Wednesday, July 4, 2018

Nature Communications - 04 July 2018

Nature Communications

Nature Sustainability publishes significant original research from a broad range of natural, social and engineering fields about sustainability, its policy dimensions and possible solutions. It brings together novel research on the drivers of human practices and their environmental and social impacts, as well as applied research that identifies viable solutions — technological, infrastructural or institutional — to sustain ecosystems and the well-being of populations across the globe. 

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04 July 2018 
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Focus on Autoimmune Disease from Nature Immunology

A series of Reviews specially commissioned by Nature Immunology discuss the genetic, environmental, microbial and cellular factors underpinning autoimmune disease as well as highlight avenues for therapeutic intervention. 

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  Latest Comment    
To catch a quake OPEN
Elizabeth S. Cochran
03 July 2018 | doi: 10.1038/s41467-018-04790-9
Natural hazards  Seismology 
  Latest Articles View all Articles  

microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site OPEN
Philipp Schult, Hanna Roth, Rebecca L. Adams, Caroline Mas, Lionel Imbert, Christian Orlik, Alessia Ruggieri, Anna M. Pyle & Volker Lohmann

The liver-specific microRNA-122 is an essential proviral host factor of Hepatitis C virus replication. Here the authors show that microRNA-122 functions as an RNA chaperone that guides the formation of a functional internal ribosome entry site by preventing energetically more favorable secondary structures within the HCV RNA genome.

04 July 2018 | doi: 10.1038/s41467-018-05053-3
Molecular modelling  NMR spectroscopy  Non-coding RNAs  Translation  Virology 

Discovery of a strain-stabilised smectic electronic order in LiFeAs OPEN
Chi Ming Yim, Christopher Trainer, Ramakrishna Aluru, Shun Chi, Walter N. Hardy, Ruixing Liang, Doug Bonn & Peter Wahl

Small structural distortions may lead to dramatic modification in the electronic states in strong correlated materials. Here, Yim et al. image a strain-stabilized smectic electronic order in LiFeAs with both broken rotational symmetry and reduced translational symmetry.

04 July 2018 | doi: 10.1038/s41467-018-04909-y
Electronic properties and materials  Superconducting properties and materials  Surfaces, interfaces and thin films 

Identifying a common backbone of interactions underlying food webs from different ecosystems OPEN
Bernat Bramon Mora, Dominique Gravel, Luis J. Gilarranz, Timothée Poisot & Daniel B. Stouffer

The structure of ecological networks can vary dramatically, yet there may be common features across networks from different ecosystem types. Here, Bramon Mora et al. use network alignment to demonstrate that there is a common backbone of interactions underlying empirical food webs.

04 July 2018 | doi: 10.1038/s41467-018-05056-0
Community ecology  Ecological networks 

Near infrared fluorescent peptide nanoparticles for enhancing esophageal cancer therapeutic efficacy OPEN
Zhen Fan, Yan Chang, Chaochu Cui, Leming Sun, David H. Wang, Zui Pan & Mingjun Zhang

Biocompatible nanoparticles for targeted drug delivery, imaging and tracking of therapeutic agents are sought-after. Here, the authors report cyclic peptide nanoparticles with structure induced fluorescence that can conjugate with biomarkers and carry drugs for application in esophageal cancer.

04 July 2018 | doi: 10.1038/s41467-018-04763-y
Biomaterials  Biomedical engineering  Cancer therapy 

Peptide density targets and impedes triple negative breast cancer metastasis OPEN
Daxing Liu, Peng Guo, Craig McCarthy, Biran Wang, Yu Tao & Debra Auguste

The C-X-C chemokine receptor type 4 (CXCR4) pathway is a key regulator of cancer metastasis. Here, the authors present a method to block CXCR4 and thereby inhibit breast cancer metastasis by developing a liposome that presents CXCR4-binding peptides in a multivalent fashion.

04 July 2018 | doi: 10.1038/s41467-018-05035-5
Biomedical materials  Breast cancer 

miR-130a and miR-145 reprogram Gr-1+CD11b+ myeloid cells and inhibit tumor metastasis through improved host immunity OPEN
Hiroki Ishii, Suman K. Vodnala, Bhagelu R. Achyut, Jae Young So, M. Christine Hollander, Tim F. Greten, Ashish Lal & Li Yang

Tumours produce soluble factors that contribute to the expansion of Gr-1+CD11b+ immature myeloid cells with TGFβ dependent immune suppressive function. Here, the authors show miR-130a and miR-145 target TβRII and reprogram these cells by altering the cytokine microenvironment, improving anti-tumour immunity and inhibiting metastasis in preclinical mouse models.

04 July 2018 | doi: 10.1038/s41467-018-05023-9
Cancer microenvironment  Metastasis 

Rapid transport of deformation-tuned nanoparticles across biological hydrogels and cellular barriers OPEN
Miaorong Yu, Lu Xu, Falin Tian, Qian Su, Nan Zheng, Yiwei Yang, Jiuling Wang, Aohua Wang, Chunliu Zhu, Shiyan Guo, XinXin Zhang, Yong Gan, Xinghua Shi & Huajian Gao

Penetration of the mucus and tumor interstitial matrix is an important consideration for drug delivery devices. Here, the authors report on a study into the optimization of rigidity for the transport of nanoparticles through biological hydrogels using core-shell polymer-lipid nanoparticles.

04 July 2018 | doi: 10.1038/s41467-018-05061-3
Applications of AFM  Cancer therapy  Microfluidics  Nanoparticles  Nanostructures 

Corrosion engineering towards efficient oxygen evolution electrodes with stable catalytic activity for over 6000 hours OPEN
Yipu Liu, Xiao Liang, Lin Gu, Yu Zhang, Guo-Dong Li, Xiaoxin Zou & Jie-Sheng Chen

Earth-abundant water splitting materials are highly desirable for renewable fuel production, but such catalysts are rarely tested for long-term use. Here, the authors prepare active water-splitting electrocatalysts via corrosion engineering that are stable for thousands of hours.

04 July 2018 | doi: 10.1038/s41467-018-05019-5
Catalyst synthesis  Electrocatalysis  Nanoscale materials  Solid-state chemistry 

Systematic discovery of germline cancer predisposition genes through the identification of somatic second hits OPEN
Solip Park, Fran Supek & Ben Lehner

Inherited germline variants and somatic mutations contribute to cancer. Here, the authors present the statistical method ALFRED that tests the two-hit hypothesis of tumorigenesis and apply it to ~10,000 tumor exomes to identify rare germline variants that affect putative cancer predisposition genes, contributing substantially to cancer risk.

04 July 2018 | doi: 10.1038/s41467-018-04900-7
Cancer genetics  Cancer genomics  Computational biology and bioinformatics  Medical genetics 

FerriTag is a new genetically-encoded inducible tag for correlative light-electron microscopy OPEN
Nicholas I. Clarke & Stephen J. Royle

Correlative light-electron microscopy (CLEM) pairs versatile fluorescence imaging with high resolution electron microscopy. Here, the authors develop a genetically-encoded, chemically-inducible tag that allows acute labeling of single proteins for CLEM.

04 July 2018 | doi: 10.1038/s41467-018-04993-0
Cellular imaging  Endocytosis  Transmission electron microscopy 

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries OPEN
Seyedeh M. Zekavat, Sanni Ruotsalainen, Robert E. Handsaker, Maris Alver, Jonathan Bloom, Timothy Poterba, Cotton Seed, Jason Ernst, Mark Chaffin, Jesse Engreitz, Gina M. Peloso, Ani Manichaikul, Chaojie Yang, Kathleen A. Ryan, Mao Fu, W. Craig Johnson, Michael Tsai, Matthew Budoff, Vasan S. Ramachandran, L. Adrienne Cupples et al.

Circulating lipoprotein(a) is an important risk factor for cardiovascular disease and shows variability between different ethnic groups. Here, Zekavat et al. perform whole-genome sequencing in individuals of European and African ancestries and find ancestry-specific genetic determinants for lipoprotein(a) levels.

04 July 2018 | doi: 10.1038/s41467-018-04668-w
Atherosclerosis  Fat metabolism  Genetic association study  Population genetics 

XPC is an RNA polymerase II cofactor recruiting ATAC to promoters by interacting with E2F1 OPEN
B. Bidon, I. Iltis, M. Semer, Z. Nagy, A. Larnicol, A. Cribier, M. Benkirane, F. Coin, J-M. Egly & N. Le May

XPC plays an important role in the nuclear exicision repair pathways. Here the authors show that in addition, XPC plays a role in transcription regulation by interacting with KAT2A and E2F1 and recruiting the ATAC coactivator complex to promoters.

