Wednesday, August 1, 2018

Nature Communications - 01 August 2018

Nature Communications

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  Latest Comments    
The must-have and nice-to-have experimental and computational requirements for functional frequency doubling deep-UV crystals OPEN
P. Shiv Halasyamani & James M. Rondinelli
30 July 2018 | doi: 10.1038/s41467-018-05411-1
Nonlinear optics 

A critical view on transgenerational epigenetic inheritance in humans OPEN
Bernhard Horsthemke
30 July 2018 | doi: 10.1038/s41467-018-05445-5
Epigenetics  Evolutionary genetics  Genetics research  Medical genetics 

How do our cells build their protein interactome? OPEN
Benoit Coulombe, Philippe Cloutier & Marie-Soleil Gauthier
27 July 2018 | doi: 10.1038/s41467-018-05448-2
Protein folding  Structural biology 
  Latest Perspectives    
A framework for enhancing ethical genomic research with Indigenous communities OPEN
Katrina G. Claw, Matthew Z. Anderson, Rene L. Begay, Krystal S. Tsosie, Keolu Fox, Nanibaa’ A. Garrison, Alyssa C. Bader, Jessica Bardill, Deborah A. Bolnick, Jada Brooks, Anna Cordova, Ripan S. Malhi, Nathan Nakatsuka, Angela Neller, Jennifer A. Raff, Jamie Singson, Kim TallBear, Tada Vargas & Joseph M. Yracheta

Indigenous peoples are still underrepresented in genetic research. Here, the authors propose an ethical framework consisting of six major principles that encourages researchers and Indigenous communities to build strong and equal partnerships to increase trust, engagement and diversity in genomic studies.

27 July 2018 | doi: 10.1038/s41467-018-05188-3
Ethics  Genetics research  Medical genomics  Policy 

Designing with living systems in the synthetic yeast project OPEN
Erika Szymanski & Jane Calvert

Synthetic biology often views the organism as a chassis into which a circuit can be inserted. Here the authors explore the idea of the organism as a core aspect of design, aiding researchers in navigating the genetic space opened up by SCRaMbLE.

27 July 2018 | doi: 10.1038/s41467-018-05332-z
Science in culture  Synthetic biology 
  Latest Articles View all Articles  

Targeted delivery of CRISPR-Cas9 ribonucleoprotein into arthropod ovaries for heritable germline gene editing OPEN
Duverney Chaverra-Rodriguez, Vanessa M. Macias, Grant L. Hughes, Sujit Pujhari, Yasutsugu Suzuki, David R. Peterson, Donghun Kim, Sage McKeand & Jason L. Rasgon

Delivery of Cas9 ribonucleoprotein complexes can be done via microinjection into eggs, though this is a technically challenging procedure. Here the authors demonstrate ReMOT Control, delivery of RNPs to the mosquito germline by tagging with peptide derived from yolk protein 1.

01 August 2018 | doi: 10.1038/s41467-018-05425-9
CRISPR-Cas9 genome editing  Genetic engineering 

A mapping framework of competition–cooperation QTLs that drive community dynamics OPEN
Libo Jiang, Xiaoqing He, Yi Jin, Meixia Ye, Mengmeng Sang, Nan Chen, Jing Zhu, Zuoran Zhang, Jinting Li & Rongling Wu

Genetic variation from coexisting species influences interspecific interactions in a community. Here, the authors develop a framework for identifying quantitative trait loci (QTLs) underlying community dynamics and validate the tool using data from co-culturing of two bacterial species.

01 August 2018 | doi: 10.1038/s41467-018-05416-w
Ecological genetics  Quantitative trait 

Linked dimensions of psychopathology and connectivity in functional brain networks OPEN
Cedric Huchuan Xia, Zongming Ma, Rastko Ciric, Shi Gu, Richard F. Betzel, Antonia N. Kaczkurkin, Monica E. Calkins, Philip A. Cook, Angel García de la Garza, Simon N. Vandekar, Zaixu Cui, Tyler M. Moore, David R. Roalf, Kosha Ruparel, Daniel H. Wolf, Christos Davatzikos, Ruben C. Gur, Raquel E. Gur, Russell T. Shinohara, Danielle S. Bassett et al.

Co-morbidity and symptom overlap make it difficult to associate psychiatric disorders with unique neural signatures. Here, the authors use a data-driven approach to show that the symptom dimensions of mood, psychosis, fear and externalizing behavior exhibit unique patterns of functional dysconnectivity.

01 August 2018 | doi: 10.1038/s41467-018-05317-y
Computational neuroscience  Network models  Psychiatric disorders 

Transient marine euxinia at the end of the terminal Cryogenian glaciation OPEN
Xianguo Lang, Bing Shen, Yongbo Peng, Shuhai Xiao, Chuanming Zhou, Huiming Bao, Alan Jay Kaufman, Kangjun Huang, Peter W. Crockford, Yonggang Liu, Wenbo Tang & Haoran Ma

The termination of the Marinoan snowball Earth event marks one of the most drastic transitions in Earth history, but the oceanic response remains unclear. Here, the authors’ integrated analysis demonstrates that the ocean experienced transient but widespread euxinia following this Snowball Earth event.

01 August 2018 | doi: 10.1038/s41467-018-05423-x
Geochemistry  Marine chemistry  Planetary science 

Transmissive silicon photonic dichroic filters with spectrally selective waveguides OPEN
Emir Salih Magden, Nanxi Li, Manan Raval, Christopher V. Poulton, Alfonso Ruocco, Neetesh Singh, Diedrik Vermeulen, Erich P. Ippen, Leslie A. Kolodziejski & Michael R. Watts

Optical filters are an integral part of many optical devices and circuits. Here, Magden et al. use a design based on mode evolution to demonstrate CMOS-compatible dichroic filters with more than an octave bandwidth, sharp roll-off and transmissive short- and long-wavelength outputs

01 August 2018 | doi: 10.1038/s41467-018-05287-1
Integrated optics  Silicon photonics 

2D perovskite stabilized phase-pure formamidinium perovskite solar cells OPEN
Jin-Wook Lee, Zhenghong Dai, Tae-Hee Han, Chungseok Choi, Sheng-Yung Chang, Sung-Joon Lee, Nicholas De Marco, Hongxiang Zhao, Pengyu Sun, Yu Huang & Yang Yang

Utilizing mixed-cation-halide can improve stability of the formamidinium perovskite films and devices but sacrifices the photocurrent due to an increase in bandgap. Here Lee et al. introduced small amounts of 2D perovskite to obtain high efficiency and stability based on phase-pure formamidinium based perovskite.

01 August 2018 | doi: 10.1038/s41467-018-05454-4
Devices for energy harvesting  Solar cells 

Tailoring van der Waals dispersion interactions with external electric charges OPEN
Andrii Kleshchonok & Alexandre Tkatchenko

The description of van der Waals interactions should often account for coupling with pervasive electric fields, but this effect has been omitted in atomistic simulations. Here, the authors develop a model to study the effects of external charge on long-range van der Waals interactions.

01 August 2018 | doi: 10.1038/s41467-018-05407-x
Chemical physics  Computational biology and bioinformatics  Theoretical chemistry  Theory and computation 

Exploring the role of stromal osmoregulation in cancer and disease using executable modelling OPEN
David Shorthouse, Angela Riedel, Emma Kerr, Luisa Pedro, Dóra Bihary, Shamith Samarajiwa, Carla P. Martins, Jacqueline Shields & Benjamin A. Hall

Aberrant ion transporter expression disrupts osmoregulation in many cancers. Here, the authors introduce an executable model of osmotic regulation and membrane transport, illuminating the mechanistic basis of multiple cellular cancer phenotypes and suggesting therapeutic avenues.

01 August 2018 | doi: 10.1038/s41467-018-05414-y
Biochemical reaction networks  Cancer microenvironment 

Brain-controlled modulation of spinal circuits improves recovery from spinal cord injury OPEN
Marco Bonizzato, Galyna Pidpruzhnykova, Jack DiGiovanna, Polina Shkorbatova, Natalia Pavlova, Silvestro Micera & Grégoire Courtine

Brain–spine interfaces have been used to enable leg movement following spinal cord injury, but movement is either involuntary or not adjustable. Here, the authors show in rats that a proportional stimulation interface permits voluntary movement and augments recovery in conjunction with rehabilitation.

01 August 2018 | doi: 10.1038/s41467-018-05282-6
Motor control  Neuroscience 

Clade diversification dynamics and the biotic and abiotic controls of speciation and extinction rates OPEN
Robin Aguilée, Fanny Gascuel, Amaury Lambert & Regis Ferriere

The history and patterns of species diversity are shaped by a variety of ecological and evolutionary factors. Here, the authors develop a computational model to predict clade diversification dynamics and rates of speciation and extinction under the influences of resource competition, genetic differentiation, and random landscape fluctuation.

