018 | doi: 10.1038/s41467-018-05196-3
Gene regulation in immune cells  Germinal centres  Humoral immunity  miRNA in immune cells 

Intravital imaging-based analysis tools for vessel identification and assessment of concurrent dynamic vascular events OPEN
Naoki Honkura, Mark Richards, Bàrbara Laviña, Miguel Sáinz-Jaspeado, Christer Betsholtz & Lena Claesson-Welsh

Different stimuli can induce dynamic changes in blood flow velocity, vessel diameter and permeability. Here the authors develop a multi-photon microscopy-based image analysis tool allowing the identification of vessels and the assessment of rapid changes in large vascular networks.

16 July 2018 | doi: 10.1038/s41467-018-04929-8
Blood flow  Imaging  Tight junctions 

Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo OPEN
Lei Li, Anton A. Shemetov, Mikhail Baloban, Peng Hu, Liren Zhu, Daria M. Shcherbakova, Ruiying Zhang, Junhui Shi, Junjie Yao, Lihong V. Wang & Vladislav V. Verkhusha

Bacterial phytochrome-based probes improved sensitivity in photoacoustic computed tomography. Here the authors engineer a small near-infrared switchable photochromic probe that allows multi-contrast imaging at depths and can be adapted to study protein–protein interactions in deep-seated tumors.

16 July 2018 | doi: 10.1038/s41467-018-05231-3
Optical imaging  Sensors and probes  Ultrasound 

Mutant ASXL1 cooperates with BAP1 to promote myeloid leukaemogenesis OPEN

ASXL1 gene is often mutated in myeloid malignancies. Here, the authors show that mutant ASXL1 and BAP1 are in a positive feedback loop such that BAP1 induces monoubiquitination of mutant ASXL1, which in turn enhances BAP1 activity to potentiate myeloid transformation via HOXA clusters and IRF8.

16 July 2018 | doi: 10.1038/s41467-018-05085-9
Epigenetics  Leukaemia 

Nanoscale imaging of charge carrier transport in water splitting photoanodes OPEN
Johanna Eichhorn, Christoph Kastl, Jason K. Cooper, Dominik Ziegler, Adam M. Schwartzberg, Ian D. Sharp & Francesca M. Toma

The performance of energy materials is affected by structural defects, as well as physicochemical heterogeneity over different length scales. Here the authors map nanoscale correlations between morphological and functional heterogeneity, quantifying the trap states limiting electronic transport in bismuth vanadate thin films.

16 July 2018 | doi: 10.1038/s41467-018-04856-8
Electrocatalysis  Solar fuels 

Act1 is a negative regulator in T and B cells via direct inhibition of STAT3 OPEN
Cun-Jin Zhang, Chenhui Wang, Meiling Jiang, Chunfang Gu, Jianxin Xiao, Xing Chen, Bradley N. Martin, Fangqiang Tang, Erin Yamamoto, Yibo Xian, Han Wang, Fengling Li, R. Balfour Sartor, Howard Smith, M. Elaine Husni, Fu-Dong Shi, Ji Gao, Julie Carman, Ashok Dongre, Susan C. McKarns et al.

Adaptor for IL-17 receptors (Act1) is known to be crucial for IL-17-mediated immune responses. Here the authors show that Act1 also functions as a negative regulator of T and B cells by direct inhibition of STAT3.

16 July 2018 | doi: 10.1038/s41467-018-04974-3
Autoimmunity  B cells  Lupus nephritis  T cells 

Molecular architecture of fungal cell walls revealed by solid-state NMR OPEN
Xue Kang, Alex Kirui, Artur Muszyński, Malitha C. Dickwella Widanage, Adrian Chen, Parastoo Azadi, Ping Wang, Frederic Mentink-Vigier & Tuo Wang

Aspergillus fumigatus is a pathogenic fungus. Here the authors perform solid-state NMR measurements with intact Aspergillus cells, which provides insights into cell wall composition and dynamics and propose a structural model for fungal cell walls.

16 July 2018 | doi: 10.1038/s41467-018-05199-0
Biophysics  Chemistry  Fungi  Solid-state NMR 

Mechanically tunable conductive interpenetrating network hydrogels that mimic the elastic moduli of biological tissue OPEN
Vivian R. Feig, Helen Tran, Minah Lee & Zhenan Bao

Conductive and stretchable materials that match the elastic moduli of biological tissue are desired for enhanced interfacial and mechanical stability. Here the authors show a method for fabricating highly conductive hydrogels comprising two interpenetrating networks.