04 July 2018 | doi: 10.1038/s41467-018-05010-0
Gene expression  Molecular biology  Transcription 

Highly stable QLEDs with improved hole injection via quantum dot structure tailoring OPEN
Weiran Cao, Chaoyu Xiang, Yixing Yang, Qi Chen, Liwei Chen, Xiaolin Yan & Lei Qian

The commercialization of light-emitting diodes based on emissive quantum dots (e.g. QLEDs) is hindered by their inherent poor operational lifetime. Using an intelligent energy-level design strategy, Qian et al. demonstrate QLEDs with operational lifetime that meets industrial display standards.

04 July 2018 | doi: 10.1038/s41467-018-04986-z
Organic LEDs  Quantum dots 

The REN4 rheostat dynamically coordinates the apical and lateral domains of Arabidopsis pollen tubes OPEN
Hui Li, Nan Luo, Weidong Wang, Zengyu Liu, Jisheng Chen, Liangtao Zhao, Li Tan, Chunyan Wang, Yuan Qin, Chao Li, Tongda Xu & Zhenbiao Yang

Polar growth of pollen tubes is established by polar localization of ROP1 GTPase activity at the apical tip. Here, Li et al. identify REN4 as a ROP1 interaction partner that restrains the ROP1 distribution to the apex by promoting ROP1 endocytosis from lateral domains of the pollen tube membrane.

03 July 2018 | doi: 10.1038/s41467-018-04838-w
Apicobasal polarity  Plant polarity  Pollen  Pollen tube 

A senataxin-associated exonuclease SAN1 is required for resistance to DNA interstrand cross-links OPEN
Alex M. Andrews, Heather J. McCartney, Tim M. Errington, Alan D. D’Andrea & Ian G. Macara

When DNA interstrand cross-links damage occurs, it causes disruption of replication and transcription. Here the authors identify FAM120B/SAN1, a 5′ exonuclease involved in the repair process of Interstrand Crosslinks independently of the Fanconi Anemia pathway.

03 July 2018 | doi: 10.1038/s41467-018-05008-8
Cell biology  DNA 

Microscopic structure of the polymer-induced liquid precursor for calcium carbonate OPEN
Yifei Xu, Koen C. H. Tijssen, Paul H. H. Bomans, Anat Akiva, Heiner Friedrich, Arno P. M. Kentgens & Nico A. J. M. Sommerdijk

There is much debate within the field about the complex processes involved in the formation of precursors and mineral crystals. Here, the authors report on a study into the structures formed in the polymer-induced liquid precursor of CaCO3 and suggest a new interpretation of the process.

03 July 2018 | doi: 10.1038/s41467-018-05006-w
Bioinspired materials  Biomineralization  Inorganic chemistry  Polymers 

Single-dose testosterone administration increases men’s preference for status goods OPEN
G. Nave, A. Nadler, D. Dubois, D. Zava, C. Camerer & H. Plassmann

Testosterone is believed to be involved in social rank-related behavior. Here, the authors show that one dose of testosterone increases men’s preference for “high status” goods and brands, suggesting a role for testosterone in modern consumer behavior in men.

03 July 2018 | doi: 10.1038/s41467-018-04923-0
Endocrinology  Human behaviour  Sexual behaviour  Social neuroscience 

Photo-tautomerization of acetaldehyde as a photochemical source of formic acid in the troposphere OPEN
Miranda F. Shaw, Bálint Sztáray, Lisa K. Whalley, Dwayne E. Heard, Dylan B. Millet, Meredith J. T. Jordan, David L. Osborn & Scott H. Kable

The concentration of formic acid in Earth’s atmosphere is under-predicted by atmospheric models. Here the authors show that acetaldehyde photo-tautomerizes to vinyl alcohol under tropospheric conditions, with subsequent oxidation via OH radicals supplying up to 60% of total modeled formic acid production over oceans.

03 July 2018 | doi: 10.1038/s41467-018-04824-2
Atmospheric chemistry  Excited states 

High energy flexible supercapacitors formed via bottom-up infilling of gel electrolytes into thick porous electrodes OPEN
Xiangming Li, Jinyou Shao, Sung-Kon Kim, Chaochao Yao, Junjie Wang, Yu-Run Miao, Qiye Zheng, Pengcheng Sun, Runyu Zhang & Paul V. Braun

The development of high performance flexible solid supercapacitors calls for an effective approach to infill gel electrolytes into porous electrodes. Here the authors report a bottom-up method to address this technical challenge, which leads to enhanced areal capacitance and durability.

03 July 2018 | doi: 10.1038/s41467-018-04937-8
Electrochemistry  Supercapacitors 

Postprandial FGF19-induced phosphorylation by Src is critical for FXR function in bile acid homeostasis OPEN
Sangwon Byun, Dong-Hyun Kim, Daniel Ryerson, Young-Chae Kim, Hao Sun, Bo Kong, Peter Yau, Grace Guo, H. Eric Xu, Byron Kemper & Jongsook Kim Kemper

FXR plays an important role in bile acid homeostasis by transcriptionally modulating several enterohepatic genes, including intestinal FGF19, that repress hepatic bile acid synthesis. Here the authors show that postprandial FGF19 regulates FXR transcriptional activity via its action on the tyrosine kinase Src, which phosphorylates FXR.

03 July 2018 | doi: 10.1038/s41467-018-04697-5
Cholestasis  Homeostasis  Phosphorylation  Primary biliary cirrhosis 

Elucidating the genetic basis of social interaction and isolation OPEN
Felix R. Day, Ken K. Ong & John R. B. Perry

Little is known about the genetic determinants of social isolation and loneliness despite their well-established importance for health. Here, using multi-trait GWAS, Day et al. identify 15 genomic loci for loneliness and further show a bidirectional causal relationship between BMI and loneliness by MR.

03 July 2018 | doi: 10.1038/s41467-018-04930-1
Genetic association study  Genome-wide association studies  Risk factors  Social behaviour 

Monoacylglycerol lipase regulates cannabinoid receptor 2-dependent macrophage activation and cancer progression OPEN
Wei Xiang, Rongchen Shi, Xia Kang, Xuan Zhang, Peng Chen, Lili Zhang, Along Hou, Rui Wang, Yuanyin Zhao, Kun Zhao, Yingzhe Liu, Yue Ma, Huan Luo, Shenglan Shang, Jinyu Zhang, Fengtian He, Songtao Yu, Lixia Gan, Chunmeng Shi, Yongsheng Li et al.

Tumour associated macrophages (TAMs) have an altered lipid metabolism. Here the authors show that downregulation of monoacylglycerols lipase MGLL in TAMs induces lipid accumulation and tumor progression by polarizing TAMs toward tumor-promoting through activation of cannabinoid receptor CB2.

03 July 2018 | doi: 10.1038/s41467-018-04999-8
Cancer microenvironment  Tumour immunology 

Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a OPEN

Uhrf1 is a known regulator of heterochromatin and DNA methylation in embryonic stem cells (ESCs). Here, the authors demonstrate that Uhrf1 acts together with the Set1/COMPASS complex regulator of active transcription to promote H3K4 methylation at bivalent loci and Uhrf1 loss results in disruption of differentiation.

03 July 2018 | doi: 10.1038/s41467-018-04818-0
DNA methylation  Embryonic stem cells  Gene regulation  Reprogramming  Stem-cell differentiation 

Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift OPEN
Satoshi Okawa, Carmen Saltó, Srikanth Ravichandran, Shanzheng Yang, Enrique M. Toledo, Ernest Arenas & Antonio del Sol

Gaining insight into cell identities from single cell RNA-seq data remains a challenge. Here, the authors introduce an approach to identify transcription factors (TFs) that synergistically determine cellular identities, and demonstrate its ability to identify TFs that can induce cellular conversion.

03 July 2018 | doi: 10.1038/s41467-018-05016-8
Computational biology and bioinformatics  Neural stem cells 

Discovery of coexisting Dirac and triply degenerate magnons in a three-dimensional antiferromagnet OPEN
Song Bao, Jinghui Wang, Wei Wang, Zhengwei Cai, Shichao Li, Zhen Ma, Di Wang, Kejing Ran, Zhao-Yang Dong, D. L. Abernathy, Shun-Li Yu, Xiangang Wan, Jian-Xin Li & Jinsheng Wen

Topological magnonic materials display exotic properties which may enable high-efficiency and low-cost spintronic devices. Here the authors demonstrate a three-dimensional antiferromagnet Cu3TeO6 that hosts symmetry-protected Dirac and triply degenerate magnons.

03 July 2018 | doi: 10.1038/s41467-018-05054-2
Magnetic properties and materials  Topological matter 

Coherent modulation of the sea-level annual cycle in the United States by Atlantic Rossby waves OPEN
Francisco M. Calafat, Thomas Wahl, Fredrik Lindsten, Joanne Williams & Eleanor Frajka-Williams

Changes in the sea-level annual cycle have a profound effect on the coast, yet little is known about their drivers. Here the authors show a considerable variability in the amplitude of the cycle along the United States Gulf and Southeast coasts and relate it to Atlantic Rossby waves.