01 August 2018 | doi: 10.1038/s41467-018-05419-7
Evolutionary genetics  Evolutionary theory  Speciation 

Regulation of T cell afferent lymphatic migration by targeting LTβR-mediated non-classical NFκB signaling OPEN
Wenji Piao, Yanbao Xiong, Konrad Famulski, C. Colin Brinkman, Lushen Li, Nicholas Toney, Chelsea Wagner, Vikas Saxena, Thomas Simon & Jonathan S. Bromberg

Lymphotoxin beta receptor (LTβR) signalling regulates leukocyte migration through the lymphatic endothelial layers. Here, the authors show that treatment of an LTβR-derived decoy peptide can target the non-classical NFκB pathway to inhibit T cell and dendritic cell migration and ameliorate contact hypersensitivity in mouse models.

01 August 2018 | doi: 10.1038/s41467-018-05412-0
Inflammatory diseases  Lymphatic vessels  NF-kappaB  Tumour-necrosis factors 

Distinct multiple fermionic states in a single topological metal OPEN
M. Mofazzel Hosen, Klauss Dimitri, Ashis K. Nandy, Alex Aperis, Raman Sankar, Gyanendra Dhakal, Pablo Maldonado, Firoza Kabir, Christopher Sims, Fangcheng Chou, Dariusz Kaczorowski, Tomasz Durakiewicz, Peter M. Oppeneer & Madhab Neupane

The existence of multiple topological phases in a single material, although theoretically possible, has not been verified. Here, the authors observe weak topological insulator surface states and a one-dimensional Dirac-node crossing surface state in a single metallic material Hf2Te2P.

01 August 2018 | doi: 10.1038/s41467-018-05233-1
Electronic properties and materials  Topological insulators 

Optimal control theory enables homonuclear decoupling without Bloch–Siegert shifts in NMR spectroscopy OPEN
Paul W. Coote, Scott A. Robson, Abhinav Dubey, Andras Boeszoermenyi, Mengxia Zhao, Gerhard Wagner & Haribabu Arthanari

Bloch–Siegert shifts prevent the accurate observation of resonance frequencies in NMR experiments. Here the authors present a method for homonuclear decoupling that avoids inducing Bloch–Siegert shifts and improves the sensitivity and resolution of HNCA experiments.

01 August 2018 | doi: 10.1038/s41467-018-05400-4
Biological physics  Experimental nuclear physics  Quantum mechanics  Solid-state NMR  Solution-state NMR 

Plk1 overexpression induces chromosomal instability and suppresses tumor development OPEN
Guillermo de Cárcer, Sharavan Vishaan Venkateswaran, Lorena Salgueiro, Aicha El Bakkali, Kalman Somogyi, Konstantina Rowald, Pablo Montañés, Manuel Sanclemente, Beatriz Escobar, Alba de Martino, Nicholas McGranahan, Marcos Malumbres & Rocío Sotillo

PLK1 is a mitotic regulator overexpressed in cancer; however, whether this overexpression causally contributes to tumor development is unclear. Here the authors produce an inducible mouse model to overexpress PLK1 and show that actually this can act as a tumor suppressor by perturbing mitotic progression and cytokinesis.

01 August 2018 | doi: 10.1038/s41467-018-05429-5
Cancer  Cell biology 

Block copolymer crystalsomes with an ultrathin shell to extend blood circulation time OPEN
Hao Qi, Hao Zhou, Qiyun Tang, Jee Young Lee, Zhiyuan Fan, Seyong Kim, Mark C. Staub, Tian Zhou, Shan Mei, Lin Han, Darrin J. Pochan, Hao Cheng, Wenbing Hu & Christopher Y. Li

In block copolymer vesicles, crystallization often leads to defects and renders the structures leaky that undermines their potential biomedical application. Here the authors use an emulsion solution method to control the crystallization of an amphiphilic block copolymer at the curved liquid/liquid interface to improve the blood circulation time.

01 August 2018 | doi: 10.1038/s41467-018-05396-x
Nanoscale materials  Polymers  Soft materials 

High protein copy number is required to suppress stochasticity in the cyanobacterial circadian clock OPEN
Justin Chew, Eugene Leypunskiy, Jenny Lin, Arvind Murugan & Michael J. Rust

Circadian clocks must maintain their fidelity despite stochasticity arising from finite protein copy numbers. Here, the authors show that a small cyanobacterium relies on an environmentally driven timer likely because its low protein copy numbers cannot support an accurate free-running clock.

01 August 2018 | doi: 10.1038/s41467-018-05109-4
Bacterial systems biology  Oscillators 

SUMO-mediated regulation of NLRP3 modulates inflammasome activity OPEN
Rachael Barry, Sidonie Wicky John, Gianmaria Liccardi, Tencho Tenev, Isabel Jaco, Chih-Hong Chen, Justin Choi, Paulina Kasperkiewicz, Teresa Fernandes-Alnemri, Emad Alnemri, Marcin Drag, Yuan Chen & Pascal Meier

The NLRP3 inflammasome is an important component of inflammatory responses, but how it is negatively regulated is still unclear. Here the authors show that post-translational modification of NLRP3 by sumoylation suppresses inflammasome activity, and that desumoylation of NLRP3 by the SENP6 and SENP7 proteases promotes NLRP3 activation.

01 August 2018 | doi: 10.1038/s41467-018-05321-2
Cell death  Inflammation  Post-translational modifications  Sumoylated proteins 

A positive feedback loop bi-stably activates fibroblasts OPEN
So-Young Yeo, Keun-Woo Lee, Dongkwan Shin, Sugyun An, Kwang-Hyun Cho & Seok-Hyung Kim

Normal adult tissue fibroblasts can be activated during wound healing, pathologic fibrosis and in cancer stroma, but the regulatory network that controls its dynamics is unknown. Here the authors show that fibroblasts are activated by a positive feedback loop formed by Twist1, Prrx1, and Tenascin-C bi-stably.

01 August 2018 | doi: 10.1038/s41467-018-05274-6
Cell proliferation  Computer modelling 

Unravelling the age of fine roots of temperate and boreal forests OPEN
Emily F. Solly, Ivano Brunner, Heljä-Sisko Helmisaari, Claude Herzog, Jaana Leppälammi-Kujansuu, Ingo Schöning, Marion Schrumpf, Fritz H. Schweingruber, Susan E. Trumbore & Frank Hagedorn

Fine-root lifetimes and carbon inputs from roots into soil impact carbon cycle-climate feedbacks yet remain poorly constrained. Here, using annual-growth rings and radiocarbon dating, the authors show that the chronological age of fine roots is substantially younger than that of the carbon used for their growth.

01 August 2018 | doi: 10.1038/s41467-018-05460-6
Biogeochemistry  Environmental sciences 

99TcO4 remediation by a cationic polymeric network OPEN
Jie Li, Xing Dai, Lin Zhu, Chao Xu, Duo Zhang, Mark A. Silver, Peng Li, Lanhua Chen, Yongzhong Li, Douwen Zuo, Hui Zhang, Chengliang Xiao, Jing Chen, Juan Diwu, Omar K. Farha, Thomas E. Albrecht-Schmitt, Zhifang Chai & Shuao Wang

Direct removal of 99TcO4− from highly radioactive and acidic nuclear waste solutions is beneficial for uranium and plutonium recovery and radioactive pollution control but this represents a huge challenge. Here the authors show a cationic polymeric network with high 99TcO4 sorption capability and stability.

01 August 2018 | doi: 10.1038/s41467-018-05380-5
Coordination polymers  Pollution remediation 

Highly-efficient extraction of entangled photons from quantum dots using a broadband optical antenna OPEN
Yan Chen, Michael Zopf, Robert Keil, Fei Ding & Oliver G. Schmidt

Cascade radiative decay in quantum dots is a promising way of generating entangled photon pairs, but the extraction efficiency is a strongly limiting factor. Here, the authors demonstrate high extraction efficiency through a broadband dielectric photonic antenna.

31 July 2018 | doi: 10.1038/s41467-018-05456-2
Quantum dots  Quantum optics  Single photons and quantum effects 

Spin-induced multiferroicity in the binary perovskite manganite Mn2O3 OPEN
Junzhuang Cong, Kun Zhai, Yisheng Chai, Dashan Shang, Dmitry D. Khalyavin, Roger D. Johnson, Denis P. Kozlenko, Sergey E. Kichanov, Artem M. Abakumov, Alexander A. Tsirlin, Leonid Dubrovinsky, Xueli Xu, Zhigao Sheng, Sergey V. Ovsyannikov & Young Sun

Multiferroic binary oxides with the perovskite structure have been very rare. Here, Cong et al. report magnetically-driven ferroelectricity and a large magnetoelectric effect in a binary perovskite compound Mn2O3 at low temperatures.

