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LinCCR2+ hematopoietic stem and progenitor cells overcome resistance to PD-1 blockade OPEN
Catherine T. Flores, Tyler J. Wildes, Jeffrey A. Drake, Ginger L. Moore, Bayli DiVita Dean, Rebecca S. Abraham & Duane A. Mitchell

Brain tumors are difficult to treat using existing immunotherapeutic strategies. Here, the authors show that in brain tumors resistant to PD-1 blockade, HSCs expressing CCR2+ can reverse treatment resistance and sensitizes mice to immunotherapy.

17 October 2018 | doi: 10.1038/s41467-018-06182-5
Cancer immunotherapy  Haematopoietic stem cells 

A hardware Markov chain algorithm realized in a single device for machine learning OPEN
He Tian, Xue-Feng Wang, Mohammad Ali Mohammad, Guang-Yang Gou, Fan Wu, Yi Yang & Tian-Ling Ren

Despite the need to develop resistive random access memory (RRAM) devices for machine learning, RRAM array-based hardware methods for algorithm require external electronics. Here, the authors realize a Markov chain algorithm in a single 2D multilayer SnSe device without external electronics.

17 October 2018 | doi: 10.1038/s41467-018-06644-w
Electronic devices  Information storage 

Recruitment of the mitotic exit network to yeast centrosomes couples septin displacement to actomyosin constriction OPEN
Davide Tamborrini, Maria Angeles Juanes, Sandy Ibanes, Giulia Rancati & Simonetta Piatti

The Mitotic Exit Network (MEN) promotes mitotic exit and cytokinesis but if and how MEN independently controls these two processes is unclear. Here, the authors report that MEN displaces septins from the cell division site to promote actomyosin ring constriction, independently of MEN control of mitotic exit.

17 October 2018 | doi: 10.1038/s41467-018-06767-0
Centrosome  Cytokinesis 

DRUG-seq for miniaturized high-throughput transcriptome profiling in drug discovery OPEN
Chaoyang Ye, Daniel J. Ho, Marilisa Neri, Chian Yang, Tripti Kulkarni, Ranjit Randhawa, Martin Henault, Nadezda Mostacci, Pierre Farmer, Steffen Renner, Robert Ihry, Leandra Mansur, Caroline Gubser Keller, Gregory McAllister, Marc Hild, Jeremy Jenkins & Ajamete Kaykas

RNA-seq is a powerful tool to investigate how drugs affect the transcriptome but library construction can be costly. Here the authors introduce DRUG-seq, an automated platform for high-throughput transcriptome profiling.

17 October 2018 | doi: 10.1038/s41467-018-06500-x
High-throughput screening  Molecular medicine  Screening  Transcriptomics 

Fundamental limits and non-reciprocal approaches in non-Hermitian quantum sensing OPEN
Hoi-Kwan Lau & Aashish A. Clerk

Non-Hermitian properties were proposed to be beneficial to sensing but it is not clear if this concept can be extended to the quantum regime. Here, Lau and Clerk self-consistently consider the impact of noise and measurement, and identify that nonreciprocity can improve sensing capabilities.

17 October 2018 | doi: 10.1038/s41467-018-06477-7
Imaging and sensing  Quantum metrology  Topological matter 

Decoding the intensity of sensory input by two glutamate receptors in one C. elegans interneuron OPEN
Wenjuan Zou, Jiajun Fu, Haining Zhang, Kang Du, Wenming Huang, Junwei Yu, Shitian Li, Yuedan Fan, Howard A. Baylis, Shangbang Gao, Rui Xiao, Wei Ji, Lijun Kang & Tao Xu

Little is known about how stimuli of different intensities result in different behavioral outcomes in C. elegans. In this study, the authors demonstrate how distinct signal patterns, involving different glutamate receptors, in a single interneuron AIB can encode differential behavioral outputs depending on the stimulus intensity

17 October 2018 | doi: 10.1038/s41467-018-06819-5
Neural circuits  Sensory processing 

Limitation of Fermi level shifts by polaron defect states in hematite photoelectrodes OPEN
Christian Lohaus, Andreas Klein & Wolfram Jaegermann

Hematite has been proposed as a suitable photocatalyst for water splitting based on its stability and appealing optical band gap, but its performance has not reached theoretical expectations. Here the authors show that this is due to intra-gap polaronic states that reduce the effective electronic band gap.