03 July 2018 | doi: 10.1038/s41467-018-04898-y
Natural hazards  Ocean sciences  Physical oceanography 

Coupling of ocean redox and animal evolution during the Ediacaran-Cambrian transition OPEN
Dan Wang, Hong-Fei Ling, Ulrich Struck, Xiang-Kun Zhu, Maoyan Zhu, Tianchen He, Ben Yang, Antonia Gamper & Graham A. Shields

The late Ediacaran to early Cambrian interval witnessed extraordinary radiations of metazoan life, in which the role of physical environment remains debated. Here, Wang et al. show that increased nutrient nitrogen availability may have exerted an important control on both macroevolution and ocean oxygenation.

03 July 2018 | doi: 10.1038/s41467-018-04980-5
Element cycles  Geochemistry  Geology 

The role of momentum-dark excitons in the elementary optical response of bilayer WSe2 OPEN
Jessica Lindlau, Malte Selig, Andre Neumann, Léo Colombier, Jonathan Förste, Victor Funk, Michael Förg, Jonghwan Kim, Gunnar Berghäuser, Takashi Taniguchi, Kenji Watanabe, Feng Wang, Ermin Malic & Alexander Högele

The electronic band structure of atomically thin transition metal dichalcogenides is strongly sensitive to the number of layers, resulting in modified light emission. Here, the authors investigate the cryogenic emission from bilayer WSe2 to identify the role of momentum-indirect excitons for its optical response.

03 July 2018 | doi: 10.1038/s41467-018-04877-3
Two-dimensional materials 

Spin–phonon couplings in transition metal complexes with slow magnetic relaxation OPEN
Duncan H. Moseley, Shelby E. Stavretis, Komalavalli Thirunavukkuarasu, Mykhaylo Ozerov, Yongqiang Cheng, Luke L. Daemen, Jonathan Ludwig, Zhengguang Lu, Dmitry Smirnov, Craig M. Brown, Anup Pandey, A. J. Ramirez-Cuesta, Adam C. Lamb, Mihail Atanasov, Eckhard Bill, Frank Neese & Zi-Ling Xue

Transition metal complexes that display slow magnetic relaxation show promise for information storage, but our mechanistic understanding of the magnetic relaxation of such compounds remains limited. Here, the authors spectroscopically and computationally characterize the strength of spin–phonon couplings, which play an important role in the relaxation process.

03 July 2018 | doi: 10.1038/s41467-018-04896-0
Electronic structure of atoms and molecules  Inorganic chemistry  Magnetic materials  Optical spectroscopy 

Fractal modes and multi-beam generation from hybrid microlaser resonators OPEN
José A. Rivera, Thomas C. Galvin, Austin W. Steinforth & J. Gary Eden

Although fractal optical patterns have been realized previously, the direct generation of fractal modes from a laser has proven challenging. Here, Rivera et al. modify an optical cavity with a microsphere array to produce fractal laser modes and probe live cells, which serve as a component of the resonator.

03 July 2018 | doi: 10.1038/s41467-018-04945-8
Biophotonics  Lasers, LEDs and light sources  Microresonators 

Dynamic strain determination using fibre-optic cables allows imaging of seismological and structural features OPEN
Philippe Jousset, Thomas Reinsch, Trond Ryberg, Hanna Blanck, Andy Clarke, Rufat Aghayev, Gylfi P. Hersir, Jan Henninges, Michael Weber & Charlotte M. Krawczyk

Imaging the internal structure of faults remains challenging using conventional seismometers. Here, the authors use fibre-optic cables used for telecommunications to obtain strain data and identify faults and volcanic dykes in Iceland and suggest that fibre-optic cables could be used for hazard assessment.

03 July 2018 | doi: 10.1038/s41467-018-04860-y
Engineering  Environmental sciences  Natural hazards  Optics and photonics  Solid Earth sciences 

Novofumigatonin biosynthesis involves a non-heme iron-dependent endoperoxide isomerase for orthoester formation OPEN
Yudai Matsuda, Tongxuan Bai, Christopher B. W. Phippen, Christina S. Nødvig, Inge Kjærbølling, Tammi C. Vesth, Mikael R. Andersen, Uffe H. Mortensen, Charlotte H. Gotfredsen, Ikuro Abe & Thomas O. Larsen

Novofumigatonin is a meroterpenoid found in the fungus Aspergillus novofumigatus. Here, the authors elucidate the biosynthetic pathway of novofumigatonin and show that the endoperoxidase NvfI and the endoperoxide isomerase NvfE are involved in it.

03 July 2018 | doi: 10.1038/s41467-018-04983-2
Biocatalysis  Isomerases 

Tunable and switchable magnetic dipole patterns in nanostructured superconductors OPEN
Jun-Yi Ge, Vladimir N. Gladilin, Jacques Tempere, Jozef T. Devreese & Victor V. Moshchalkov

By designing superconducting materials the behavior of supercurrents can be controlled to give different emergent behavior. Ge et al. fabricate superconducting films in which currents form geometrically frustrated magnetic dipoles that can be tuned further by coupling to a vortex lattice.

03 July 2018 | doi: 10.1038/s41467-018-05045-3
Magnetic properties and materials  Superconducting properties and materials 

Evidence for line width and carrier screening effects on excitonic valley relaxation in 2D semiconductors OPEN
Yuhei Miyauchi, Satoru Konabe, Feijiu Wang, Wenjin Zhang, Alexander Hwang, Yusuke Hasegawa, Lizhong Zhou, Shinichiro Mouri, Minglin Toh, Goki Eda & Kazunari Matsuda

Atomically thin transition metal dichalcogenides offer a platform to explore the valley degree of freedom originating from their electronic band structure. Here, the authors use polarization- and time-resolved spectroscopy to investigate the temperature-dependent valley pseudospin relaxation processes in WSe2 monolayers.

03 July 2018 | doi: 10.1038/s41467-018-04988-x
Two-dimensional materials 

Synthesis of polymers with on-demand sequence structures via dually switchable and interconvertible polymerizations OPEN
Ze Zhang, Tian-You Zeng, Lei Xia, Chun-Yan Hong, De-Cheng Wu & Ye-Zi You

The synthesis of polymers with on-demand sequence structures is difficult but highly desirable. Here the authors show a dual switchable and controlled interconvertible polymerization involving two orthogonal polymerizations that are switched ON/OFF independent of each other with an external stimulus.

03 July 2018 | doi: 10.1038/s41467-018-05000-2
Polymer chemistry  Polymer synthesis 

Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase OPEN
Ivan Laponogov, Xiao-Su Pan, Dennis A. Veselkov, Galyna B. Skamrova, Trishant R. Umrekar, L. Mark Fisher & Mark R. Sanderson

Type 2 topoisomerases alter DNA supercoiling by an ATP-dependent reaction involving DNA passage through a cleaved DNA duplex. Here the authors present the crystal structure of the ParE ATPase domains of S. pneumoniae topoisomerase IV, in complex with a captured DNA oligonucleotide.

03 July 2018 | doi: 10.1038/s41467-018-05005-x
DNA recombination  X-ray crystallography 

Task-dependent representations of stimulus and choice in mouse parietal cortex OPEN
Gerald N. Pho, Michael J. Goard, Jonathan Woodson, Benjamin Crawford & Mriganka Sur

The precise role of PPC in transforming sensory signals to relevant actions is not yet clear. Here, the authors show that unlike V1, which is largely driven by visual input, PPC is strongly task-dependent and exhibits a mixture of stimulus and choice signals in a visual decision task.

03 July 2018 | doi: 10.1038/s41467-018-05012-y
Decision  Visual system 

Control over the emerging chirality in supramolecular gels and solutions by chiral microvortices in milliseconds OPEN
Jiashu Sun, Yike Li, Fusheng Yan, Chao Liu, Yutao Sang, Fei Tian, Qiang Feng, Pengfei Duan, Li Zhang, Xinghua Shi, Baoquan Ding & Minghua Liu

Symmetry breaking and chiral amplification are fundamental principles in chemistry and biology but the control of initial chiral bias remains a great challenge. Here the authors show that chiral microvortices can lead to a selection of initial chiral bias of supramolecular systems composed of achiral molecules.