16 July 2018 | doi: 10.1038/s41467-018-05222-4
Electronic materials  Gels and hydrogels  Polymers 

ZNF506-dependent positive feedback loop regulates H2AX signaling after DNA damage OPEN
Somaira Nowsheen, Khaled Aziz, Kuntian Luo, Min Deng, Bo Qin, Jian Yuan, Karthik B. Jeganathan, Jia Yu, Henan Zhang, Wei Ding, Jan M. van Deursen & Zhenkun Lou

Following double-strand break a cascade of events leads to the recruitment of repair factors to damaged sites. Here the authors identify ZNF506 as a key factor that mediates post-translational modification changes in H2AX affecting the DNA damage response.

16 July 2018 | doi: 10.1038/s41467-018-05161-0
DNA damage response  Double-strand DNA breaks  Histone post-translational modifications  Phosphorylation  Radiotherapy 

Anterior cingulate cortex and its input to the basolateral amygdala control innate fear response OPEN
Jinho Jhang, Hyoeun Lee, Min Soo Kang, Han-Sol Lee, Hyungju Park & Jin-Hee Han

Brain circuits that control innate fear response are essential for an animal’s survival. Here, the authors report how the anterior cingulate cortex and its projection to amygdala control the innate fear response in mice.

16 July 2018 | doi: 10.1038/s41467-018-05090-y
Amygdala  Neural circuits  Prefrontal cortex 

A diuranium carbide cluster stabilized inside a C80 fullerene cage OPEN
Xingxing Zhang, Wanlu Li, Lai Feng, Xin Chen, Andreas Hansen, Stefan Grimme, Skye Fortier, Dumitru-Claudiu Sergentu, Thomas J. Duignan, Jochen Autschbach, Shuao Wang, Yaofeng Wang, Giorgios Velkos, Alexey A. Popov, Nabi Aghdassi, Steffen Duhm, Xiaohong Li, Jun Li, Luis Echegoyen, W. H. Eugen Schwarz et al.

While metal–carbon double bonds are common in transition metal chemistry and catalysis, unsupported uranium–carbon double bonds remain highly challenging to prepare. Here, the authors stabilize and characterize a U=C=U cluster containing unusually short, unsupported double bonds inside an Ih(7)-C80 fullerene cage.

16 July 2018 | doi: 10.1038/s41467-018-05210-8
Carbon nanotubes and fullerenes  Chemical bonding  Nuclear chemistry 

Gene expression drives the evolution of dominance OPEN
Christian D. Huber, Arun Durvasula, Angela M. Hancock & Kirk E. Lohmueller

Dominance is difficult to measure in natural populations as it is confounded with fitness. Here, Huber et al. developed a new approach to co-estimate dominance and selection coefficients, and found that the observed relationship is best fit by a new model of dominance based on gene expression level.

16 July 2018 | doi: 10.1038/s41467-018-05281-7
Evolutionary biology  Evolutionary genetics  Gene expression  Genetic variation 

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination OPEN
Margaret M. C. Lam, Kelly L. Wyres, Sebastian Duchêne, Ryan R. Wick, Louise M. Judd, Yunn-Hwen Gan, Chu-Han Hoh, Sophia Archuleta, James S. Molton, Shirin Kalimuddin, Tse Hsien Koh, Virginie Passet, Sylvain Brisse & Kathryn E. Holt

Since the 1980s, hypervirulent clonal-group CG23 serotype K1 Klebsiella pneumoniae has been recognised as a prominent cause of community-acquired liver abscess and other severe infections. Here, the authors investigate the genomic evolutionary history of CG23 and suggest a new reference strain for CG23.

13 July 2018 | doi: 10.1038/s41467-018-05114-7
Bacterial evolution  Bacterial genetics  Bacterial genomics  Genetic variation  Pathogens 

Highly efficient RNA-guided base editing in rabbit OPEN
Zhiquan Liu, Mao Chen, Siyu Chen, Jichao Deng, Yuning Song, Liangxue Lai & Zhanjun Li

Base editors can make targeted changes without inducing a double-stranded break. Here, the authors apply the BE3 and ABE7.10 systems to rabbit to create highly efficient targeted base substitutions and various mutation types, and show reduced frequency of undesired by-products with the updated BE4-Gam system.