31 July 2018 | doi: 10.1038/s41467-018-05296-0
Ferroelectrics and multiferroics  Magnetic properties and materials 

Biodiversity across trophic levels drives multifunctionality in highly diverse forests OPEN
Andreas Schuldt, Thorsten Assmann, Matteo Brezzi, François Buscot, David Eichenberg, Jessica Gutknecht, Werner Härdtle, Jin-Sheng He, Alexandra-Maria Klein, Peter Kühn, Xiaojuan Liu, Keping Ma, Pascal A. Niklaus, Katherina A. Pietsch, Witoon Purahong, Michael Scherer-Lorenzen, Bernhard Schmid, Thomas Scholten, Michael Staab, Zhiyao Tang et al.

Biodiversity change can impact ecosystem functioning, though this is primarily studied at lower trophic levels. Here, Schuldt et al. find that biodiversity components other than tree species richness are particularly important, and higher trophic level diversity plays a role in multifunctionality.

31 July 2018 | doi: 10.1038/s41467-018-05421-z
Biodiversity  Ecology  Ecosystem services  Forest ecology  Tropical ecology 

Systems analysis of intracellular pH vulnerabilities for cancer therapy OPEN
Erez Persi, Miquel Duran-Frigola, Mehdi Damaghi, William R. Roush, Patrick Aloy, John L. Cleveland, Robert J. Gillies & Eytan Ruppin

Tumors often exhibit a pH gradient, with an acidic extracellular space and alkaline cytoplasm. Here the authors develop a computational model to show how alkaline pHi supports changes inherent to cancer cell metabolism and acidification disables these adaptations, and demonstrate the effect of acidic pHi on breast cancer cell survival.

31 July 2018 | doi: 10.1038/s41467-018-05261-x
Biochemical networks  Biochemical reaction networks  Cancer metabolism  Computational biology and bioinformatics 

New insights into the design of conjugated polymers for intramolecular singlet fission OPEN
Jiahua Hu, Ke Xu, Lei Shen, Qin Wu, Guiying He, Jie-Yu Wang, Jian Pei, Jianlong Xia & Matthew Y. Sfeir

Further mechanistic insight of intramolecular singlet fission (iSF) in conjugated polymers can enable novel material design for solar cells. Here, the authors use transient spectroscopy to show iSF in an isoindigo-based conjugated polymer and propose a design rule based on morphology-dependent iSF.

31 July 2018 | doi: 10.1038/s41467-018-05389-w
Devices for energy harvesting  Semiconductors  Solar cells  Ultrafast photonics 

Predictable evolution towards larger brains in birds colonizing oceanic islands OPEN
Ferran Sayol, Philip A. Downing, Andrew N. Iwaniuk, Joan Maspons & Daniel Sol

Islands may impose a distinct set of selective pressures, leading to the repeated evolution of certain traits. Here, Sayol et al. compare brain sizes of more than 1900 bird species in a phylogenetic context, finding a consistent trend for in situ evolution of increased brain size in island birds.

31 July 2018 | doi: 10.1038/s41467-018-05280-8
Behavioural ecology  Macroecology  Phylogenetics 

North China Plain threatened by deadly heatwaves due to climate change and irrigation OPEN
Suchul Kang & Elfatih A. B. Eltahir

Irrigation increases the intensity of heatwaves over the North China Plain but how this will be exacerbated by climate change has not been quantified. Here the authors show that irrigation enhances magnitude of extreme wet-bulb temperature and intensity of heatwaves in this region.

31 July 2018 | doi: 10.1038/s41467-018-05252-y
Environmental health  Fluid dynamics 

Distributed forward Brillouin sensor based on local light phase recovery OPEN
Desmond M. Chow, Zhisheng Yang, Marcelo A. Soto & Luc Thévenaz

Conventional distributed Brillouin sensing allows real-time sampling at high spatial resolution, but is so far restricted to measuring quantities inside the fibre core. Here, Chow et al. demonstrate a distributed forward Brillouin sensor that is sensitive to quantities outside the fibre bulk.

31 July 2018 | doi: 10.1038/s41467-018-05410-2
Fibre optics and optical communications  Imaging and sensing  Nonlinear optics  Optical sensors  Photoacoustics 

Facile transformation of imine covalent organic frameworks into ultrastable crystalline porous aromatic frameworks OPEN
Xinle Li, Changlin Zhang, Songliang Cai, Xiaohe Lei, Virginia Altoe, Fang Hong, Jeffrey J. Urban, Jim Ciston, Emory M. Chan & Yi Liu

Despite recent success in developing new covalent organic frameworks (COFs) materials, synthesis of chemically stable COFs still remains challenging. Here the authors demonstrate a facile strategy that transforms imine-linked COFs into robust porous aromatic frameworks by kinetically fixing the reversible imine linkage via an aza-Diels-Alder cycloaddition reaction.

31 July 2018 | doi: 10.1038/s41467-018-05462-4
Polymer synthesis  Polymers  Porous materials 

Topical ferumoxytol nanoparticles disrupt biofilms and prevent tooth decay in vivo via intrinsic catalytic activity OPEN
Yuan Liu, Pratap C. Naha, Geelsu Hwang, Dongyeop Kim, Yue Huang, Aurea Simon-Soro, Hoi-In Jung, Zhi Ren, Yong Li, Sarah Gubara, Faizan Alawi, Domenick Zero, Anderson T. Hara, David P. Cormode & Hyun Koo

Ferumoxytol is a nanoparticle formulation approved for systemic use to treat iron deficiency. Liu et al. show that topical use of ferumoxytol, in combination with low concentrations of H2O2, disrupts intractable oral biofilms and prevents tooth decay in vitro and in an animal model.

31 July 2018 | doi: 10.1038/s41467-018-05342-x
Biofilms  Biomaterials  Biomedical materials  Dental caries  Diseases 

Manic Fringe deficiency imposes Jagged1 addiction to intestinal tumor cells OPEN
Erika López-Arribillaga, Verónica Rodilla, Carlota Colomer, Anna Vert, Amy Shelton, Jason H. Cheng, Bing Yan, Abel Gonzalez-Perez, Melissa R. Junttila, Mar Iglesias, Ferran Torres, Joan Albanell, Alberto Villanueva, Anna Bigas, Christian W. Siebel & LLuís Espinosa

In intestinal adenomas carrying active β-catenin, Jagged1 (Jag1) ligand is responsible for Notch1 activation. Here, the authors show the reliance of Notch on Jag1 in cancer, and investigate how Jag1–Notch1 signaling interference may provide therapeutic benefits in some colorectal cancer patients

31 July 2018 | doi: 10.1038/s41467-018-05385-0
Cancer  Gastroenterology 

Optomechanical time-domain reflectometry OPEN
Gil Bashan, Hilel Hagai Diamandi, Yosef London, Eyal Preter & Avi Zadok

Distributed fibre sensors are so far restricted to the monitoring of conditions within the core. Here, Bashan et al. introduce distributed optomechanical mapping of outside media, where light cannot reach. The sensor resolves forward stimulated Brillouin scattering through Rayleigh back-scatter.

31 July 2018 | doi: 10.1038/s41467-018-05404-0
Fibre optics and optical communications  Nonlinear optics  Optomechanics 

Long noncoding RNA licensing of obesity-linked hepatic lipogenesis and NAFLD pathogenesis OPEN
Xu-Yun Zhao, Xuelian Xiong, Tongyu Liu, Lin Mi, Xiaoling Peng, Crystal Rui, Liang Guo, Siming Li, Xiaoying Li & Jiandie D. Lin

The LXR-SREBP1c pathway promotes hepatic lipogenesis that is deregualted in fatty liver disease. Here the authors show that the long noncoding RNA Blnc1 contributes to the development of obesity-driven steatosis by enabling SREBP1c trascriptional activity in response to LXR activation.

30 July 2018 | doi: 10.1038/s41467-018-05383-2
CRISPR-Cas systems  Long non-coding RNAs  Non-alcoholic fatty liver disease  Non-alcoholic steatohepatitis  Transcription 

Operando and three-dimensional visualization of anion depletion and lithium growth by stimulated Raman scattering microscopy OPEN
Qian Cheng, Lu Wei, Zhe Liu, Nan Ni, Zhe Sang, Bin Zhu, Weiheng Xu, Meijie Chen, Yupeng Miao, Long-Qing Chen, Wei Min & Yuan Yang

The relationship between Li-ion concentration and Li deposition remains an issue to be addressed. Here the authors show that stimulated Raman scattering microscopy offers insight into the concentration evolution and its impact on the dendrite growth, which is not possible by existing techniques.