03 July 2018 | doi: 10.1038/s41467-018-05017-7
Mechanical engineering  Self-assembly 

Topochemical conversion of an imine- into a thiazole-linked covalent organic framework enabling real structure analysis OPEN
Frederik Haase, Erik Troschke, Gökcen Savasci, Tanmay Banerjee, Viola Duppel, Susanne Dörfler, Martin M. J. Grundei, Asbjörn M. Burow, Christian Ochsenfeld, Stefan Kaskel & Bettina V. Lotsch

Stabilization of covalent organic frameworks (COFs) by post-synthetic locking is a powerful tool to push the limits of COF utilization. Here the authors demonstrate a sulfur-assisted conversion of an imine-linked COF into a thiazole-linked COF, with retention of crystallinity and porosity, allowing for direct imaging of defects in COFs.

03 July 2018 | doi: 10.1038/s41467-018-04979-y
Organic molecules in materials science  Structural properties 

Transparent and flexible fingerprint sensor array with multiplexed detection of tactile pressure and skin temperature OPEN
Byeong Wan An, Sanghyun Heo, Sangyoon Ji, Franklin Bien & Jang-Ung Park

Next-generation mobile security devices require fingerprint sensors that can be incorporated directly into the display. Here, Park et al. demonstrate a highly transparent, multifunctional capacitive fingerprint sensor array that simultaneously detects tactile pressure and finger skin temperature.

03 July 2018 | doi: 10.1038/s41467-018-04906-1
Electronic devices  Electronic properties and materials 

Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics OPEN
Sarah Auburn, Ernest D. Benavente, Olivo Miotto, Richard D. Pearson, Roberto Amato, Matthew J. Grigg, Bridget E. Barber, Timothy William, Irene Handayuni, Jutta Marfurt, Hidayat Trimarsanto, Rintis Noviyanti, Kanlaya Sriprawat, Francois Nosten, Susana Campino, Taane G. Clark, Nicholas M. Anstey, Dominic P. Kwiatkowski & Ric N. Price

Plasmodium vivax incidence in Malaysia has declined markedly over the last decade, despite evidence of chloroquine resistance. Here, Auburn et al. compare population structure of P. vivax in Malaysia to regions with intermediate and high transmission and identify genetic regions under putative selection.

03 July 2018 | doi: 10.1038/s41467-018-04965-4
Epidemiology  Parasite genetics  Parasite genomics  Population genetics 

Immediate action is the best strategy when facing uncertain climate change OPEN
Maria Abou Chakra, Silke Bumann, Hanna Schenk, Andreas Oschlies & Arne Traulsen

Reducing the adverse effects of climate change triggered by human activity requires cooperation on a global scale. Modelling this challenge as an evolutionary game shows that the emerging contributions of selfish players depend strongly on the risk scenario at stake.

02 July 2018 | doi: 10.1038/s41467-018-04968-1
Climate-change mitigation  Cultural evolution  Social sciences 

Vapor sublimation and deposition to build porous particles and composites OPEN
Hsing-Ying Tung, Zhen-Yu Guan, Ting-Yu Liu & Hsien-Yeh Chen

Fabrication of porous nanoparticles is often hampered by low efficiency production methods, challenging isolation of the material and poor control over the fabrication process. Here the authors demonstrate a facile ice-template vapor-phase synthesis which allows for production of porous poly-para-xylylene particles on a large scale.

02 July 2018 | doi: 10.1038/s41467-018-04975-2
Chemical engineering  Materials chemistry  Materials science  Nanoscale materials 

Unmasking chloride attack on the passive film of metals OPEN
B. Zhang, J. Wang, B. Wu, X. W. Guo, Y. J. Wang, D. Chen, Y. C. Zhang, K. Du, E. E. Oguzie & X. L. Ma

Collecting experimental evidence of chloride ion attack on protective passive metallic films due to corrosion remains challenging. Here, the authors show that the boundaries between nanocrystals and amorphous regions in the passive film ease chloride transport even as they do not coincide with areas of high chloride concentration.

02 July 2018 | doi: 10.1038/s41467-018-04942-x
Corrosion  Metals and alloys  Microscopy 

TGF-β signaling alters H4K20me3 status via miR-29 and contributes to cellular senescence and cardiac aging OPEN
Guoliang Lyu, Yiting Guan, Chao Zhang, Le Zong, Lei Sun, Xiaoke Huang, Li Huang, Lijun Zhang, Xiao-Li Tian, Zhongjun Zhou & Wei Tao

Cellular senescence is associated with epigenetic remodeling. Here, the authors report that TGF-β signaling promotes miR-29 mediated loss of H4K20me3 thus accelerating senescence.

02 July 2018 | doi: 10.1038/s41467-018-04994-z
Cell biology  Senescence 

BrlR from Pseudomonas aeruginosa is a receptor for both cyclic di-GMP and pyocyanin OPEN
Feng Wang, Qing He, Jia Yin, Sujuan Xu, Wei Hu & Lichuan Gu

The virulence factor pyocyanin and the second messenger c-di-GMP regulate biofilm formation and antibiotic tolerance in Pseudomonas aeruginosa. Here, the authors perform structural and biochemical analyses to show that a transcriptional regulator, BrlR, acts as a receptor for both pyocyanin and c-di-GMP.

02 July 2018 | doi: 10.1038/s41467-018-05004-y
Biofilms  Transcription 

Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway OPEN
Tsing-Lee Tang-Huau, Paul Gueguen, Christel Goudot, Mélanie Durand, Mylène Bohec, Sylvain Baulande, Benoit Pasquier, Sebastian Amigorena & Elodie Segura

Cross-presentation, or the presentation of exogenous antigens on MHC-I, is thought to be restricted to dendritic cells (DCs). Here the authors show that human DCs and macrophages developed in vivo from monocytes can both perform cross-presentation using a non-conventional pathway, but only DCs are capable of inducing cytotoxic CD8+ T cells.

02 July 2018 | doi: 10.1038/s41467-018-04985-0
Antigen processing and presentation  Cellular immunity  Dendritic cells  Peritoneal macrophages 

Nuclear microtubule filaments mediate non-linear directional motion of chromatin and promote DNA repair OPEN
Roxanne Oshidari, Jonathan Strecker, Daniel K. C. Chung, Karan J. Abraham, Janet N. Y. Chan, Christopher J. Damaren & Karim Mekhail

Following DNA damage, different processes come to action to aid repair. The authors here find that microtubule filaments within the cell nucleus capture and non-randomly mobilize damaged chromatin to mediate DNA repair.

02 July 2018 | doi: 10.1038/s41467-018-05009-7
Fungi  Genomic instability  Motor protein function  Nuclear envelope  Nucleoskeleton 

Early Palaeozoic ocean anoxia and global warming driven by the evolution of shallow burrowing OPEN
Sebastiaan van de Velde, Benjamin J. W. Mills, Filip J. R. Meysman, Timothy M. Lenton & Simon W. Poulton

The extent to which the onset of bioturbation affected global biogeochemistry during the Palaeozoic remains unclear. Here, the authors integrate bioturbation into the COPSE model, compare output with geochemical proxies, and suggest shallow burrowing contributed to a global low oxygen state during the early Cambrian.

02 July 2018 | doi: 10.1038/s41467-018-04973-4
Element cycles  Marine chemistry 

Synthetic molecular evolution of hybrid cell penetrating peptides OPEN
W. Berkeley Kauffman, Shantanu Guha & William C. Wimley

Therapeutic peptide nucleic acids can be delivered into cells by conjugation to cell penetrating peptides (CPPs), but efficiency is usually low. Here the authors use synthetic molecular evolution and a luciferase-based library screen to generate new CPPs with improved efficiency and lower toxicity.

02 July 2018 | doi: 10.1038/s41467-018-04874-6
Biotechnology  Cell delivery 

Placental H3K27me3 establishes female resilience to prenatal insults OPEN
Bridget M. Nugent, Carly M. O’Donnell, C. Neill Epperson & Tracy L. Bale

Sex differences in placental O-linked N-acetylglucosamine transferase (OGT) activity mediate the effects of prenatal stress on neurodevelopmental programming. Here authors provide evidence that OGT confers variation in vulnerability to prenatal insults by establishing sex-specific trophoblast gene expression via regulation of H3K27me3.

02 July 2018 | doi: 10.1038/s41467-018-04992-1
Epigenetics  Neural patterning  Reprogramming  Stress and resilience 

Early-warning signals for Dansgaard-Oeschger events in a high-resolution ice core record OPEN
Niklas Boers

The Dansgaard-Oeschger events are remarkable examples of abrupt climate changes during the last ice age, yet a physical explanation remains debated. Here, Boers shows that these events are preceded by early-warning signals in the high-frequency variability, providing valuable constraints regarding physical causes.

02 July 2018 | doi: 10.1038/s41467-018-04881-7
Cryospheric science  Palaeoclimate 

Osteocytic oxygen sensing controls bone mass through epigenetic regulation of sclerostin OPEN
Steve Stegen, Ingrid Stockmans, Karen Moermans, Bernard Thienpont, Patrick H. Maxwell, Peter Carmeliet & Geert Carmeliet

Osteocytes reside in a low oxygen environment, but it is not clear if oxygen sensing regulates their function. Here, the authors show that deletion of the oxygen sensor prolyl hydroxylase 2 in osteocytes leads to increased bone mass via regulation of sclerostin, and reduces bone loss in mouse models of osteoporosis.