13 July 2018 | doi: 10.1038/s41467-018-05232-2
CRISPR-Cas9 genome editing  CRISPR-Cas systems 

KIF20A/MKLP2 regulates the division modes of neural progenitor cells during cortical development OPEN
Anqi Geng, Runxiang Qiu, Kiyohito Murai, Jiancheng Liu, Xiwei Wu, Heying Zhang, Henry Farhoodi, Nam Duong, Meisheng Jiang, Jiing-kuan Yee, Walter Tsark & Qiang Lu

The division of neural progenitors is closely regulated but how is unclear. Here, the authors show that mitotic kinesin KIF20A/MKLP2 interacts with a regulator of G protein signaling RGS3 in neural progenitor cells, dislodging it from the intercellular bridge of dividing cortical cells.

13 July 2018 | doi: 10.1038/s41467-018-05152-1
Developmental neurogenesis  Neural stem cells 

Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors OPEN
Thomas Duhen, Rebekka Duhen, Ryan Montler, Jake Moses, Tarsem Moudgil, Noel F. de Miranda, Cheri P. Goodall, Tiffany C. Blair, Bernard A. Fox, Jason E. McDermott, Shu-Ching Chang, Gary Grunkemeier, Rom Leidner, Richard Bryan Bell & Andrew D. Weinberg

Identifying and enumerating tumor-specific CD8 T cells are important for assessing cancer prognosis and therapy efficacy. Here the authors show that CD39 and CD103 mark a subset of tumor-infiltrating CD8 T cells that are tumor-reactive and exhibit characteristics of exhausted or tissue-resident memory T cells.

13 July 2018 | doi: 10.1038/s41467-018-05072-0
CD8-positive T cells  Immunological memory  Immunotherapy  Tumour immunology 

Single neurons may encode simultaneous stimuli by switching between activity patterns OPEN
Valeria C. Caruso, Jeff T. Mohl, Christopher Glynn, Jungah Lee, Shawn M. Willett, Azeem Zaman, Akinori F. Ebihara, Rolando Estrada, Winrich A. Freiwald, Surya T. Tokdar & Jennifer M. Groh

The neural mechanisms through which neurons represent simultaneously presented stimuli are not well understood. Here the authors demonstrate that the two stimuli are alternately encoded through fluctuations in the activity patterns of single neurons.

13 July 2018 | doi: 10.1038/s41467-018-05121-8
Neural encoding  Perception  Sensorimotor processing 

Neutralization of the Plasmodium-encoded MIF ortholog confers protective immunity against malaria infection OPEN
Alvaro Baeza Garcia, Edwin Siu, Tiffany Sun, Valerie Exler, Luis Brito, Armin Hekele, Gib Otten, Kevin Augustijn, Chris J. Janse, Jeffrey B. Ulmer, Jürgen Bernhagen, Erol Fikrig, Andrew Geall & Richard Bucala

Plasmodium species produce an ortholog of the cytokine macrophage migration inhibitory factor, PMIF, which modulates the host inflammatory response to malaria. Here, the authors show that inhibition of PMIF may have translational benefits for managing malaria infections.

13 July 2018 | doi: 10.1038/s41467-018-05041-7
Immunology  Infectious diseases  Malaria  Vaccines 

ATP synthase F1 subunits recruited to centromeres by CENP-A are required for male meiosis OPEN
Caitríona M. Collins, Beatrice Malacrida, Colin Burke, Patrick A. Kiely & Elaine M. Dunleavy

The histone H3 CENP-A is known to play a role during meiosis but its role in the testes in the fly is unknown. Here, the authors identify the mitochondrial metabolic protein complex ATP synthase F1 as interacting with CENP-A, promoting centromere cohesion during meiosis and affecting fly fertility.

13 July 2018 | doi: 10.1038/s41467-018-05093-9
Centromeres  Meiosis 

UTX is an escape from X-inactivation tumor-suppressor in B cell lymphoma OPEN
Xiaoxi Li, Yanli Zhang, Liting Zheng, Mingxian Liu, Charlie Degui Chen & Hai Jiang

UTX is a tumor suppressor gene located on the X-chromosome so it could potentially contribute to the cancer gender bias. Here the authors, using a mouse model of B cell lymphoma, show that UTX is a dosage sensitive tumor suppressor and may be responsible for some of the increased incidence and possibly aggressiveness of male cancers that harbour UTX mutations.

13 July 2018 | doi: 10.1038/s41467-018-05084-w
Lymphoma  Tumour-suppressor proteins 

Reactive astrocytic S1P3 signaling modulates the blood–tumor barrier in brain metastases OPEN
Brunilde Gril, Anurag N. Paranjape, Stephan Woditschka, Emily Hua, Emma L. Dolan, Jeffrey Hanson, Xiaolin Wu, Wojciech Kloc, Ewa Izycka-Swieszewska, Renata Duchnowska, Rafał Pęksa, Wojciech Biernat, Jacek Jassem, Naema Nayyar, Priscilla K. Brastianos, O. Morgan Hall, Cody J. Peer, William D. Figg, Gary T. Pauly, Christina Robinson et al.