17 October 2018 | doi: 10.1038/s41467-018-06838-2
Electrochemistry  Electronic properties and materials  Photocatalysis  Surfaces, interfaces and thin films 

Superresolution mapping of energy landscape for single charge carriers in plastic semiconductors OPEN
Yifei Jiang & Jason McNeill

To understand the complex nanoscale structure-property relationships in conjugated polymers for device applications, new methods for tracking charge transport are required. Here, the authors employ superresolution mapping to study the charge carrier dynamics in conjugated polymer nanoparticles.

17 October 2018 | doi: 10.1038/s41467-018-06846-2
Fluorescence spectroscopy 

Photo-induced semimetallic states realised in electron–hole coupled insulators OPEN
Kozo Okazaki, Yu Ogawa, Takeshi Suzuki, Takashi Yamamoto, Takashi Someya, Shoya Michimae, Mari Watanabe, Yangfan Lu, Minoru Nohara, Hidenori Takagi, Naoyuki Katayama, Hiroshi Sawa, Masami Fujisawa, Teruto Kanai, Nobuhisa Ishii, Jiro Itatani, Takashi Mizokawa & Shik Shin

Ultrafast light pulses can manipulate and probe materials faster than relaxation timescales, leading to new electronic states and insights into equilibrium properties. Okazaki et al. use the properties of photo-induced metallic states to investigate unconventional correlated behaviour in Ta2NiSe5 and Ta2NiS5.

17 October 2018 | doi: 10.1038/s41467-018-06801-1
Electronic properties and materials  Phase transitions and critical phenomena 

Nanoscale metal-organic frameworks for mitochondria-targeted radiotherapy-radiodynamic therapy OPEN
Kaiyuan Ni, Guangxu Lan, Samuel S. Veroneau, Xiaopin Duan, Yang Song & Wenbin Lin

Photosensitizers delivered to mitochondria of cancer cells can enhance photodynamic therapy. Here, the authors report mitochondria-targeted radiation therapy and radiodynamic therapy of colorectal cancer models with a cationic nanoscale metal-organic framework to overcome shallow light penetration of Ru-based photosensitizers.

17 October 2018 | doi: 10.1038/s41467-018-06655-7
Biomaterials  Cancer therapy  Drug delivery  Metal–organic frameworks  Nanomedicine 

Targeting SPINK1 in the damaged tumour microenvironment alleviates therapeutic resistance OPEN

Tumour microenvironment actively contributes to drug resistance in clinical oncology. Here, the authors show that genotoxic stress induces senescence in human stromal cells, which in turn secrete serine protease inhibitor Kazal type 1 (SPINK1) and promote acquired resistance of cancer cells via EGFR-mediated paracrine signaling.

17 October 2018 | doi: 10.1038/s41467-018-06860-4
Cancer microenvironment  Cancer therapeutic resistance 

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance OPEN
Erol S. Kavvas, Edward Catoiu, Nathan Mih, James T. Yurkovich, Yara Seif, Nicholas Dillon, David Heckmann, Amitesh Anand, Laurence Yang, Victor Nizet, Jonathan M. Monk & Bernhard O. Palsson

Mycobacterium tuberculosis exhibits complex evolution of antimicrobial resistance (AMR). Here, the authors perform machine learning and structural analysis to identify signatures of AMR evolution to 13 antibiotics.