30 July 2018 | doi: 10.1038/s41467-018-05289-z
Batteries  Raman spectroscopy 

The actin cytoskeletal architecture of estrogen receptor positive breast cancer cells suppresses invasion OPEN
Marco Padilla-Rodriguez, Sara S. Parker, Deanna G. Adams, Thomas Westerling, Julieann I. Puleo, Adam W. Watson, Samantha M. Hill, Muhammad Noon, Raphael Gaudin, Jesse Aaron, Daoqin Tong, Denise J. Roe, Beatrice Knudsen & Ghassan Mouneimne

Whilst estrogen is known to be tumorigenic in some breast cancer, in some contexts it can be protective against invasion and dissemination. Here, the authors show estrogen can promote generation of Suppressive Cortical Actin Bundles that can inhibit motility dynamics through EVL-mediated actin cytoskeletal remodeling.

30 July 2018 | doi: 10.1038/s41467-018-05367-2
Breast cancer  Cell invasion 

Transforming ground mica into high-performance biomimetic polymeric mica film OPEN
Xiao-Feng Pan, Huai-Ling Gao, Yang Lu, Chun-Yan Wu, Ya-Dong Wu, Xiang-Ying Wang, Zhi-Qiang Pan, Liang Dong, Yong-Hong Song, Huai-Ping Cong & Shu-Hong Yu

Biomimetic assembly of nanosheets into nacre-like structures and films is of interest for a range of applications; the abundance of mica makes it a good candidate. Here, the authors report on the large-scale exfoliation of ground mica into nanosheets and the assembly into polymeric mica films.

30 July 2018 | doi: 10.1038/s41467-018-05355-6
Composites  Electronic devices  Nanoscale materials 

Stability criteria for complex microbial communities OPEN
Stacey Butler & James P. O’Dwyer

Network stability is a central topic in theoretical ecology, with most work focusing on mutualistic or food web networks. Here, the authors explore the stability of microbial networks based on the consumption and exchange of resources, showing that asymmetry in crossfeeding relationships can destabilize networks.

30 July 2018 | doi: 10.1038/s41467-018-05308-z
Ecological networks  Microbial ecology  Theoretical ecology 

Overexpression of endophilin A1 exacerbates synaptic alterations in a mouse model of Alzheimer’s disease OPEN
Qing Yu, Yongfu Wang, Fang Du, Shijun Yan, Gang Hu, Nicola Origlia, Grazia Rutigliano, Qinru Sun, Haiyang Yu, James Ainge, Shi Fang Yan, Frank Gunn-Moore & Shirley ShiDu Yan

Endophilin A1 protein is known to be elevated in Alzheimer’s disease (AD). Here the authors show that endophilin A1 overexpression exacerbates synaptic deficits in a mouse model of AD.

30 July 2018 | doi: 10.1038/s41467-018-04389-0
Alzheimer's disease  Long-term potentiation 

Organoid cultures recapitulate esophageal adenocarcinoma heterogeneity providing a model for clonality studies and precision therapeutics OPEN
Xiaodun Li, Hayley E. Francies, Maria Secrier, Juliane Perner, Ahmad Miremadi, Núria Galeano-Dalmau, William J. Barendt, Laura Letchford, Genevieve M. Leyden, Emma K. Goffin, Andrew Barthorpe, Howard Lightfoot, Elisabeth Chen, James Gilbert, Ayesha Noorani, Ginny Devonshire, Lawrence Bower, Amber Grantham, Shona MacRae, Nicola Grehan et al.

Esophageal adenocarcinoma (EAC) has a poor 5-year survival rate and lacks robust preclinical models for use in research. Here, the authors show that newly derived organoids recapitulate the transcriptomic, genetic, and morphological landscape of the primary EAC tumors and provide a platform to test drug sensitivity and study tumor clonality.

30 July 2018 | doi: 10.1038/s41467-018-05190-9
Cancer genetics  Cancer models 

Enhanced immunocompatibility of ligand-targeted liposomes by attenuating natural IgM absorption OPEN
Juan Guan, Qing Shen, Zui Zhang, Zhuxuan Jiang, Yang Yang, Meiqing Lou, Jun Qian, Weiyue Lu & Changyou Zhan

Targeting ligands on drug carriers can trigger immune responses. Here, the authors modify liposomes with a peptidomimetic that preserves bioactivity of the nanocarrier in blood circulation and attenuates IgM absorption, thereby improving the immunocompatibility of brain-targeted liposomes.

30 July 2018 | doi: 10.1038/s41467-018-05384-1
Drug delivery 

Surfaces away from horizons are not thermodynamic OPEN
Zhi-Wei Wang & Samuel L. Braunstein

It has been conjectured that gravity may emerge from an entropic force arising on a holographic screen due to its purportedly intrinsic thermodynamic properties. Here, the authors test this conjecture by demonstrating that this key assumption of entropic force is inconsistent with general relativity.

30 July 2018 | doi: 10.1038/s41467-018-05433-9
General relativity and gravity  Thermodynamics 

Structural insights into SorCS2–Nerve Growth Factor complex formation OPEN
Nadia Leloup, Lucas M. P. Chataigner & Bert J. C. Janssen

The Sortilin-related CNS-expressed receptor 2 (SorCS2)–proneurotrophin signaling system regulates neuronal plasticity and its dysfunction is linked to schizophrenia. Here the authors present the structures of the SorCS2 ectodomain alone and in complex with Nerve Growth Factor, which provides insights into SorCS2 ligand binding and signaling.

30 July 2018 | doi: 10.1038/s41467-018-05405-z
Extracellular signalling molecules  Neurological disorders  X-ray crystallography 

Asymmetric migration decreases stability but increases resilience in a heterogeneous metapopulation OPEN
Anurag Limdi, Alfonso Pérez-Escudero, Aming Li & Jeff Gore

Asymmetrical movement among patches could affect the stability of ecological metapopulations, but this is difficult to test empirically. Here, Limdi et al. use experimental yeast metapopulations to show that asymmetric migration decreases stability but increases resilience to transient shocks.

30 July 2018 | doi: 10.1038/s41467-018-05424-w
Microbial ecology  Population dynamics 

Controllable protein phase separation and modular recruitment to form responsive membraneless organelles OPEN
Benjamin S. Schuster, Ellen H. Reed, Ranganath Parthasarathy, Craig N. Jahnke, Reese M. Caldwell, Jessica G. Bermudez, Holly Ramage, Matthew C. Good & Daniel A. Hammer

Designer organelles with new biochemical functionalities are of great interest in synthetic biology and cellular engineering. Here the authors present a single-protein-based platform for generating synthetic membraneless compartments that is capable of enzymatically-triggered alterations to phase behavior and of recruiting and concentrating cargo proteins.

30 July 2018 | doi: 10.1038/s41467-018-05403-1
Bioinspired materials  Intrinsically disordered proteins  Organelles  Self-assembly  Synthetic biology 

Statistical mechanics for metabolic networks during steady state growth OPEN
Daniele De Martino, Anna MC Andersson, Tobias Bergmiller, Călin C. Guet & Gašper Tkačik

Single cell growth rate variability has been difficult to understand. Here, the authors apply a generalization of flux balance analysis to single cells based on maximum entropy modeling, and find that growth rate fluctuations of E. coli reflect metabolic flux variability and growth sub-optimality, in turn highlighting information costs for growth optimization.

30 July 2018 | doi: 10.1038/s41467-018-05417-9
Biochemical networks  Biological physics  Computational biophysics 

Genetic dissection of clonal lineage relationships with hydroxytamoxifen liposomes OPEN
Ryan C. Ransom, Deshka S. Foster, Ankit Salhotra, Ruth Ellen Jones, Clement D. Marshall, Tripp Leavitt, Matthew P. Murphy, Alessandra L. Moore, Charles P. Blackshear, Derrick C. Wan & Michael T. Longaker

Targeted genetic dissection of tissues can be used to identify cell populations and lineages. Here the authors develop 4-hydroxytamoxifen liposomes for the localized induction of CreERT2.

30 July 2018 | doi: 10.1038/s41467-018-05436-6
Cell biology  Stem cells 

Long range electronic phase separation in CaFe3O5 OPEN
Ka. H. Hong, Angel M. Arevalo-Lopez, James Cumby, Clemens Ritter & J. Paul Attfield

Electronic phase separation is an important feature of many correlated perovskite compounds but hasn’t been seen in other complex oxides with similar physical behaviour such as magnetite. Hong et al. find phase separation between a magnetite-like charge ordered phase and a charge averaged phase in CaFe3O5.