02 July 2018 | doi: 10.1038/s41467-018-04679-7
Bone  Osteoporosis 

CEACAM1 promotes CD8+ T cell responses and improves control of a chronic viral infection OPEN
Vishal Khairnar, Vikas Duhan, Ashwini M. Patil, Fan Zhou, Hilal Bhat, Christine Thoens, Piyush Sharma, Tom Adomati, Sarah-Kim Friendrich, Judith Bezgovsek, Janine D. Dreesen, Gunther Wennemuth, Astrid M. Westendorf, Gennadiy Zelinskyy, Ulf Dittmer, Cornelia Hardt, Jörg Timm, Joachim R. Göthert, Philipp A. Lang, Bernhard B. Singer et al.

Chronic viral infections are frequently associated with the dysfunction of CD8+ T cells which includes loss of function and results in CD8+ T cell exhaustion. Here the authors show a role of CEACAM1 in promoting responsive CD8+ T cells in the context of a chronic lymphocytic choriomeningitis virus (LCMV) infection model.

02 July 2018 | doi: 10.1038/s41467-018-04832-2
CD8-positive T cells  Cellular immunity  Viral infection 

Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria OPEN
Zbigniew Pietras, Magdalena A. Wojcik, Lukasz S. Borowski, Maciej Szewczyk, Tomasz M. Kulinski, Dominik Cysewski, Piotr P. Stepien, Andrzej Dziembowski & Roman J. Szczesny

G-rich RNAs encoded in mitochondrial DNA are prone to form four-stranded structures called G-quadruplexes (G4s). Here the authors show using in vitro and in vivo approaches that GRSF1 promotes melting of G4 RNA structures in mtRNAs, thus leading to their decay by the hSuv3–PNPase complex.

02 July 2018 | doi: 10.1038/s41467-018-05007-9
Gene expression  Mitochondria  RNA decay  RNA quality control 

Taxonomic and functional diversity change is scale dependent OPEN
Marta A. Jarzyna & Walter Jetz

The evidence for and implications of biodiversity change remain widely debated. Jarzyna and Jetz demonstrate a strong and varying scale dependence of avian taxonomic and functional diversity, highlighting the importance of scale when assessing biodiversity change.

02 July 2018 | doi: 10.1038/s41467-018-04889-z
Biodiversity  Macroecology 

A moisture function of soil heterotrophic respiration that incorporates microscale processes OPEN
Zhifeng Yan, Ben Bond-Lamberty, Katherine E. Todd-Brown, Vanessa L. Bailey, SiLiang Li, CongQiang Liu & Chongxuan Liu

Empirical moisture functions that describe the relationship between soil heterotrophic respiration and moisture introduce considerable uncertainty in soil CO2 flux predictions. Here, the authors derive a process-based moisture function by incorporating mechanisms that control soil heterotrophic respiration.

02 July 2018 | doi: 10.1038/s41467-018-04971-6
Carbon cycle 

Giant antidamping orbital torque originating from the orbital Rashba-Edelstein effect in ferromagnetic heterostructures OPEN
Xi Chen, Yang Liu, Guang Yang, Hui Shi, Chen Hu, Minghua Li & Haibo Zeng

The emerging spintronics applications are hampered by low current-induced torque efficiency in, for example, inversion-symmetry-breaking ferromagnetic heterostructures. Here the authors demonstrate an orbital Rashba-Edelstein effect which can enhance the torque efficiency in Pt/Co/SiO2/Pt films due to the intrinsic Co 3d orbital anisotropy.

02 July 2018 | doi: 10.1038/s41467-018-05057-z
Electronic devices  Magnetic properties and materials  Spintronics 

Prognostic significance of frequent CLDN18-ARHGAP26/6 fusion in gastric signet-ring cell cancer OPEN
Yang Shu, Weihan Zhang, Qianqian Hou, Linyong Zhao, Shouyue Zhang, Jiankang Zhou, Xiaohai Song, Yan Zhang, Dan Jiang, Xinzu Chen, Peiqi Wang, Xuyang Xia, Fei Liao, Dandan Yin, Xiaolong Chen, Xueyan Zhou, Duyu Zhang, Senlin Yin, Kun Yang, Jianping Liu et al.

Signet-ring cell carcinoma (SRCC) is a unique type of gastric cancer with no prognostic features. Here, the authors report a CLDN18-ARHGAP26/6 gene fusion in patients with a high signet-ring cell content, poor survival outcomes, and who experience no benefit from platinum/fluoropyrimidines-based chemotherapy.

30 June 2018 | doi: 10.1038/s41467-018-04907-0
Cancer genomics  Gastric cancer 

High-performance bifunctional porous non-noble metal phosphide catalyst for overall water splitting OPEN
Fang Yu, Haiqing Zhou, Yufeng Huang, Jingying Sun, Fan Qin, Jiming Bao, William A. Goddard III, Shuo Chen & Zhifeng Ren

Water electrolysis provides a carbon-neutral means to generate hydrogen fuel from water, but the process typically requires expensive, rare metal catalysts. Here, the authors prepare hydrogen- and oxygen-evolving electrocatalysts from earth-abundant elements that outperform noble-metal counterparts.

29 June 2018 | doi: 10.1038/s41467-018-04746-z
Electrocatalysis  Materials chemistry  Nanoscale materials 

Targeting EZH2 reactivates a breast cancer subtype-specific anti-metastatic transcriptional program OPEN
Alison Hirukawa, Harvey W. Smith, Dongmei Zuo, Catherine R. Dufour, Paul Savage, Nicholas Bertos, Radia M. Johnson, Tung Bui, Guillaume Bourque, Mark Basik, Vincent Giguère, Morag Park & William J. Muller

Histone modifications in cancer can contribute to pathogenesis. Here, the authors demonstrate that targeting epigenetic modifier Ezh2 hinders metastatic behaviour in Luminal B breast cancer models, and highlight a mechanism where Ezh2 contributes to metastatic behaviour by repression of FOXC1.

29 June 2018 | doi: 10.1038/s41467-018-04864-8
Breast cancer  Metastasis 

One-second coherence for a single electron spin coupled to a multi-qubit nuclear-spin environment OPEN
M. H. Abobeih, J. Cramer, M. A. Bakker, N. Kalb, M. Markham, D. J. Twitchen & T. H. Taminiau

The coherence of quantum registers is limited by unwanted interactions, both between the qubits and with the environment. Here the authors extend the coherence time of a nitrogen-vacancy centre beyond a second by characterizing and decoupling its interactions with a multi-qubit nuclear spin environment.

29 June 2018 | doi: 10.1038/s41467-018-04916-z
Condensed-matter physics  Quantum information  Qubits 

Oridonin is a covalent NLRP3 inhibitor with strong anti-inflammasome activity OPEN
Hongbin He, Hua Jiang, Yun Chen, Jin Ye, Aoli Wang, Chao Wang, Qingsong Liu, Gaolin Liang, Xianming Deng, Wei Jiang & Rongbin Zhou

The small molecule oridonin (Ori) from the traditional Chinese herb Rabdosia rubescens has anti-inflammatory activity. Here the authors show that Ori can be covalently linked to NLRP3 to prevent assembly of the NLRP3 inflammasome, and to ameliorate inflammation in several mouse disease models.

29 June 2018 | doi: 10.1038/s41467-018-04947-6
Chronic inflammation  Inflammasome  Target identification  Target validation 

Auditory cortical activity drives feedback-dependent vocal control in marmosets OPEN
Steven J. Eliades & Joji Tsunada

During vocalization, mammals change their vocal production to compensate for altered auditory feedback. Here, Eliades and Tsunada show that neural activity in the marmoset’s auditory cortex mediates this effect, and that stimulation of the auditory cortex evokes similar changes in vocalization.

29 June 2018 | doi: 10.1038/s41467-018-04961-8
Auditory system  Cortex  Neuroscience 

2D transition metal dichalcogenides with glucan multivalency for antibody-free pathogen recognition OPEN
Tae Woog Kang, Juhee Han, Sin Lee, In-Jun Hwang, Su-Ji Jeon, Jong-Min Ju, Man-Jin Kim, Jin-Kyoung Yang, Byoengsun Jun, Chi Ho Lee, Sang Uck Lee & Jong-Ho Kim

The detection of pathogenic microorganisms is key consideration for safety across a wide range of fields. Here, the authors report on the simultaneous exfoliation and functionalisation of transition metal dichalcogenides with dextran for antibody-free detection of pathogenic Escherichia coli.