17 October 2018 | doi: 10.1038/s41467-018-06634-y
Bacterial genetics  Machine learning  Pathogens  Tuberculosis 

Integrated extracellular microRNA profiling for ovarian cancer screening OPEN
Akira Yokoi, Juntaro Matsuzaki, Yusuke Yamamoto, Yutaka Yoneoka, Kenta Takahashi, Hanako Shimizu, Takashi Uehara, Mitsuya Ishikawa, Shun-ichi Ikeda, Takumi Sonoda, Junpei Kawauchi, Satoko Takizawa, Yoshiaki Aoki, Shumpei Niida, Hiromi Sakamoto, Ken Kato, Tomoyasu Kato & Takahiro Ochiya

Screening methods for early detection of ovarian cancer is technically difficult. Here, the authors investigated circulating microRNA in human blood serum and developed a model using 10 microRNAs to discern between ovarian cancer and being ovarian tumors, solid tumors, and non-cancer patients.

17 October 2018 | doi: 10.1038/s41467-018-06434-4
Cancer screening  Gynaecological cancer  Tumour biomarkers 

Caenorhabditis elegans sperm carry a histone-based epigenetic memory of both spermatogenesis and oogenesis OPEN
Tomoko M. Tabuchi, Andreas Rechtsteiner, Tess E. Jeffers, Thea A. Egelhofer, Coleen T. Murphy & Susan Strome

Paternal contributions to epigenetic inheritance via nucleosomes are poorly understood, as sperm in many organisms replace the majority of nucleosomes with protamines. Here the authors provide evidence that Caenorhabditis elegans sperm retain histone packaging of the genome and provide a histone-based epigenetic memory that is important for germ cell development in offspring.

17 October 2018 | doi: 10.1038/s41467-018-06236-8
Epigenetic memory  Histone post-translational modifications  Oogenesis  Spermatogenesis 

Rare truncating variants in the sarcomeric protein titin associate with familial and early-onset atrial fibrillation OPEN
Gustav Ahlberg, Lena Refsgaard, Pia R. Lundegaard, Laura Andreasen, Mattis F. Ranthe, Nora Linscheid, Jonas B. Nielsen, Mads Melbye, Stig Haunsø, Ahmad Sajadieh, Lu Camp, Søren-Peter Olesen, Simon Rasmussen, Alicia Lundby, Patrick T. Ellinor, Anders G. Holst, Jesper H. Svendsen & Morten S. Olesen

Common genetic variants in structural proteins contribute to risk of atrial fibrillation (AF). Here, using whole-exome sequencing, the authors identify rare truncating variants in TTN that associate with familial and early-onset AF and show defects in cardiac sarcomere assembly in ttn.2-mutant zebrafish.

17 October 2018 | doi: 10.1038/s41467-018-06618-y
Atrial fibrillation  Cardiac hypertrophy  Cardiovascular genetics  Medical genetics 

Phenome-wide association studies across large population cohorts support drug target validation OPEN
Dorothée Diogo, Chao Tian, Christopher S. Franklin, Mervi Alanne-Kinnunen, Michael March, Chris C. A. Spencer, Ciara Vangjeli, Michael E. Weale, Hannele Mattsson, Elina Kilpeläinen, Patrick M. A. Sleiman, Dermot F. Reilly, Joshua McElwee, Joseph C. Maranville, Arnaub K. Chatterjee, Aman Bhandari, Khanh-Dung H. Nguyen, Karol Estrada, Mary-Pat Reeve, Janna Hutz et al.

Testing the association between genetic variants and a range of phenotypes can assist drug development. Here, in a phenome-wide association study in up to 697,815 individuals, Diogo et al. identify genotype–phenotype associations predicting efficacy, alternative indications or adverse drug effects.

16 October 2018 | doi: 10.1038/s41467-018-06540-3
Drug discovery  Genetic association study  Genetic predisposition to disease  Genetics research 

Action sharpens sensory representations of expected outcomes OPEN
Daniel Yon, Sam J. Gilbert, Floris P. de Lange & Clare Press

Our brains predict the likely sensory consequences of actions we take; one theory is that these sensory responses are suppressed, but another theory is that they are sharpened. Here, the authors show using fMRI evidence consistent with the sharpening account for sensory consequences of hand movements.