30 July 2018 | doi: 10.1038/s41467-018-05363-6
Electronic materials  Electronic properties and materials  Magnetic properties and materials 

Spontaneous cortical activity transiently organises into frequency specific phase-coupling networks OPEN
Diego Vidaurre, Laurence T. Hunt, Andrew J. Quinn, Benjamin A. E. Hunt, Matthew J. Brookes, Anna C. Nobre & Mark W. Woolrich

Coordination of neural activity between distant brain areas is necessary for cognition. Here, the authors report using MEG that various brain networks show dynamic phase coupling through specific frequency bands in the alpha and delta/theta range transiently during the resting state.

30 July 2018 | doi: 10.1038/s41467-018-05316-z
Dynamical systems  Network models 

A reliable murine model of bone metastasis by injecting cancer cells through caudal arteries OPEN
Takahiro Kuchimaru, Naoya Kataoka, Kenji Nakagawa, Tatsuhiro Isozaki, Hitomi Miyabara, Misa Minegishi, Tetsuya Kadonosono & Shinae Kizaka-Kondoh

Reliably modelling bone metastasis in mice is essential for research. Here, the authors present a new murine model for cancer metastasis based on intra-caudal artery injection that reliably recapitulates bone metastasis.

30 July 2018 | doi: 10.1038/s41467-018-05366-3
Bone cancer  Bone metastases 

Evolution of cooperativity in the spin transition of an iron(II) complex on a graphite surface OPEN
Lalminthang Kipgen, Matthias Bernien, Sascha Ossinger, Fabian Nickel, Andrew J. Britton, Lucas M. Arruda, Holger Naggert, Chen Luo, Christian Lotze, Hanjo Ryll, Florin Radu, Enrico Schierle, Eugen Weschke, Felix Tuczek & Wolfgang Kuch

Spin-crossover molecules offer a potential route towards molecular spintronics, but retaining the bistability of the spin state upon surface deposition is challenging. Here, the authors study the spin-crossover behaviours of an Fe(II) complex deposited on graphite, determining the scale limit at which cooperative spin switching becomes effective.

30 July 2018 | doi: 10.1038/s41467-018-05399-8
Magnetic materials  Magnetic properties and materials  Molecular electronics  Molecular self-assembly 

Stabilization of three-dimensional charge order in YBa2Cu3O6+x via epitaxial growth OPEN
M. Bluschke, A. Frano, E. Schierle, D. Putzky, F. Ghorbani, R. Ortiz, H. Suzuki, G. Christiani, G. Logvenov, E. Weschke, R. J. Birgeneau, E. H. da Silva Neto, M. Minola, S. Blanco-Canosa & B. Keimer

In many cuprates the high temperature superconducting state competes with a charge ordered phase that has been difficult to investigate in detail. Here the authors show three-dimensional charge order can be stabilized in YBCO films and studied without using the high magnetic fields that are necessary in the bulk material.

30 July 2018 | doi: 10.1038/s41467-018-05434-8
Superconducting properties and materials  Surfaces, interfaces and thin films 

Multiethnic meta-analysis identifies ancestry-specific and cross-ancestry loci for pulmonary function OPEN
Annah B. Wyss, Tamar Sofer, Mi Kyeong Lee, Natalie Terzikhan, Jennifer N. Nguyen, Lies Lahousse, Jeanne C. Latourelle, Albert Vernon Smith, Traci M. Bartz, Mary F. Feitosa, Wei Gao, Tarunveer S. Ahluwalia, Wenbo Tang, Christopher Oldmeadow, Qing Duan, Kim de Jong, Mary K. Wojczynski, Xin-Qun Wang, Raymond Noordam, Fernando Pires Hartwig et al.

Pulmonary function is influenced by environmental factors, lifestyle, and genetics. Here, in a multiethnic GWAS meta-analysis for pulmonary function traits, the authors identify over 50 additional genetic loci, a subset of which are specific for European, African, Asian, or Hispanic/Latino ancestry.

30 July 2018 | doi: 10.1038/s41467-018-05369-0
Epidemiology  Genetics research  Genome-wide association studies  Respiratory tract diseases 

A user-friendly herbicide derived from photo-responsive supramolecular vesicles OPEN
Cheng Gao, Qiaoxian Huang, Qingping Lan, Yu Feng, Fan Tang, Maggie P. M. Hoi, Jianxiang Zhang, Simon M. Y. Lee & Ruibing Wang

Paraquat is a widely used herbicide that is highly toxic to humans upon acute ingestion or chronic exposure. Here, the authors generate a photosensitive formulation that releases paraquat upon exposure to UV light or sunlight, which shows an improved safety profile in zebrafish and mouse models, while maintaining substantial herbicidal activity.

27 July 2018 | doi: 10.1038/s41467-018-05437-5
Agriculture  Nanoscale materials  Supramolecular chemistry 

Spindle tubulin and MTOC asymmetries may explain meiotic drive in oocytes OPEN
Tianyu Wu, Simon I. R. Lane, Stephanie L. Morgan & Keith T. Jones

During ‘meiotic drive’, some chromosomes can bias their spindle orientation and thus be retained in the egg. Here, the authors find that this phenomenon can be driven by microtubule force asymmetry on chromosomes with differently sized centromeres and kinetochores.

27 July 2018 | doi: 10.1038/s41467-018-05338-7
Animal physiology  Centromeres  Embryology  Evolutionary biology 

Scutoids are a geometrical solution to three-dimensional packing of epithelia OPEN
Pedro Gómez-Gálvez, Pablo Vicente-Munuera, Antonio Tagua, Cristina Forja, Ana M. Castro, Marta Letrán, Andrea Valencia-Expósito, Clara Grima, Marina Bermúdez-Gallardo, Óscar Serrano-Pérez-Higueras, Florencia Cavodeassi, Sol Sotillos, María D. Martín-Bermudo, Alberto Márquez, Javier Buceta & Luis M. Escudero

Cell arrangement in the plane of epithelia is well studied, but its three-dimensional packing is largely unknown. Here the authors model curved epithelia and predict that cells adopt a geometrical shape they call “scutoid”, resulting in different apical and basal neighbours, and confirm the presence of scutoids in curved tissues.

27 July 2018 | doi: 10.1038/s41467-018-05376-1
Computational models  Morphogenesis 

Lipid droplet and peroxisome biogenesis occur at the same ER subdomains OPEN
Amit S. Joshi, Benjamin Nebenfuehr, Vineet Choudhary, Prasanna Satpute-Krishnan, Tim P. Levine, Andy Golden & William A. Prinz

Lipid droplets (LDs) and peroxisomes are both generated by budding off the endoplasmic reticulum (ER). Here, the authors show that the yeast protein Pex30 marks ER subdomains where both LD and peroxisome biogenesis occurs, and identify MCTP2 as the putative mammalian Pex30 ortholog.

27 July 2018 | doi: 10.1038/s41467-018-05277-3
Endoplasmic reticulum  Peroxisomes 

Coherent deglacial changes in western Atlantic Ocean circulation OPEN
Hong Chin Ng, Laura F. Robinson, Jerry F. McManus, Kais J. Mohamed, Allison W. Jacobel, Ruza F. Ivanovic, Lauren J. Gregoire & Tianyu Chen

The exact timing and magnitude of past changes in Atlantic Ocean circulation, and its relation to abrupt climate changes remains elusive. Here, the authors show a spatially coherent picture of western Atlantic circulation changes, which reveals a two-step AMOC slowdown at the beginning of the deglacial period.

27 July 2018 | doi: 10.1038/s41467-018-05312-3
Climate change  Marine chemistry  Palaeoceanography  Palaeoclimate 

Persistent CO2 emissions and hydrothermal unrest following the 2015 earthquake in Nepal OPEN
Frédéric Girault, Lok Bijaya Adhikari, Christian France-Lanord, Pierre Agrinier, Bharat P. Koirala, Mukunda Bhattarai, Sudhan S. Mahat, Chiara Groppo, Franco Rolfo, Laurent Bollinger & Frédéric Perrier

Earthquakes rarely affect hydrothermal systems in non-magmatic context. Here the authors report outbursts of CO2 and hydrothermal disturbances triggered by the 2015 Nepal earthquake, revealing high sensitivity of Himalayan hydrothermal systems to co-, post- and possibly pre- seismic deformation.