When brain metastases form, the blood–brain barrier morphs into the blood–tumor barrier (BTB), surrounded by neuroinflammatory response. Here, the authors show that S1P3 is upregulated in neuroinflammatory response in highly BTB permeable lesions, and modulation of S1P3 could impact BTB permeability.

13 July 2018 | doi: 10.1038/s41467-018-05030-w
Blood–brain barrier  Breast cancer  Metastasis 

Infralimbic cortex is required for learning alternatives to prelimbic promoted associations through reciprocal connectivity OPEN
Arghya Mukherjee & Pico Caroni

Prelimbic (PL) and infralimbic (IL) cortical areas are known to have complementary roles in learning and decision making. Here the authors report reciprocal connectivity between the two areas and elucidate their functional impact on different aspects of learning.

13 July 2018 | doi: 10.1038/s41467-018-05318-x
Consolidation  Decision  Extinction 

A rigid and healable polymer cross-linked by weak but abundant Zn(II)-carboxylate interactions OPEN
Jian-Cheng Lai, Lan Li, Da-Peng Wang, Min-Hao Zhang, Sheng-Ran Mo, Xue Wang, Ke-Yu Zeng, Cheng-Hui Li, Qing Jiang, Xiao-Zeng You & Jing-Lin Zuo

Combining solid-like properties with fast self-healing is a great challenge due to slow diffusion dynamics. Here the authors demonstrate a rigid and healable material by using weak but abundant coordination bonds to crosslink a PDMS polymer.

13 July 2018 | doi: 10.1038/s41467-018-05285-3
Coordination chemistry  Polymer chemistry 

Controlled gene and drug release from a liposomal delivery platform triggered by X-ray radiation OPEN
Wei Deng, Wenjie Chen, Sandhya Clement, Anna Guller, Zhenjun Zhao, Alexander Engel & Ewa M. Goldys

X-ray radiation has excellent tissue penetration depth, making it a useful trigger for deep tissue cancer therapy. Here, the authors design X-ray triggered drug/gene-loaded liposomes by embedding photosensitizers and gold nanoparticles in the liposome bilayer, and demonstrate their efficacy in cancer and gene therapy.

13 July 2018 | doi: 10.1038/s41467-018-05118-3
Chemotherapy  Drug delivery  Nanoparticles  Transfection 

Nonstimulatory peptide–MHC enhances human T-cell antigen-specific responses by amplifying proximal TCR signaling OPEN
Xiang Zhao, Shvetha Sankaran, Jiawei Yap, Chien Tei Too, Zi Zong Ho, Garry Dolton, Mateusz Legut, Ee Chee Ren, Andrew K. Sewell, Antonio Bertoletti, Paul A. MacAry, Joanna Brzostek & Nicholas R. J. Gascoigne

Coagonism, the ability of nonstimulatory antigens to promote T-cell activation, has been reported in mice. Here the authors show that coagonism also occurs in human CD8 T cells, in which a nonstimulatory HIV GAG peptide enhances a specific T-cell response to a hepatitis B virus epitope by amplifying T-cell receptor signals.

13 July 2018 | doi: 10.1038/s41467-018-05288-0
Adaptive immunity  Lymphocyte activation  MHC  T-cell receptor 

Magnetostatic twists in room-temperature skyrmions explored by nitrogen-vacancy center spin texture reconstruction OPEN
Y. Dovzhenko, F. Casola, S. Schlotter, T. X. Zhou, F. Büttner, R. L. Walsworth, G. S. D. Beach & A. Yacoby

The Dzyaloshinskii-Moriya interaction (DMI) is crucial to the stabilization of skyrmions but the contribution is not well understood. Here, the authors provide a methodology using the single electron spin of a nitrogen-vacancy center to image the fine structure of skyrmions which is attributed to the competition between the DMI and stray fields.

13 July 2018 | doi: 10.1038/s41467-018-05158-9
Characterization and analytical techniques  Magnetic properties and materials 

Limits to growth of forest biomass carbon sink under climate change OPEN
Kai Zhu, Jian Zhang, Shuli Niu, Chengjin Chu & Yiqi Luo

The recovery of North American forests is likely to impact their capacity as a carbon sink. Here, Zhu et al. show a growth in aboveground biomass in various climate change scenarios, with these forests expected to sequester no more than 22% more carbon than current levels by the 2080s.