29 June 2018 | doi: 10.1038/s41467-018-04997-w
Bacteria  Biosensors  Two-dimensional materials 

Clustering huge protein sequence sets in linear time OPEN
Martin Steinegger & Johannes Söding

Billions of metagenomic and genomic sequences fill up public datasets, which makes similarity clustering an important and time-critical analysis step. Here, the authors develop Linclust, an algorithm with linear time complexity that can cluster over a billion sequences within hours on a single server.

29 June 2018 | doi: 10.1038/s41467-018-04964-5
Environmental microbiology  Functional clustering  Protein sequence analyses  Software 

Understanding crystallization pathways leading to manganese oxide polymorph formation OPEN
Bor-Rong Chen, Wenhao Sun, Daniil A. Kitchaev, John S. Mangum, Vivek Thampy, Lauren M. Garten, David S. Ginley, Brian P. Gorman, Kevin H. Stone, Gerbrand Ceder, Michael F. Toney & Laura T. Schelhas

Minor variations in synthesis conditions can redirect crystallization pathways through different nonequilibrium intermediates. Here, the authors present a theoretical framework to predict which polymorphs appear during MnO2 precipitation, which is validated by in situ X-ray scattering of reaction progression.

29 June 2018 | doi: 10.1038/s41467-018-04917-y
Computational chemistry  Materials chemistry  Materials for energy and catalysis 

Prioritizing network communities OPEN
Marinka Zitnik, Rok Sosič & Jure Leskovec

Community detection allows one to decompose a network into its building blocks. While communities can be identified with a variety of methods, their relative importance can’t be easily derived. Here the authors introduce an algorithm to identify modules which are most promising for further analysis.

29 June 2018 | doi: 10.1038/s41467-018-04948-5
Complex networks  Computational models  Data mining  Network topology 

Surface ocean pH variations since 1689 CE and recent ocean acidification in the tropical South Pacific OPEN
Henry C. Wu, Delphine Dissard, Eric Douville, Dominique Blamart, Louise Bordier, Aline Tribollet, Florence Le Cornec, Edwige Pons-Branchu, Arnaud Dapoigny & Claire E. Lazareth

Ocean acidification due to the industrial era is a major marine environmental concern, yet little is known on the historical ocean pH changes prior to human influence. Here, Wu et al. show that tropical South Pacific seawater pH is linked to ENSO pacing and has recently been decreasing rapidly.

29 June 2018 | doi: 10.1038/s41467-018-04922-1
Biogeochemistry  Climate change  Climate sciences  Ocean sciences  Palaeoceanography 

Stable complete methane oxidation over palladium based zeolite catalysts OPEN
Andrey W. Petrov, Davide Ferri, Frank Krumeich, Maarten Nachtegaal, Jeroen A. van Bokhoven & Oliver Kröcher

Palladium supported on zeolite is a highly active catalyst for complete methane oxidation, but its stability needs to be improved. Here, the authors design a highly active catalyst resistant to steam-induced sintering under reaction conditions by alleviating the high mobility of palladium nanoparticles and zeolite degradation.

29 June 2018 | doi: 10.1038/s41467-018-04748-x
Catalyst synthesis  Chemical engineering  Heterogeneous catalysis 

Pervasive genetic interactions modulate neurodevelopmental defects of the autism-associated 16p11.2 deletion in Drosophila melanogaster OPEN
Janani Iyer, Mayanglambam Dhruba Singh, Matthew Jensen, Payal Patel, Lucilla Pizzo, Emily Huber, Haley Koerselman, Alexis T. Weiner, Paola Lepanto, Komal Vadodaria, Alexis Kubina, Qingyu Wang, Abigail Talbert, Sneha Yennawar, Jose Badano, J. Robert Manak, Melissa M. Rolls, Arjun Krishnan & Santhosh Girirajan

The 16p11.2 deletion leads to a range of neurodevelopmental phenotypes, but to date, sequencing studies have not been able to pinpoint individual genes that are causative for the disease on their own. Here, using Drosophila homologs of 14 16p11.2 genes, the authors take a combinatorial approach to show that gene interactions contribute to a neurological phenotype.

29 June 2018 | doi: 10.1038/s41467-018-04882-6
Autism spectrum disorders  Medical genomics 

Harnessing synthetic lethality to predict the response to cancer treatment OPEN
Joo Sang Lee, Avinash Das, Livnat Jerby-Arnon, Rand Arafeh, Noam Auslander, Matthew Davidson, Lynn McGarry, Daniel James, Arnaud Amzallag, Seung Gu Park, Kuoyuan Cheng, Welles Robinson, Dikla Atias, Chani Stossel, Ella Buzhor, Gidi Stein, Joshua J. Waterfall, Paul S. Meltzer, Talia Golan, Sridhar Hannenhalli et al.

Synthetic lethality (SL) offers a new precision oncology approach, which is based on targeting cancer-specific vulnerabilities across the whole genome, going beyond cancer drivers. The authors develop an approach termed ISLE to identify clinically relevant SL interactions and use them for patient stratification and novel target identification.

29 June 2018 | doi: 10.1038/s41467-018-04647-1
Cancer genomics  Predictive markers  Statistical methods 

Continuous biomarker monitoring by particle mobility sensing with single molecule resolution OPEN
Emiel W. A. Visser, Junhong Yan, Leo J. van IJzendoorn & Menno W. J. Prins

Biomarkers are natural indicators of some biological conditions, often used in diagnostics. Here, the authors developed a biosensor that continuously measures concentrations of DNA or protein biomarkers, and is based on particles that change mobility by directly interacting with individual molecules.

29 June 2018 | doi: 10.1038/s41467-018-04802-8
Biosensors  Sensors  Single-molecule biophysics 

Very large tunneling magnetoresistance in layered magnetic semiconductor CrI3 OPEN
Zhe Wang, Ignacio Gutiérrez-Lezama, Nicolas Ubrig, Martin Kroner, Marco Gibertini, Takashi Taniguchi, Kenji Watanabe, Ataç Imamoğlu, Enrico Giannini & Alberto F. Morpurgo

Layered van der Waals compounds offer opportunities to visit new physical phenomena in two dimensional materials. Here the authors report large tunneling magnetoresistance through exfoliated CrI3 crystals and attribute its evolution to the multiple transitions to different magnetic states.

28 June 2018 | doi: 10.1038/s41467-018-04953-8
Electronic and spintronic devices  Electronic properties and materials  Magnetic properties and materials  Two-dimensional materials 

Long-haul optical transmission link using low-noise phase-sensitive amplifiers OPEN
Samuel L.I. Olsson, Henrik Eliasson, Egon Astra, Magnus Karlsson & Peter A. Andrekson

Phase-sensitive amplifiers are known for low-noise amplification and nonlinearity mitigation, but their long-haul implementation is challenging. The authors use these amplifiers to show a long-haul optical link with a 5.6-times reach improvement over conventional amplifier performance, affirming their viability as an alternative technology.

28 June 2018 | doi: 10.1038/s41467-018-04956-5
Fibre optics and optical communications  Nonlinear optics 

Layered liquid crystal elastomer actuators OPEN
Tyler Guin, Michael J. Settle, Benjamin A. Kowalski, Anesia D. Auguste, Richard V. Beblo, Gregory W. Reich & Timothy J. White

Liquid crystalline elastomers (LCE) exhibit shape transformation when subjected to various stimuli, but the achievable thickness of LCE films is limited. Here the authors demonstrate arbitrarily thick LCE films that are continuous in composition and maintain the director orientation, prescribed into the material.

28 June 2018 | doi: 10.1038/s41467-018-04911-4
Actuators  Liquid crystals  Polymers 

An all-dielectric metasurface as a broadband optical frequency mixer OPEN
Sheng Liu, Polina P. Vabishchevich, Aleksandr Vaskin, John L. Reno, Gordon A. Keeler, Michael B. Sinclair, Isabelle Staude & Igal Brener

Frequency mixers are hard to achieve at optical frequencies because it is difficult to meet different phase-matching conditions. Here, the authors show that GaAs metasurfaces can mix laser beams to generate eleven new wavelengths through different nonlinear optical processes occurring simultaneously.

28 June 2018 | doi: 10.1038/s41467-018-04944-9
Metamaterials  Nanophotonics and plasmonics  Nonlinear optics 

The origin and remolding of genomic islands of differentiation in the European sea bass OPEN
Maud Duranton, François Allal, Christelle Fraïsse, Nicolas Bierne, François Bonhomme & Pierre-Alexandre Gagnaire

The speciation process tends to generate ‘genomic islands’ of increased divergence. Here, the authors use haplotype–resolved whole-genome sequences of European sea bass lineages to infer divergence history and show that linked selection generated genomic islands that resist introgression at secondary contact.