16 October 2018 | doi: 10.1038/s41467-018-06752-7
Cognitive neuroscience  Learning algorithms  Perception  Sensorimotor processing 

Human breast tumor-infiltrating CD8+ T cells retain polyfunctionality despite PD-1 expression OPEN
Colt A. Egelston, Christian Avalos, Travis Y. Tu, Diana L. Simons, Grecia Jimenez, Jae Y. Jung, Laleh Melstrom, Kim Margolin, John H. Yim, Laura Kruper, Joanne Mortimer & Peter P. Lee

Expression of the checkpoint molecule programmed cell death protein 1 (PD-1) is considered a marker of T cells exhaustion. Here the authors show that CD8T cells isolated from breast cancer patients are perfectly functional despite PD-1 expression while those isolated from melanoma patients are not.

16 October 2018 | doi: 10.1038/s41467-018-06653-9
Breast cancer  Tumour immunology 

Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features OPEN
Jason J. Pitt, Markus Riester, Yonglan Zheng, Toshio F. Yoshimatsu, Ayodele Sanni, Olayiwola Oluwasola, Artur Veloso, Emma Labrot, Shengfeng Wang, Abayomi Odetunde, Adeyinka Ademola, Babajide Okedere, Scott Mahan, Rebecca Leary, Maura Macomber, Mustapha Ajani, Ryan S. Johnson, Dominic Fitzgerald, A. Jason Grundstad, Jigyasa H. Tuteja et al.

Research on racial and ethnic influence on breast cancer mortality is stymied by a lack of genomic studies in diverse populations. Here, the authors genomically interrogate 194 Nigerian breast cancers, unveiling molecular features that could explain the high mortality rate from breast cancer in an indigenous African population.

16 October 2018 | doi: 10.1038/s41467-018-06616-0
Breast cancer  Cancer genomics 

Narrow bandgap oxide nanoparticles coupled with graphene for high performance mid-infrared photodetection OPEN
Xuechao Yu, Yangyang Li, Xiaonan Hu, Daliang Zhang, Ye Tao, Zhixiong Liu, Yongmin He, Md. Azimul Haque, Zheng Liu, Tom Wu & Qi Jie Wang

Coupling graphene with narrow band-gap Ti2O3 nanoparticles can enable efficient mid-infrared photodetection. Here, the authors report a graphene-Ti2O3 based hybrid photodetector with high responsivity of ~300 A W-1 up to 10 μm by varying the number of graphene layers and size of Ti2O3 nanoparticles.

16 October 2018 | doi: 10.1038/s41467-018-06776-z
Nanoparticles  Optical properties and devices  Two-dimensional materials 

Tailoring near-field thermal radiation between metallo-dielectric multilayers using coupled surface plasmon polaritons OPEN
Mikyung Lim, Jaeman Song, Seung S. Lee & Bong Jae Lee

Here, the authors report on an experimental demonstration of near-field thermal radiation enhancement between metallo-dielectric multilayers separated by submicron gap distances and that near-field thermal radiation can be readily tuned by modifying the resonance condition of coupled surface plasmon polaritons.

16 October 2018 | doi: 10.1038/s41467-018-06795-w
Nanophotonics and plasmonics  Nanoscale materials  Optical materials and structures 

An intrinsic association between olfactory identification and spatial memory in humans OPEN
Louisa Dahmani, Raihaan M. Patel, Yiling Yang, M. Mallar Chakravarty, Lesley K. Fellows & Véronique D. Bohbot

Olfaction, the sense of smell, may have originally evolved to aid navigation in space, but there is no direct evidence of a link between olfaction and navigation in humans. Here the authors show that olfaction and spatial memory abilities are correlated and rely on similar brain regions in humans.

16 October 2018 | doi: 10.1038/s41467-018-06569-4
Brain injuries  Cognitive neuroscience  Navigation  Olfactory system 

Multi-stage bioengineering of a layered oesophagus with in vitro expanded muscle and epithelial adult progenitors OPEN
Luca Urbani, Carlotta Camilli, Demetra-Ellie Phylactopoulos, Claire Crowley, Dipa Natarajan, Federico Scottoni, Panayiotis Maghsoudlou, Conor J. McCann, Alessandro Filippo Pellegata, Anna Urciuolo, Koichi Deguchi, Sahira Khalaf, Salvatore Ferdinando Aruta, Maria Cristina Signorelli, David Kiely, Edward Hannon, Matteo Trevisan, Rui Rachel Wong, Marc Olivier Baradez, Dale Moulding et al.