13 July 2018 | doi: 10.1038/s41467-018-05132-5
Ecology  Environmental sciences 

Skilful forecasting of global fire activity using seasonal climate predictions OPEN
Marco Turco, Sonia Jerez, Francisco J. Doblas-Reyes, Amir AghaKouchak, Maria Carmen Llasat & Antonello Provenzale

Societal exposure to large fires has been increasing in recent years and fire forecasting is required for fire management strategies. Here the authors use seasonal climate models to provide skilful predictions of global fire activity.

13 July 2018 | doi: 10.1038/s41467-018-05250-0
Climate sciences  Natural hazards 

Modulation of anti-tumor immunity by the brain’s reward system OPEN
Tamar L Ben-Shaanan, Maya Schiller, Hilla Azulay-Debby, Ben Korin, Nadia Boshnak, Tamar Koren, Maria Krot, Jivan Shakya, Michal A. Rahat, Fahed Hakim & Asya Rolls

Neural activation can have wide ranging effects beyond central and peripheral nervous system. This work shows that chemogenetic activation of the brain’s reward system ventral tegmental area (VTA) can boost mice’s immune function, confer anti-tumor immunity, and reduce tumor mass in experimental rodent models of lung carcinoma and melanoma.

13 July 2018 | doi: 10.1038/s41467-018-05283-5
Neuroimmunology  Tumour immunology 

SUMO2 conjugation of PCNA facilitates chromatin remodeling to resolve transcription-replication conflicts OPEN
Min Li, Xiaohua Xu, Chou-Wei Chang, Li Zheng, Binghui Shen & Yilun Liu

Transcription-replication conflicts need to be resolved to minimize genome instability. Here the authors show that SUMO2-conjugated PCNA destabilizes RNAPII from chromatin, enhances replication progression and limits transcription-induced DNA damage at common fragile sites.

13 July 2018 | doi: 10.1038/s41467-018-05236-y
Chromatin remodelling  Double-strand DNA breaks  Fragile sites  Replisome  Stalled forks 

Influence of atomic site-specific strain on catalytic activity of supported nanoparticles OPEN
Torben Nilsson Pingel, Mikkel Jørgensen, Andrew B. Yankovich, Henrik Grönbeck & Eva Olsson

Detailed knowledge of how strain influences catalytic reactions remains elusive. Here, the authors experimentally measure the strain in supported Pt nanoparticles on alumina and ceria with atomic resolution and computationally explore how the strain affects the CO oxidation reaction.

13 July 2018 | doi: 10.1038/s41467-018-05055-1
Computational chemistry  Heterogeneous catalysis  Materials for energy and catalysis  Nanoparticles  Transmission electron microscopy 

Strong plates enhance mantle mixing in early Earth OPEN
Roberto Agrusta, Jeroen van Hunen & Saskia Goes

The subducting plates can either penetrate straight into the lower mantle or flatten in the mantle transition zone, yet slab dynamics in the past remains unclear. Here, using subduction models, the authors predict that a hotter early Earth was probably more favourable to lower mantle slab penetration.

13 July 2018 | doi: 10.1038/s41467-018-05194-5
Geodynamics  Planetary science  Solid Earth sciences 

Single-molecule insights into surface-mediated homochirality in hierarchical peptide assembly OPEN
Yumin Chen, Ke Deng, Shengbin Lei, Rong Yang, Tong Li, Yuantong Gu, Yanlian Yang, Xiaohui Qiu & Chen Wang

Most chiral molecules and structures in living organisms exist as single enantiomers, but why? Here, the authors investigated surface-mediated homochirality on the single-molecule level and show that it can be triggered by the chirality unbalance of two adsorption configuration monomers.

13 July 2018 | doi: 10.1038/s41467-018-05218-0
Biophysical chemistry  Molecular conformation 

HHEX is a transcriptional regulator of the VEGFC/FLT4/PROX1 signaling axis during vascular development OPEN
Sébastien Gauvrit, Alethia Villasenor, Boris Strilic, Philip Kitchen, Michelle M. Collins, Rubén Marín-Juez, Stefan Guenther, Hans-Martin Maischein, Nana Fukuda, Maurice A. Canham, Joshua M. Brickman, Clifford W. Bogue, Padma-Sheela Jayaraman & Didier Y. R. Stainier

VEGFC, its receptor FLT4, and transcriptional effector PROX1 control formation of the lymphatic system but how is unclear. Here, the authors show that the transcription factor hematopoietically expressed homeobox (HHEX) regulates VEGFC, FLT4 and PROX1 in fish and mammals during angiogenic sprouting and lymphatic formation.