27 July 2018 | doi: 10.1038/s41467-018-05138-z
Hydrology  Natural hazards  Solid Earth sciences 

Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes OPEN
Angli Xue, Yang Wu, Zhihong Zhu, Futao Zhang, Kathryn E. Kemper, Zhili Zheng, Loic Yengo, Luke R. Lloyd-Jones, Julia Sidorenko, Yeda Wu, Mawussé Agbessi, Habibul Ahsan, Isabel Alves, Anand Andiappan, Philip Awadalla, Alexis Battle, Frank Beutner, Marc Jan Bonder, Dorret Boomsma, Mark Christiansen et al.

GWAS have so far identified 129 loci associated with type 2 diabetes (T2D). Here, the authors meta-analyse three large T2D GWA studies which uncovers 42 additional loci, further prioritize 33 functional genes using eQTL and mQTL data and propose regulatory mechanisms for three putative T2D genes.

27 July 2018 | doi: 10.1038/s41467-018-04951-w
Gene regulation  Genome-wide association studies  Quantitative trait loci  Type 2 diabetes 

Contact inhibition controls cell survival and proliferation via YAP/TAZ-autophagy axis OPEN
Mariana Pavel, Maurizio Renna, So Jung Park, Fiona M. Menzies, Thomas Ricketts, Jens Füllgrabe, Avraham Ashkenazi, Rebecca A. Frake, Alejandro Carnicer Lombarte, Carla F. Bento, Kristian Franze & David C. Rubinsztein

At high cell density or when plated on soft matrix, YAP/TAZ are redistributed from the nucleus to the cytosol, becoming transcriptionally inactive. Here the authors show that at high cell density, autophagosome formation is impaired due to reduced YAP/TAZ-dependent transcription of actomyosin genes

27 July 2018 | doi: 10.1038/s41467-018-05388-x
Cell proliferation  Cell signalling  Macroautophagy 

Predicting treatment benefit in multiple myeloma through simulation of alternative treatment effects OPEN
Joske Ubels, Pieter Sonneveld, Erik H. van Beers, Annemiek Broijl, Martin H. van Vliet & Jeroen de Ridder

Selection of the right cancer treatment is still a challenge. Here, the authors introduce a framework to analyze treatment benefits, using the idea that patients with similar genetic tumor profiles receiving different treatments can be used to model their responses to the alternative treatment.

27 July 2018 | doi: 10.1038/s41467-018-05348-5
Myeloma  Predictive markers  Predictive medicine 

Strongly-coupled quantum critical point in an all-in-all-out antiferromagnet OPEN
Yishu Wang, T. F. Rosenbaum, A. Palmer, Y. Ren, J.-W. Kim, D. Mandrus & Yejun Feng

The critical behavior of a continuous phase transition is determined by both symmetry and dimensionality. Wang et al. present evidence that the cubic all-in-all-out spin order in Cd2Os2O7 leads to a realization of a non-mean-field strongly-coupled quantum phase transition in three dimensions.

27 July 2018 | doi: 10.1038/s41467-018-05435-7
Magnetic properties and materials  Phase transitions and critical phenomena 

Exploiting a cognitive bias promotes cooperation in social dilemma experiments OPEN
Zhen Wang, Marko Jusup, Lei Shi, Joung-Hun Lee, Yoh Iwasa & Stefano Boccaletti

The decoy effect refers to the fact that the presence of a third option can shift people’s preferences between two other options even though the third option is inferior to both. Here, the authors show how the decoy effect can enhance cooperation in a social dilemma, the repeated prisoner’s dilemma.

27 July 2018 | doi: 10.1038/s41467-018-05259-5
Human behaviour  Interdisciplinary studies  Social evolution 

Seipin and the membrane-shaping protein Pex30 cooperate in organelle budding from the endoplasmic reticulum OPEN
Sihui Wang, Fatima-Zahra Idrissi, Martin Hermansson, Alexandra Grippa, Christer S. Ejsing & Pedro Carvalho

Lipid droplets (LDs) and peroxisomes both emerge from the endoplasmic reticulum (ER). Here, the authors show that yeast Seipin and Pex30 proteins act together to regulate budding of these organelles from the same subdomain of the ER.

27 July 2018 | doi: 10.1038/s41467-018-05278-2
Endoplasmic reticulum  Peroxisomes 

Macrophages are exploited from an innate wound healing response to facilitate cancer metastasis OPEN
Tamara Muliaditan, Jonathan Caron, Mary Okesola, James W. Opzoomer, Paris Kosti, Mirella Georgouli, Peter Gordon, Sharanpreet Lall, Desislava M. Kuzeva, Luisa Pedro, Jacqueline D. Shields, Cheryl E. Gillett, Sandra S. Diebold, Victoria Sanz-Moreno, Tony Ng, Esther Hoste & James N. Arnold

The relationship between wound healing and cancer is intricate and complex. Here, the authors show that in breast cancer models an IL-6 driven co-expression of FAP and HO-1 in tumour-associated macrophages, similar to the wound healing response, facilitates migration and metastatic spread.

27 July 2018 | doi: 10.1038/s41467-018-05346-7
Cancer  Cancer microenvironment  Metastasis 

Real-space imaging with pattern recognition of a ligand-protected Ag374 nanocluster at sub-molecular resolution OPEN
Qin Zhou, Sami Kaappa, Sami Malola, Hui Lu, Dawei Guan, Yajuan Li, Haochen Wang, Zhaoxiong Xie, Zhibo Ma, Hannu Häkkinen, Nanfeng Zheng, Xueming Yang & Lansun Zheng

Translating high-resolution imaging methods to the curved organic surface of a nanoparticle has been challenging. Here, the authors are able to spatially resolve the sub-molecular surface details of a silver nanocluster by comparing scanning tunneling microscopy images and simulated topography data through a pattern recognition algorithm.

27 July 2018 | doi: 10.1038/s41467-018-05372-5
Electronic structure  Nanoparticles  Scanning probe microscopy 

Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells OPEN
Josh Tycko, Luis A. Barrera, Nicholas C. Huston, Ari E. Friedland, Xuebing Wu, Jonathan S. Gootenberg, Omar O. Abudayyeh, Vic E. Myer, Christopher J. Wilson & Patrick D. Hsu

A rigorous understanding of off-target effects is necessary for SaCas9 to be used in therapeutic genome editing. Here the authors measure SaCas9 mismatch tolerance across a pairwise library screen of 88,000 guides and targets in human cells and develop a model which ranks off-target sites.

27 July 2018 | doi: 10.1038/s41467-018-05391-2
CRISPR-Cas9 genome editing  Computational models  Genetic engineering  Synthetic biology 

Chemically specific termination control of oxide interfaces via layer-by-layer mean inner potential engineering OPEN

Precisely controlled growth of oxide interfaces at the atomic layer level is critical for device applications but quite challenging. Here Sun et al. show real time monitoring and control of the surface composition of epitaxial strontium titanate perovskite films by analysing the Kikuchi lines.

27 July 2018 | doi: 10.1038/s41467-018-04903-4
Electronic properties and materials  Surfaces, interfaces and thin films 

Neutrophil extracellular trap formation requires OPA1-dependent glycolytic ATP production OPEN
Poorya Amini, Darko Stojkov, Andrea Felser, Christopher B. Jackson, Carolina Courage, André Schaller, Laurent Gelman, Maria Eugenia Soriano, Jean-Marc Nuoffer, Luca Scorrano, Charaf Benarafa, Shida Yousefi & Hans-Uwe Simon

Optic atrophy 1 (OPA1) is known to be important for mitochondrial fusion and structural integrity. Here, using OPA1 knockout mice, the authors show a detrimental effect on host defense capabilities against pathogen infections. This study reports a critical role for OPA1 in innate immunity.

27 July 2018 | doi: 10.1038/s41467-018-05387-y
Cell biology  Innate immunity 

Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes OPEN

The rapidly evolving Y chromosome accumulates male-benefit genes but is often poorly characterized in many mammals. Here, the authors assemble the male specific region of the horse Y chromosome and investigate its evolution and function.

27 July 2018 | doi: 10.1038/s41467-018-05290-6
Comparative genomics  Molecular evolution 

Lighting up silicon nanoparticles with Mie resonances OPEN
Chengyun Zhang, Yi Xu, Jin Liu, Juntao Li, Jin Xiang, Hui Li, Jinxiang Li, Qiaofeng Dai, Sheng Lan & Andrey E. Miroshnichenko

As an indirect semiconductor, silicon shows notoriously inefficient luminescence. Here, the authors utilize the Mie resonances in silicon nanoparticles to demonstrate visible white-light emission, both from free-standing spheres and particles etched on a silicon-on-insulator substrate.