Combining decellularised scaffolds with patient-derived cells holds promise for bioengineering of functional tissues. Here the authors develop a two-stage approach to engineer an oesophageal graft that retains the structural organisation of native oesophagus.

16 October 2018 | doi: 10.1038/s41467-018-06385-w
Regenerative medicine  Stem cells  Tissue engineering  Translational research 

Early redox activities modulate Xenopus tail regeneration OPEN
Fernando Ferreira, VijayKrishna Raghunathan, Guillaume Luxardi, Kan Zhu & Min Zhao

Reactive oxygen species (ROS) and hypoxia-inducible factors (HIF) mediate regeneration but how is unclear. Here, the authors use an optic-based probe ('optrode') to monitor oxygen (O2) during Xenopus tail regeneration, identifying crosstalk between O2 influx, ROS production, and HIF-1α stabilization.

16 October 2018 | doi: 10.1038/s41467-018-06614-2
Developmental biology  Physiology 

DNA engineered micromotors powered by metal nanoparticles for motion based cellphone diagnostics OPEN
Mohamed Shehata Draz, Kamyar Mehrabi Kochehbyoki, Anish Vasan, Dheerendranath Battalapalli, Aparna Sreeram, Manoj Kumar Kanakasabapathy, Shantanu Kallakuri, Athe Tsibris, Daniel R. Kuritzkes & Hadi Shafiee

Micromotors have a range of potential healthcare applications. Here, the authors describe the development of a metal nanoparticle DNA micromotor which can be used to detect human HIV-1 by a change in the motion of the micromotors, monitored by cell phone camera, triggered by binding of HIV-1 RNA.

16 October 2018 | doi: 10.1038/s41467-018-06727-8
Biosensors  Diagnosis  HIV infections  Molecular machines and motors 

Shaping the topology of folding pathways in mechanical systems OPEN
Menachem Stern, Viraaj Jayaram & Arvind Murugan

Self-folding origami have applications for mechanical metamaterials but one of their pitfalls is that many undesirable folding modes exist. Here the authors propose an algorithm to determine which folding joints to make stiffer in order to ensure that the sheet is folded into the chosen state.

16 October 2018 | doi: 10.1038/s41467-018-06720-1
Applied mathematics  Nonlinear phenomena  Soft materials 

Cancer exosomes induce tumor innervation OPEN
Marianna Madeo, Paul L. Colbert, Daniel W. Vermeer, Christopher T. Lucido, Jacob T. Cain, Elisabeth G. Vichaya, Aaron J. Grossberg, DesiRae Muirhead, Alex P. Rickel, Zhongkui Hong, Jing Zhao, Jill M. Weimer, William C. Spanos, John H. Lee, Robert Dantzer & Paola D. Vermeer

Tumors can induce axonogenesis which is commonly associated with worse outcomes. Here, the authors show that this phenomenon is mediated by cancer exosomes.

16 October 2018 | doi: 10.1038/s41467-018-06640-0
Head and neck cancer  Mechanisms of disease 

Tracing the transitions from pluripotency to germ cell fate with CRISPR screening OPEN
Jamie A. Hackett, Yun Huang, Ufuk Günesdogan, Kristjan A. Gretarsson, Toshihiro Kobayashi & M. Azim Surani

Primordial Germ Cell-Like Cells (PGCLCs) are an in vitro model for primordial germ cell development. Here, the authors couple a novel compound reporter with CRISPR screening to identify key genes for exit from pluripotency and acquisition of PGCLC fate; specifically identifying Nr5a2 and Zfp296.