13 July 2018 | doi: 10.1038/s41467-018-05039-1
Development  Growth factor signalling  Lymphangiogenesis 

Nicotine aversion is mediated by GABAergic interpeduncular nucleus inputs to laterodorsal tegmentum OPEN
Shannon L. Wolfman, Daniel F. Gill, Fili Bogdanic, Katie Long, Ream Al-Hasani, Jordan G. McCall, Michael R. Bruchas & Daniel S. McGehee

Despite its known effects in brain reward centers, nicotine can be aversive in high doses. Here, the authors show that nicotine aversion depends on low-affinity nicotinic acetylcholine receptors expressed on projections from the interpeduncular nucleus to the laterodorsal tegmentum.

13 July 2018 | doi: 10.1038/s41467-018-04654-2
Neurophysiology  Reward  Synaptic plasticity 

Anomalous mechanical behavior of nanocrystalline binary alloys under extreme conditions OPEN
S. A. Turnage, M. Rajagopalan, K. A. Darling, P. Garg, C. Kale, B. G. Bazehhour, I. Adlakha, B. C. Hornbuckle, C. L. Williams, P. Peralta & K. N. Solanki

Metals deformed at very high rates experience a rapid increase in flow stress due to dislocation drag. Here, the authors stabilise a nanocrystalline microstructure to suppress dislocation velocity and limit drag effects, conserving low strain-rate deformation mechanisms up to higher strain rates and temperatures.

12 July 2018 | doi: 10.1038/s41467-018-05027-5
Metals and alloys  Nanoscale materials  Structural properties 

Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm OPEN
Michael K. Strasser, Philipp S. Hoppe, Dirk Loeffler, Konstantinos D. Kokkaliaris, Timm Schroeder, Fabian J. Theis & Carsten Marr

The timing of cell fate choices is usually unknown, because we have to rely on indirect evidence of their molecular basis. Here, the authors introduce a method to infer decision times from marker onset in cell genealogies, and find evidence refuting the paradigmatic PU.1/GATA1 cell fate switch.

12 July 2018 | doi: 10.1038/s41467-018-05037-3
Computational models  Haematopoiesis  Regulatory networks  Statistical methods 

Self-assembly of metal–organic polyhedra into supramolecular polymers with intrinsic microporosity OPEN
Arnau Carné-Sánchez, Gavin A. Craig, Patrick Larpent, Takashi Hirose, Masakazu Higuchi, Susumu Kitagawa, Kenji Matsuda, Kenji Urayama & Shuhei Furukawa

Porosity in metal–organic materials typically relies on highly ordered crystalline networks, which hinders material processing and morphological control. Here, the authors use metal–organic polyhedra as porous monomers in supramolecular polymerization to produce colloidal spheres and gels with intrinsic microporosity.

12 July 2018 | doi: 10.1038/s41467-018-04834-0
Coordination chemistry  Porous materials  Soft materials  Supramolecular chemistry 

A molecular neuromorphic network device consisting of single-walled carbon nanotubes complexed with polyoxometalate OPEN
Hirofumi Tanaka, Megumi Akai-Kasaya, Amin TermehYousefi, Liu Hong, Lingxiang Fu, Hakaru Tamukoh, Daisuke Tanaka, Tetsuya Asai & Takuji Ogawa

Neuromorphic hardware is based on principles of neuroscience, and has the potential to provide higher-level brain functions. Here, the authors develop a neuromorphic network device, constructed from single-walled carbon nanotubes and polyoxometalate, that mimics nerve impulse generation.

12 July 2018 | doi: 10.1038/s41467-018-04886-2
Carbon nanotubes and fullerenes  Computer science  Electronic properties and materials  Materials for devices 

Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery OPEN
Thapakorn Jaroentomeechai, Jessica C. Stark, Aravind Natarajan, Cameron J. Glasscock, Laura E. Yates, Karen J. Hsu, Milan Mrksich, Michael C. Jewett & Matthew P. DeLisa

The ability to produce homogeneous glycoproteins is expected to advance fundamental understanding in glycoscience, but current in vivo-based production systems have several limitations. Here, the authors develop an E. coli extract-based one-pot system for customized production of N-linked glycoproteins.