27 July 2018 | doi: 10.1038/s41467-018-05394-z
Nonlinear optics  Silicon photonics  Supercontinuum generation 

A novel enhancer regulates MGMT expression and promotes temozolomide resistance in glioblastoma OPEN
Xiaoyue Chen, Minjie Zhang, Haiyun Gan, Heping Wang, Jeong-Heon Lee, Dong Fang, Gaspar J. Kitange, Lihong He, Zeng Hu, Ian F. Parney, Fredric B. Meyer, Caterina Giannini, Jann N. Sarkaria & Zhiguo Zhang

Temozolomide (TMZ) resistance in glioblastomas (GBM) is associated with increased MGMT expression. Here, the authors identify an enhancer between the promoters of MKI67 and MGMT, that when activated drives MGMT expression despite MGMT promoter methylation to confer TMZ resistance in GBM.

27 July 2018 | doi: 10.1038/s41467-018-05373-4
Biochemistry  CNS cancer 

Mechanical dissipation from charge and spin transitions in oxygen-deficient SrTiO3 surfaces OPEN
Marcin Kisiel, Oleg O. Brovko, Dilek Yildiz, Rémy Pawlak, Urs Gysin, Erio Tosatti & Ernst Meyer

Non-contact atomic force microscope (AFM) dissipation contains rich information on the electron, phonon and spin states, but has been poorly understood. Here the authors demonstrated that tip-induced charge and spin state transitions in oxygen vacancies at SrTiO3 surface are revealed by AFM dissipation measurements.

27 July 2018 | doi: 10.1038/s41467-018-05392-1
Electronic properties and materials  Quantum dots  Surfaces, interfaces and thin films 

Two-dimensional multibit optoelectronic memory with broadband spectrum distinction OPEN
Du Xiang, Tao Liu, Jilian Xu, Jun Y. Tan, Zehua Hu, Bo Lei, Yue Zheng, Jing Wu, A. H. Castro Neto, Lei Liu & Wei Chen

Continued device miniaturization and feasibility of integrating two-dimensional materials into circuits have enabled flexible and transparent optoelectronic memories. Here, the authors show a WSe2–hBN-based heterostructure memory with switching ratio of ~1.1 × 106, ensuring over 128 distinct storage states and retention time of ~4.5 × 104 s.

27 July 2018 | doi: 10.1038/s41467-018-05397-w
Electronic devices  Information storage  Optical data storage  Two-dimensional materials 

A facile strategy for realizing room temperature phosphorescence and single molecule white light emission OPEN
Jianguo Wang, Xinggui Gu, Huili Ma, Qian Peng, Xiaobo Huang, Xiaoyan Zheng, Simon H. P. Sung, Guogang Shan, Jacky W. Y. Lam, Zhigang Shuai & Ben Zhong Tang

The demonstration of pure organic room temperature phosphorescence (RTP) luminogens with complementary emission is a key requirement for developing low-cost white light emitters. Here, the authors construct RTP-active organic salt compounds by exchanging the counterion with a heavy halide ion.

27 July 2018 | doi: 10.1038/s41467-018-05298-y
Chemical physics  Optical materials 

Concerted ESCRT and clathrin recruitment waves define the timing and morphology of intraluminal vesicle formation OPEN
Eva Maria Wenzel, Sebastian Wolfgang Schultz, Kay Oliver Schink, Nina Marie Pedersen, Viola Nähse, Andreas Carlson, Andreas Brech, Harald Stenmark & Camilla Raiborg

Intraluminal vesicles are formed by the endosomal sorting complex required for transport (ESCRT) machinery. Here, the authors unravel the timing of vesicle budding, and that endosomal clathrin regulates concerted recruitment of ESCRT subcomplexes, required for efficient membrane remodeling.

26 July 2018 | doi: 10.1038/s41467-018-05345-8
Cellular imaging  ESCRT 

Bottom-up growth of n-type monolayer molecular crystals on polymeric substrate for optoelectronic device applications OPEN
Yanjun Shi, Lang Jiang, Jie Liu, Zeyi Tu, Yuanyuan Hu, Qinghe Wu, Yuanping Yi, Eliot Gann, Christopher R. McNeill, Hongxiang Li, Wenping Hu, Daoben Zhu & Henning Sirringhaus

New methods for obtaining large-area monolayer molecular crystals (MMCs) on hydrophobic surfaces are needed to realize the full potential of MMCs for organic electronics. Here, the authors demonstrate bottom-up growth of high-grade n-type MMCs, which show superior performance in device applications.

26 July 2018 | doi: 10.1038/s41467-018-05390-3
Electronic devices 

Non-hysteretic first-order phase transition with large latent heat and giant low-field magnetocaloric effect OPEN
F. Guillou, A. K. Pathak, D. Paudyal, Y. Mudryk, F. Wilhelm, A. Rogalev & V. K. Pecharsky

First order magnetic phase transitions have many practical applications but they often involve structural changes that make it difficult to control energy losses. Guillou et al. show that Eu2In has an isostructural transition with a mechanism distinct from other known magnetoelastic transitions.

26 July 2018 | doi: 10.1038/s41467-018-05268-4
Electronic properties and materials  Magnetic properties and materials  Phase transitions and critical phenomena 

Exploring the performance of nanostructured reagents with organic-group-defined morphology in cross-coupling reaction OPEN
Alexey S. Kashin, Evgeniya S. Degtyareva, Dmitry B. Eremin & Valentine P. Ananikov

Direct visualization and characterization of the influence of nanoscale organization on the reactivity of organic functional groups in solution remain a challenge. Here, the authors report the real-time observation of the involvement of a nanostructured reagent in a cross-coupling reaction using advanced liquid-phase electron microscopy.

26 July 2018 | doi: 10.1038/s41467-018-05350-x
Catalytic mechanisms  Heterogeneous catalysis  Two-dimensional materials 

FABP4 as a key determinant of metastatic potential of ovarian cancer OPEN
Kshipra M. Gharpure, Sunila Pradeep, Marta Sans, Rajesha Rupaimoole, Cristina Ivan, Sherry Y. Wu, Emine Bayraktar, Archana S. Nagaraja, Lingegowda S. Mangala, Xinna Zhang, Monika Haemmerle, Wei Hu, Cristian Rodriguez-Aguayo, Michael McGuire, Celia Sze Ling Mak, Xiuhui Chen, Michelle A. Tran, Alejandro Villar-Prados, Guillermo Armaiz Pena, Ragini Kondetimmanahalli et al.

In ovarian cancer, metastatic phenotype may impact surgical outcomes. Here, the authors show miR-409-3p regulates FABP4 which can increase metastatic potential of ovarian cancer, and treatment with DOPC nanoliposomes containing either miR-409--3p mimic or FABP4 siRNA inhibits tumor progression in mice.

26 July 2018 | doi: 10.1038/s41467-018-04987-y
Cancer therapy  Metastasis  Ovarian cancer 

The influence of retardation and dielectric environments on interatomic Coulombic decay OPEN
Joshua Leo Hemmerich, Robert Bennett & Stefan Yoshi Buhmann

Interatomic Coulombic Decay is a non-radiative relaxation process between excited systems. Here the authors report a theoretical framework based on macroscopic quantum electrodynamics that shows the role of retardation and an environment in the enhancement or suppression of the ICD rate.

26 July 2018 | doi: 10.1038/s41467-018-05091-x
Atomic and molecular interactions with photons  Energy transfer  Macromolecules and clusters 

Glucose promotes cell growth by suppressing branched-chain amino acid degradation OPEN
Dan Shao, Outi Villet, Zhen Zhang, Sung Won Choi, Jie Yan, Julia Ritterhoff, Haiwei Gu, Danijel Djukovic, Danos Christodoulou, Stephen C. Kolwicz Jr, Daniel Raftery & Rong Tian

Hypertrophic cardiomyocytes switch their metabolism from fatty acid oxidation to glucose use, but the functional role of this change is unclear. Here the authors show that high intracellular glucose inhibits the degradation of branched-chain amino acids, which is required for the activation of pro-growth mTOR signaling.

26 July 2018 | doi: 10.1038/s41467-018-05362-7
Cardiac hypertrophy  Metabolism  TOR signalling 

High sensitivity organic inorganic hybrid X-ray detectors with direct transduction and broadband response OPEN
H. M. Thirimanne, K. D. G. I. Jayawardena, A. J. Parnell, R. M. I. Bandara, A. Karalasingam, S. Pani, J. E. Huerdler, D. G. Lidzey, S. F. Tedde, A. Nisbet, C. A. Mills & S. R. P. Silva

X-ray detectors based on low-cost organic semiconductors have inherently low detector sensitivity due to poor X-ray to charge conversion and charge collection. Here, the authors demonstrate a flexible, high-sensitivity X-ray detector based on an organic bulk heterojunction-nanoparticle composite.