28 June 2018 | doi: 10.1038/s41467-018-04963-6
Population genetics  Speciation 

Glutamic acid–valine–citrulline linkers ensure stability and efficacy of antibody–drug conjugates in mice OPEN
Yasuaki Anami, Chisato M. Yamazaki, Wei Xiong, Xun Gui, Ningyan Zhang, Zhiqiang An & Kyoji Tsuchikama

The valine-citrulline dipeptide, which is used as a cleavable linker for antibody-drug conjugates, is instable in mouse plasma. Here, the authors developed a glutamic acid–valine–citrulline tripeptide sequence as a stable alternative that still is susceptible to cathepsin-mediated cleavage.

28 June 2018 | doi: 10.1038/s41467-018-04982-3
Drug delivery  Targeted therapies 

Direct evidence for hula twist and single-bond rotation photoproducts OPEN
Aaron Gerwien, Monika Schildhauer, Stefan Thumser, Peter Mayer & Henry Dube

Photoisomerization mechanisms govern important (bio)catalytic reactions and lie at the core of many functional materials. Here, the authors report a molecular setup that allows for the direct and separate observation of three fundamental photoreactions, namely the hula twist, single-bond rotation, as well as double-bond isomerization.

28 June 2018 | doi: 10.1038/s41467-018-04928-9
Organic chemistry  Photochemistry  Physical chemistry 

A model for super El Niños OPEN
Saji N. Hameed, Dachao Jin & Vishnu Thilakan

Despite advances in ENSO modeling, super El Niño events remain largely unpredictable. Hameed et al. postulate that ENSO-IOD interaction is crucial for super El Niño development and identify a self-limiting factor that constrains ENSO dynamics from generating these extreme events on their own.

28 June 2018 | doi: 10.1038/s41467-018-04803-7
Atmospheric dynamics  Computational science  Physical oceanography 

Doping-induced structural phase transition in cobalt diselenide enables enhanced hydrogen evolution catalysis OPEN
Ya-Rong Zheng, Ping Wu, Min-Rui Gao, Xiao-Long Zhang, Fei-Yue Gao, Huan-Xin Ju, Rui Wu, Qiang Gao, Rui You, Wei-Xin Huang, Shou-Jie Liu, Shan-Wei Hu, Junfa Zhu, Zhenyu Li & Shu-Hong Yu

Transition metal dichalcogenides represent an exciting class of earth-abundant hydrogen-from-water electrocatalysts, although low efficiencies limit commercialization. Here, authors present a doping strategy to induce a phase transition in cobalt selenide and boost H2-evolution performance.

28 June 2018 | doi: 10.1038/s41467-018-04954-7
Electrocatalysis  Solid-state chemistry  Structural properties 

Quantitative spatial analysis of haematopoiesis-regulating stromal cells in the bone marrow microenvironment by 3D microscopy OPEN
Alvaro Gomariz, Patrick M. Helbling, Stephan Isringhausen, Ute Suessbier, Anton Becker, Andreas Boss, Takashi Nagasawa, Grégory Paul, Orcun Goksel, Gábor Székely, Szymon Stoma, Simon F. Nørrelykke, Markus G. Manz & César Nombela-Arrieta

The bone marrow microenvironment modulates haematopoiesis, stem cell maintenance and differentiation. Here, the authors use 3D microscopy to map the topography of haematopoietic stem cell niche stromal components.

28 June 2018 | doi: 10.1038/s41467-018-04770-z
Confocal microscopy  Haematopoiesis  Image processing  Statistical methods  Stem-cell niche 

Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta OPEN
Chloé S. Baron, Lennart Kester, Anna Klaus, Jean-Charles Boisset, Roshana Thambyrajah, Laurent Yvernogeau, Valérie Kouskoff, Georges Lacaud, Alexander van Oudenaarden & Catherine Robin

Haematopoietic stem cells (HSCs) are generated from haemogenic endothelial (HE) cells in vertebrate embryo aortas. Here, the authors perform single-cell RNA-sequencing of cells isolated from embryonic mouse aortas to identify genes and transcription factor networks activated during the endothelial-to-haematopoietic switch.

28 June 2018 | doi: 10.1038/s41467-018-04893-3
Cell signalling  Haematopoietic stem cells 

Neuromorphic computing with multi-memristive synapses OPEN
Irem Boybat, Manuel Le Gallo, S. R. Nandakumar, Timoleon Moraitis, Thomas Parnell, Tomas Tuma, Bipin Rajendran, Yusuf Leblebici, Abu Sebastian & Evangelos Eleftheriou

Memristive technology is a promising avenue towards realizing efficient non-von Neumann neuromorphic hardware. Boybat et al. proposes a multi-memristive synaptic architecture with a counter-based global arbitration scheme to address challenges associated with the non-ideal memristive device behavior.

28 June 2018 | doi: 10.1038/s41467-018-04933-y
Computational science  Electronic devices  Network models 

Go/No-Go task engagement enhances population representation of target stimuli in primary auditory cortex OPEN
Sophie Bagur, Martin Averseng, Diego Elgueda, Stephen David, Jonathan Fritz, Pingbo Yin, Shihab Shamma, Yves Boubenec & Srdjan Ostojic

Sensory areas are thought to process stimulus information while higher-order processing occurs in association cortices. Here the authors report that during task engagement population activity in ferret primary auditory cortex shifts away from encoding stimulus features toward detection of the behaviourally relevant targets.

28 June 2018 | doi: 10.1038/s41467-018-04839-9
Cortex  Neural decoding  Sensory processing 

Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris OPEN
Alexander Vogel, Rainer Schwacke, Alisandra K. Denton, Björn Usadel, Julien Hollmann, Karsten Fischer, Anthony Bolger, Maximilian H.-W. Schmidt, Marie E. Bolger, Heidrun Gundlach, Klaus F. X. Mayer, Hanna Weiss-Schneeweiss, Eva M. Temsch & Kirsten Krause

Parasitic lifestyles leave unique genomic footprints. Here, the authors describe the genome sequence of a parasitic plant, Cuscuta campestris, and find that gene losses and host gene acquisitions reflect the independence from photosynthesis and the ability to retain and express chunks of foreign genomic DNA.

28 June 2018 | doi: 10.1038/s41467-018-04344-z
Genome evolution  Plant molecular biology 

FRET-enhanced photostability allows improved single-molecule tracking of proteins and protein complexes in live mammalian cells OPEN
Srinjan Basu, Lisa-Maria Needham, David Lando, Edward J. R. Taylor, Kai J. Wohlfahrt, Devina Shah, Wayne Boucher, Yi Lei Tan, Lawrence E. Bates, Olga Tkachenko, Julie Cramard, B. Christoffer Lagerholm, Christian Eggeling, Brian Hendrich, Dave Klenerman, Steven F. Lee & Ernest D. Laue

Single molecule tracking of fluorescent proteins in live cells is temporally limited by fluorophore photobleaching. Here the authors show using fluorophore pairs that FRET competes with photobleaching to improve photostability and allow longer-term tracking of both single proteins and complexes.

28 June 2018 | doi: 10.1038/s41467-018-04486-0
Cellular imaging  Fluorescence imaging  Single-molecule biophysics  Super-resolution microscopy 

Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks OPEN
Mun-Kit Choy, Biola M. Javierre, Simon G. Williams, Stephanie L. Baross, Yingjuan Liu, Steven W. Wingett, Artur Akbarov, Chris Wallace, Paula Freire-Pritchett, Peter J. Rugg-Gunn, Mikhail Spivakov, Peter Fraser & Bernard D. Keavney

Human embryonic stem cell-derived cardiomyocytes (hESC-CM) are a widely used model to study cardiac genomics. Here, Choy et al. perform promoter capture Hi-C to map long-range chromosomal interactions of hESC-CMs and to study overlap of such regions with genetic loci associated with cardiac phenotypes.

28 June 2018 | doi: 10.1038/s41467-018-04931-0
Cardiovascular genetics  Chromatin structure  Gene regulation  Genetic variation 

Global pairwise RNA interaction landscapes reveal core features of protein recognition OPEN
Qin Zhou, Nikesh Kunder, José Alberto De la Paz, Alexandra E. Lasley, Vandita D. Bhat, Faruck Morcos & Zachary T. Campbell

RNA–protein interactions often depend on the recognition of extended RNA elements but the identification of these motifs is challenging. Here, the authors present a global integrated approach to analyze RNA–protein binding landscapes, mapping extended RNA interaction motifs for four RNA-binding proteins.