12 July 2018 | doi: 10.1038/s41467-018-05110-x
Biosynthesis  Expression systems  Glycobiology  Post-translational modifications  Synthetic biology 

Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system OPEN
Adrian C. D. Fuchs, Lorena Maldoner, Matthias Wojtynek, Marcus D. Hartmann & Jörg Martin

Ubiquitin modification also occurs in archaea. Here, the authors characterize an archaeal ancestral ubiquitination system, present the crystal structure of the archaeal deubiquitinase Rpn11 from Caldiarchaeum subterraneum bound to ubiquitin and provide insights into evolutionary relationships.

12 July 2018 | doi: 10.1038/s41467-018-05198-1
Archaeal physiology  Deubiquitylating enzymes  Ubiquitins  X-ray crystallography 

Ratiometric nanothermometer in vivo based on triplet sensitized upconversion OPEN
Ming Xu, Xianmei Zou, Qianqian Su, Wei Yuan, Cong Cao, Qiuhong Wang, Xingjun Zhu, Wei Feng & Fuyou Li

Though luminescence imaging is a promising approach for contactless thermometry in vivo, the low thermal sensitivity of existing thermometers limits its potential. Here, the authors develop a high-sensitivity ratiometric nanothermometer based on triplet-sensitized upconversion.

12 July 2018 | doi: 10.1038/s41467-018-05160-1
Biosensors  Fluorescence imaging 

Molecular basis for the inhibition of the methyl-lysine binding function of 53BP1 by TIRR OPEN
Jiaxu Wang, Zenglin Yuan, Yaqi Cui, Rong Xie, Guang Yang, Muzaffer A. Kassab, Mengxi Wang, Yinliang Ma, Chen Wu, Xiaochun Yu & Xiuhua Liu

Tudor interacting repair regulator (TIRR) is a negative regulator of 53BP1 in DNA damage repair processes. Here the authors give mechanistic insights into how TIRR mediates suppression by solving the crystal structure of TIRR bound to the 53BP1 tandem Tudor domain (TTD).

12 July 2018 | doi: 10.1038/s41467-018-05174-9
Double-strand DNA breaks  X-ray crystallography 

Predicting marsh vulnerability to sea-level rise using Holocene relative sea-level data OPEN
Benjamin P. Horton, Ian Shennan, Sarah L. Bradley, Niamh Cahill, Matthew Kirwan, Robert E. Kopp & Timothy A. Shaw

Quantifying the vulnerability of tidal marsh ecosystems to relative sea-level rise (RSLR) is essential if the threat is to be mitigated. Here, the authors analyze the response of Great Britain’s tidal marshes to RSLR during the Holocene and predict an almost inevitable loss of this ecosystem by 2100 under rapid RSLR scenarios.

12 July 2018 | doi: 10.1038/s41467-018-05080-0
Palaeoclimate  Palaeoecology 

The origin and adaptive evolution of domesticated populations of yeast from Far East Asia OPEN
Shou-Fu Duan, Pei-Jie Han, Qi-Ming Wang, Wan-Qiu Liu, Jun-Yan Shi, Kuan Li, Xiao-Ling Zhang & Feng-Yan Bai

An understanding of the domestication of the yeast Saccharomyces cerevisiae has important implications for studying its evolution and diversity. Here, the authors show that Far East Asia is likely the center of origin of the domesticated populations of the yeast based on genomic and phenotypic characterization of a large collection of isolates.

12 July 2018 | doi: 10.1038/s41467-018-05106-7
Evolutionary genetics  Fungal evolution  Population genetics 

Attosecond coherent control of free-electron wave functions using semi-infinite light fields OPEN
G. M. Vanacore, I. Madan, G. Berruto, K. Wang, E. Pomarico, R. J. Lamb, D. McGrouther, I. Kaminer, B. Barwick, F. Javier García de Abajo & F. Carbone

Manipulation of the electron–photon coupling is crucial for quantum circuits and exploration of electronic motions and nuclear phenomena. Here the authors discuss a scheme to coherently control the electron wave function from attosecond to zeptosecond timescales by using semi-infinite light fields.

12 July 2018 | doi: 10.1038/s41467-018-05021-x
Attosecond science  Nanophotonics and plasmonics  Ultrafast photonics 

Domino-like multi-emissions across red and near infrared from solid-state 2-/2,6-aryl substituted BODIPY dyes OPEN
Dan Tian, Fen Qi, Huili Ma, Xiaoqing Wang, Yue Pan, Runfeng Chen, Zhen Shen, Zhipeng Liu, Ling Huang & Wei Huang

The class of BODIPY dyes has high solubility and high quantum yields and is widely used in imaging applications. Here Tian et al. synthesize new dye molecules and demonstrate extended emission properties and application scope controllable both by the excitation wavelength and aggregation states.