26 July 2018 | doi: 10.1038/s41467-018-05301-6
Nanoparticles  Organic–inorganic nanostructures 

Mechanical mismatch-driven rippling in carbon-coated silicon sheets for stress-resilient battery anodes OPEN
Jaegeon Ryu, Tianwu Chen, Taesoo Bok, Gyujin Song, Jiyoung Ma, Chihyun Hwang, Langli Luo, Hyun-Kon Song, Jaephil Cho, Chongmin Wang, Sulin Zhang & Soojin Park

Maintaining the structural stability during electrochemical cycling remains a big challenge facing the silicon anode material. Here, the authors have developed 2D silicon nanosheets coated with carbon layers, which show a unique mechanism in releasing internal stress by forming ripple structures.

26 July 2018 | doi: 10.1038/s41467-018-05398-9
Energy science and technology  Materials science 

Epigenome-wide DNA methylation profiling in Progressive Supranuclear Palsy reveals major changes at DLX1 OPEN
Axel Weber, Sigrid C. Schwarz, Jörg Tost, Dietrich Trümbach, Pia Winter, Florence Busato, Pawel Tacik, Anita C. Windhorst, Maud Fagny, Thomas Arzberger, Catriona McLean, John C. van Swieten, Johannes Schwarz, Daniela Vogt Weisenhorn, Wolfgang Wurst, Till Adhikary, Dennis W. Dickson, Günter U. Höglinger & Ulrich Müller

Progressive supranuclear palsy (PSP) is a neurodegenerative disease characterized by aggregation of Tau, encoded by MAPT. Here, the authors perform an EWAS for PSP in prefrontal lobe tissue and find hypermethylation of DLX1 and its antisense transcript DLX1AS to associate with MAPT expression.

26 July 2018 | doi: 10.1038/s41467-018-05325-y
DNA methylation  Epigenetics in the nervous system  Epigenomics  Neurodegenerative diseases 

Digital acoustofluidics enables contactless and programmable liquid handling OPEN
Steven Peiran Zhang, James Lata, Chuyi Chen, John Mai, Feng Guo, Zhenhua Tian, Liqiang Ren, Zhangming Mao, Po-Hsun Huang, Peng Li, Shujie Yang & Tony Jun Huang

Contamination is an obstacle to the functioning of microfluidic devices. Here the authors exploit acoustic streaming to manipulate droplets which float on a layer of immiscible oil. This prevents contamination and enables rewritability by which different fluids can be used on the same substrate.

26 July 2018 | doi: 10.1038/s41467-018-05297-z
Acoustics  Fluid dynamics  Lab-on-a-chip 

Immediate hydroxylation of arenes to phenols via V-containing all-silica ZSM-22 zeolite triggered non-radical mechanism OPEN
Yu Zhou, Zhipan Ma, Junjie Tang, Ning Yan, Yonghua Du, Shibo Xi, Kai Wang, Wei Zhang, Haimeng Wen & Jun Wang

Hydroxylation of arenes via activation of aromatic Csp2–H bond remains a challenge. Here, the authors have managed to get various arenes hydroxylated to corresponding phenols using stoichiometric hydrogen peroxide and a series of robust V–Si–ZSM-22 catalysts synthesized via an ionic liquid involved dry-gel-conversion route.

26 July 2018 | doi: 10.1038/s41467-018-05351-w
Catalyst synthesis  Catalytic mechanisms  Heterogeneous catalysis 

Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates OPEN
Ronen Gabizon, Antony Lee, Hanif Vahedian-Movahed, Richard H. Ebright & Carlos J. Bustamante

Transcription elongation by RNA polymerase (RNAP) is interspersed with sequence-dependent pausing which is difficult to study due to spatiotemporal limitations of available methods. Here authors use a high-resolution optical tweezers assay and find that pause sites modify the dynamics of nearly all RNAP molecules.

26 July 2018 | doi: 10.1038/s41467-018-05344-9
Single-molecule biophysics  Transcription 

Inverted signaling by bacterial chemotaxis receptors OPEN
Shuangyu Bi, Fan Jin & Victor Sourjik

Bacteria use chemotaxis receptors to perceive environmental factors. Here, the authors show that mutations in a chemotaxis receptor can invert the sensory response, e.g. from attractant to repellent, and use these mutants to map regions that enable the receptor to sense multiple environmental factors.

26 July 2018 | doi: 10.1038/s41467-018-05335-w
Cell signalling  Cellular microbiology 

Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq OPEN
Johannes W. Bagnoli, Christoph Ziegenhain, Aleksandar Janjic, Lucas E. Wange, Beate Vieth, Swati Parekh, Johanna Geuder, Ines Hellmann & Wolfgang Enard

Single-cell RNA-barcoding and sequencing is an efficient, genome-wide method to characterize cellular identities. Here the authors systematically evaluate the protocol and develop molecular crowding SCRB-seq with improved sensitivity and cost-efficiency.

26 July 2018 | doi: 10.1038/s41467-018-05347-6
Genome-wide analysis of gene expression  Transcriptomics 
Nature Communications
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  Latest Correspondence    
Challenging PD-L1 expressing cytotoxic T cells as a predictor for response to immunotherapy in melanoma OPEN
Lieve Brochez, Annabel Meireson, Inès Chevolet, Nora Sundahl, Piet Ost & Vibeke Kruse
26 July 2018 | doi: 10.1038/s41467-018-05047-1
Cancer immunotherapy  Melanoma  Tumour immunology 

Reply to ‘Challenging PD-L1 expressing cytotoxic T cells as a predictor for response to immunotherapy in melanoma’ OPEN
Nicolas Jacquelot, Laurence Zitvogel & Alexander M. Eggermont
26 July 2018 | doi: 10.1038/s41467-018-05048-0
Immunotherapy  Tumour immunology 
  Latest Author Corrections    
Author Correction: TLR9 activation via microglial glucocorticoid receptors contributes to degeneration of midbrain dopamine neurons OPEN
Layal Maatouk, Anne-Claire Compagnion, Maria-Angeles Carrillo-de Sauvage, Alexis-Pierre Bemelmans, Sabrina Leclere-Turbant, Vincent Cirotteau, Mira Tohme, Allen Beke, Michaël Trichet, Virginie Bazin, Bobby N. Trawick, Richard M. Ransohoff, François Tronche, Bénédicte Manoury & Sheela Vyas
01 August 2018 | doi: 10.1038/s41467-018-05680-w
Neuroimmunology  Parkinson's disease 

Author Correction: The nature of spin excitations in the one-third magnetization plateau phase of Ba3CoSb2O9 OPEN
Y. Kamiya, L. Ge, Tao Hong, Y. Qiu, D. L. Quintero-Castro, Z. Lu, H. B. Cao, M. Matsuda, E. S. Choi, C. D. Batista, M. Mourigal, H. D. Zhou & J. Ma
01 August 2018 | doi: 10.1038/s41467-018-05679-3
Magnetic properties and materials 

Author Correction: RPAP3 provides a flexible scaffold for coupling HSP90 to the human R2TP co-chaperone complex OPEN
Fabrizio Martino, Mohinder Pal, Hugo Muñoz-Hernández, Carlos F. Rodríguez, Rafael Núñez-Ramírez, David Gil-Carton, Gianluca Degliesposti, J. Mark Skehel, S. Mark Roe, Chrisostomos Prodromou, Laurence H. Pearl & Oscar Llorca
31 July 2018 | doi: 10.1038/s41467-018-05546-1
Biochemistry  Cryoelectron microscopy  Structural biology 

Author Correction: Direct measurement of superdiffusive energy transport in disordered granular chains OPEN
Eunho Kim, Alejandro J. Martínez, Sean E. Phenisee, P. G. Kevrekidis, Mason A. Porter & Jinkyu Yang
27 July 2018 | doi: 10.1038/s41467-018-05576-9
Applied mathematics  Condensed-matter physics 

Author Correction: Checkpoint blockade immunotherapy reshapes the high-dimensional phenotypic heterogeneity of murine intratumoural neoantigen-specific CD8+ T cells OPEN
M. Fehlings, Y. Simoni, H. L. Penny, E. Becht, C. Y. Loh, M. M. Gubin, J. P. Ward, S. C. Wong, R. D. Schreiber & E. W. Newell
26 July 2018 | doi: 10.1038/s41467-018-05468-y
Applied immunology  High-throughput screening  Immunotherapy  Tumour heterogeneity 
  Latest Publisher Corrections    
Publisher Correction: 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
31 July 2018 | doi: 10.1038/s41467-018-05591-w
Fibre optics and optical communications  Nonlinear optics 

Publisher Correction: 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
27 July 2018 | doi: 10.1038/s41467-018-05359-2
Population genetics  Speciation 

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