28 June 2018 | doi: 10.1038/s41467-018-04729-0
High-throughput screening  RNA-binding proteins  RNA sequencing  Statistical methods 

Natural selection of a GSK3 determines rice mesocotyl domestication by coordinating strigolactone and brassinosteroid signaling OPEN
Shiyong Sun, Tao Wang, Linlin Wang, Xiaoming Li, Yancui Jia, Chang Liu, Xuehui Huang, Weibo Xie & Xuelu Wang

Long mesocotyl is a critical trait for the application of rice deep direct seeding or mechanized dry seeding cultivation method. Here, Sun et al. find OsGSK2 is selected for mesocotyl length variation during domestication and it coordinates strigolactone and brassinosteroid signaling to determine mesocotyl elongation.

28 June 2018 | doi: 10.1038/s41467-018-04952-9
Brassinosteroid  Natural variation in plants  Plant domestication  Strigolactone 

Prolonged abstinence from cocaine or morphine disrupts separable valuations during decision conflict OPEN
Brian M. Sweis, A. David Redish & Mark J. Thomas

Neuroeconomic theories suggest that conflict during decision, such as exhibited by relapsing drug addicts who continue drug use despite stated wishes not to, might arise from separable processes in decision making. Here the authors test mice in a foraging task designed to separate these processes and find that mice show alterations in separable components of decision conflict following abstinence from cocaine versus morphine.

28 June 2018 | doi: 10.1038/s41467-018-04967-2
Motivation  Reward 

Possible nitrogen fertilization of the early Earth Ocean by microbial continental ecosystems OPEN
Christophe Thomazo, Estelle Couradeau & Ferran Garcia-Pichel

How the Early Earth transitioned from an abiotic world to the modern biogeochemical Earth system remains unclear. Here, the authors show that colonization of a minor fraction of Archean landmasses by topsoil bacteria would have been enough to match the modern land-to-ocean nitrogen export of ammonium and nitrate.

28 June 2018 | doi: 10.1038/s41467-018-04995-y
Element cycles 

Coherent two-dimensional electronic mass spectrometry OPEN
Sebastian Roeding & Tobias Brixner

Multidimensional spectroscopy is a powerful tool in exploring photo-induced dynamics and electron coupling processes in molecules. Here the authors demonstrate coherent two-dimensional electronic mass spectrometry on molecular beams and its application to photoionization studies of the NO2 molecule.

28 June 2018 | doi: 10.1038/s41467-018-04927-w
Atomic and molecular interactions with photons  Excited states  Reaction kinetics and dynamics  Optical spectroscopy 

Designing a magnesium alloy with high strength and high formability OPEN
T. T. T. Trang, J. H. Zhang, J. H. Kim, A. Zargaran, J. H. Hwang, B.-C. Suh & N. J. Kim

Despite being the lightest structural alloys, obtaining magnesium alloys with both high strength and high formability remains a challenge. Here, the authors use precipitation and elemental segregation to design a magnesium alloy with high strength and high formability.

28 June 2018 | doi: 10.1038/s41467-018-04981-4
Mechanical properties  Metals and alloys 

Zero-static power radio-frequency switches based on MoS2 atomristors OPEN
Myungsoo Kim, Ruijing Ge, Xiaohan Wu, Xing Lan, Jesse Tice, Jack C. Lee & Deji Akinwande

The wide application of wireless communications in various technologies calls for the development of robust yet compact radio-frequency switches. Here, Kim et al. utilize MoS2 based non-volatile memristors to switch up to THz frequencies in sub µm2 areas, whilst the switches consume zero-static energy.

28 June 2018 | doi: 10.1038/s41467-018-04934-x
Nanoscale devices  Nanoscale materials 

Molecular basis of Tousled-Like Kinase 2 activation OPEN
Gulnahar B. Mortuza, Dario Hermida, Anna-Kathrine Pedersen, Sandra Segura-Bayona, Blanca López-Méndez, Pilar Redondo, Patrick Rüther, Irina Pozdnyakova, Ana M. Garrote, Inés G. Muñoz, Marina Villamor-Payà, Cristina Jauset, Jesper V. Olsen, Travis H. Stracker & Guillermo Montoya

The Tousled-like kinase (TLKs) family belongs to a distinct branch of Ser/Thr kinases that exhibit the highest levels of activity during DNA replication. Here the authors present the crystal structure of the kinase domain from human TLK2 and propose an activation model for TLK2 based on biochemical and phosphoproteomics experiments.

28 June 2018 | doi: 10.1038/s41467-018-04941-y
Biophysics  Chromatin  Molecular biology  X-ray crystallography 

Excited-state vibrational dynamics toward the polaron in methylammonium lead iodide perovskite OPEN
Myeongkee Park, Amanda J. Neukirch, Sebastian E. Reyes-Lillo, Minliang Lai, Scott R. Ellis, Daniel Dietze, Jeffrey B. Neaton, Peidong Yang, Sergei Tretiak & Richard A. Mathies

Elucidating electron-phonon coupling in hybrid organic-inorganic perovskites may help us to understand the high photovoltaic efficiency. Here, the authors observe low-frequency Raman modes and related nuclear displacements of the Pb–I framework, indicating how these vibrational motions lead to polaron formation in perovskites.

28 June 2018 | doi: 10.1038/s41467-018-04946-7
Chemistry  Materials science 

Astrometrically registered maps of H2O and SiO masers toward VX Sagittarii OPEN
Dong-Hwan Yoon, Se-Hyung Cho, Youngjoo Yun, Yoon Kyung Choi, Richard Dodson, María Rioja, Jaeheon Kim, Hiroshi Imai, Dongjin Kim, Haneul Yang & Do-Young Byun

The red supergiant VX Sagittarii is a strong emitter of H2O and SiO masers, however its mass loss dynamics are still poorly understood. Here, the authors present astrometrically registered, simultaneous maps of SiO and H2O maser regions, and provide observational evidence for a break in spherical symmetry between the SiO and H2O maser zone.

28 June 2018 | doi: 10.1038/s41467-018-04767-8
Interstellar medium  Stars 
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  Latest Correspondence    
On the origin of molecular oxygen in cometary comae OPEN
K. L. Heritier, K. Altwegg, J.-J. Berthelier, A. Beth, C. M. Carr, J. De Keyser, A. I. Eriksson, S. A. Fuselier, M. Galand, T. I. Gombosi, P. Henri, F. L. Johansson, H. Nilsson, M. Rubin, C. Simon Wedlund, M. G. G. T. Taylor & E Vigren
03 July 2018 | doi: 10.1038/s41467-018-04972-5
Asteroids, comets and Kuiper belt  Astronomy and planetary science 

Reply to “On the origin of molecular oxygen in cometary comae” OPEN
Y. Yao & K. P. Giapis
03 July 2018 | doi: 10.1038/s41467-018-04943-w
Asteroids, comets and Kuiper belt  Astronomical instrumentation 

Reply to ‘Misestimation of heritability and prediction accuracy of male-pattern baldness’ OPEN
Nicola Pirastu, Peter K. Joshi, Paul S. de Vries, Marilyn C. Cornelis, NaNa Keum, Nora Franceschini, Marco Colombo, Edward L. Giovannucci, Athina Spiliopoulou, Lude Franke, Kari E. North, Peter Kraft, Alanna C. Morrison, Tõnu Esko & James F. Wilson
29 June 2018 | doi: 10.1038/s41467-018-04808-2
Genetic predisposition to disease  Genome-wide association studies 

Misestimation of heritability and prediction accuracy of male-pattern baldness OPEN
Chloe X. Yap, Julia Sirodenko, Riccardo E. Marioni, Loic Yengo, Naomi R. Wray & Peter M. Visscher
29 June 2018 | doi: 10.1038/s41467-018-04807-3
Genetics  Heritable quantitative trait 
  Latest Author Corrections    
Author Correction: GWAS for male-pattern baldness identifies 71 susceptibility loci explaining 38% of the risk OPEN
Nicola Pirastu, Peter K. Joshi, Paul S. de Vries, Marilyn C. Cornelis, Paul M. McKeigue, NaNa Keum, Nora Franceschini, Marco Colombo, Edward L. Giovannucci, Athina Spiliopoulou, Lude Franke, Kari E. North, Peter Kraft, Alanna C. Morrison, Tõnu Esko & James F. Wilson
29 June 2018 | doi: 10.1038/s41467-018-04857-7
Genetic predisposition to disease  Genome-wide association studies 

Author Correction: TRPV1 SUMOylation regulates nociceptive signaling in models of inflammatory pain OPEN
Yan Wang, Yingwei Gao, Quan Tian, Qi Deng, Yangbo Wang, Tian Zhou, Qiang Liu, Kaidi Mei, Yingping Wang, Huiqing Liu, Ruining Ma, Yuqiang Ding, Weifang Rong, Jinke Cheng, Jing Yao, Tian-Le Xu, Michael X. Zhu & Yong Li
28 June 2018 | doi: 10.1038/s41467-018-05022-w
Chronic pain  Post-translational modifications  Transient receptor potential channels 

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