12 July 2018 | doi: 10.1038/s41467-018-05040-8
Fluorescence spectroscopy  Optical materials 

Network-based approach to prediction and population-based validation of in silico drug repurposing OPEN
Feixiong Cheng, Rishi J. Desai, Diane E. Handy, Ruisheng Wang, Sebastian Schneeweiss, Albert-László Barabási & Joseph Loscalzo

Repurposing approved drugs could accelerate treatment options for various diseases. Here, the authors use network proximity of disease gene products and drug targets in the human protein interactome to identify drug-disease associations for cardiovascular disease, and validate these using longitudinal healthcare data.

12 July 2018 | doi: 10.1038/s41467-018-05116-5
Cellular signalling networks  Predictive medicine  Systems biology 

Collapse and rescue of cooperation in evolving dynamic networks OPEN
Erol Akçay

The evolution of cooperation depends on social structure, which may evolve in response. Here, Akçay models coevolution between cooperation and social network formation strategies, showing that coevolutionary feedbacks lead cooperation to collapse unless constrained by costs of social connections.

12 July 2018 | doi: 10.1038/s41467-018-05130-7
Behavioural ecology  Coevolution  Evolutionary theory  Social evolution 
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  Latest Addendum    
Addendum: Heliconical smectic phases formed by achiral molecules OPEN
Jordan P. Abberley, Ross Killah, Rebecca Walker, John M. D. Storey, Corrie T. Imrie, Mirosław Salamończyk, Chenhui Zhu, Ewa Gorecka & Damian Pociecha
17 July 2018 | doi: 10.1038/s41467-018-05334-x
Liquid crystals  Molecular self-assembly  Structure of solids and liquids 
  Latest Author Corrections    
Author Correction: Generation and characterization of ultrathin free-flowing liquid sheets OPEN
Jake D. Koralek, Jongjin B. Kim, Petr Brůža, Chandra B. Curry, Zhijiang Chen, Hans A. Bechtel, Amy A. Cordones, Philipp Sperling, Sven Toleikis, Jan F. Kern, Stefan P. Moeller, Siegfried H. Glenzer & Daniel P. DePonte
17 July 2018 | doi: 10.1038/s41467-018-05365-4
Infrared spectroscopy  Microfluidics  Microscopy  Physics 

Author Correction: Zebrafish and medaka offer insights into the neurobehavioral correlates of vertebrate magnetoreception OPEN
Ahne Myklatun, Antonella Lauri, Stephan H. K. Eder, Michele Cappetta, Denis Shcherbakov, Wolfgang Wurst, Michael Winklhofer & Gil G. Westmeyer
17 July 2018 | doi: 10.1038/s41467-018-05323-0
Animal behaviour  Model vertebrates  Navigation  Sensory processing 

Author Correction: A novel atypical sperm centriole is functional during human fertilization OPEN
Emily L. Fishman, Kyoung Jo, Quynh P. H. Nguyen, Dong Kong, Rachel Royfman, Anthony R. Cekic, Sushil Khanal, Ann L. Miller, Calvin Simerly, Gerald Schatten, Jadranka Loncarek, Vito Mennella & Tomer Avidor-Reiss
13 July 2018 | doi: 10.1038/s41467-018-05324-z
Centrosome  Spermatogenesis 

Author Correction: Dynamics of a qubit while simultaneously monitoring its relaxation and dephasing OPEN
Q. Ficheux, S. Jezouin, Z. Leghtas & B. Huard
13 July 2018 | doi: 10.1038/s41467-018-05207-3
Quantum information  Quantum mechanics  Superconducting devices 
  Latest Publisher Corrections    
Publisher Correction: FGF signalling controls the specification of hair placode-derived SOX9 positive progenitors to Merkel cells OPEN
Minh Binh Nguyen, Idan Cohen, Vinod Kumar, Zijian Xu, Carmit Bar, Katherine L. Dauber-Decker, Pai-Chi Tsai, Pauline Marangoni, Ophir D. Klein, Ya-Chieh Hsu, Ting Chen, Marja L. Mikkola & Elena Ezhkova
17 July 2018 | doi: 10.1038/s41467-018-05361-8
Differentiation  Skin stem cells  Stem-cell differentiation 

Publisher Correction: Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom OPEN
C.-Elisa Schaum, A. Buckling, N. Smirnoff, D. J. Studholme & G. Yvon-Durocher
13 July 2018 | doi: 10.1038/s41467-018-05353-8
Climate change  Evolutionary ecology  Experimental evolution  Microbiology 

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