16 October 2018 | doi: 10.1038/s41467-018-06230-0
CRISPR-Cas9 genome editing  Cell lineage  Embryonic germ cells  Epigenetics  Transcriptomics 

Heat conduction measurements in ballistic 1D phonon waveguides indicate breakdown of the thermal conductance quantization OPEN
Adib Tavakoli, Kunal Lulla, Thierry Crozes, Natalio Mingo, Eddy Collin & Olivier Bourgeois

At low temperatures and dimensionality it has become possible to probe the quantum limits of heat transport. Tavakoli et al. show that heat transport through a one-dimensional device can be dominated by non-ideal transmission instead of reaching the regime of thermal conductance quantization.

16 October 2018 | doi: 10.1038/s41467-018-06791-0
Condensed-matter physics  Nanoscale devices  Quantum physics  Statistical physics, thermodynamics and nonlinear dynamics 

Daily humidity oscillation regulates the circadian clock to influence plant physiology OPEN
Musoki Mwimba, Sargis Karapetyan, Lijing Liu, Jorge Marqués, Erin M. McGinnis, Nicolas E. Buchler & Xinnian Dong

Humidity has been shown to influence many aspects of plant physiology. Here Mwimba et al. show that oscillating humidity entrains the circadian clock under constant light conditions and enhances clock amplitude in simulated natural environments, while also improving immunity and overall growth.

16 October 2018 | doi: 10.1038/s41467-018-06692-2
Plant immunity  Plant molecular biology 

Hidden hearing loss selectively impairs neural adaptation to loud sound environments OPEN
Warren Michael Henry Bakay, Lucy Anne Anderson, Jose Alberto Garcia-Lazaro, David McAlpine & Roland Schaette

Hidden hearing loss (HHL) arises through subtle damage to the synapses of hair cells in the inner ear before audiograms reveal hearing threshold shifts. Here, the authors report that HHL in a mouse model disrupts the neural encoding of loud sound environments in the central auditory system.

16 October 2018 | doi: 10.1038/s41467-018-06777-y
Cochlea  Experimental models of disease  Midbrain  Sensory processing 

Structural basis for arginine glycosylation of host substrates by bacterial effector proteins OPEN
Jun Bae Park, Young Hun Kim, Youngki Yoo, Juyeon Kim, Sung-Hoon Jun, Jin Won Cho, Samir El Qaidi, Samuel Walpole, Serena Monaco, Ana A. García-García, Miaomiao Wu, Michael P. Hays, Ramon Hurtado-Guerrero, Jesus Angulo, Philip R. Hardwidge, Jeon-Soo Shin & Hyun-Soo Cho

The type III secretion system effectors NleB and SseK are glycosyltransferases (GT) that specifically glycosylate arginine residues. Here the authors provide insights into their mechanism by combining X-ray crystallography, NMR, enzyme kinetics measurements, molecular dynamics simulations and in vivo experiments and show that SseK/NleB enzymes are retaining GTs.

16 October 2018 | doi: 10.1038/s41467-018-06680-6
Glycobiology  NMR spectroscopy  X-ray crystallography 

MicroRNA-27a controls the intracellular survival of Mycobacterium tuberculosis by regulating calcium-associated autophagy OPEN
Feng Liu, Jianxia Chen, Peng Wang, Haohao Li, Yilong Zhou, Haipeng Liu, Zhonghua Liu, Ruijuan Zheng, Lin Wang, Hua Yang, Zhenling Cui, Fei Wang, Xiaochen Huang, Jie Wang, Wei Sha, Heping Xiao & Baoxue Ge

How Mycobacterium tuberculosis (Mtb) escapes autophagy-mediated clearance is poorly understood. Here, Liu et al. show that Mtb-induced MicroRNA-27a targets the ER-associated calcium transporter CACNA2D3, leading to suppression of antimicrobial autophagy and to enhanced intracellular survival of Mtb.

16 October 2018 | doi: 10.1038/s41467-018-06836-4
Bacterial host response  Bacterial pathogenesis  Infection  Pathogenesis 

A shear-dependent NO-cGMP-cGKI cascade in platelets acts as an auto-regulatory brake of thrombosis OPEN
Lai Wen, Susanne Feil, Markus Wolters, Martin Thunemann, Frank Regler, Kjestine Schmidt, Andreas Friebe, Marcus Olbrich, Harald Langer, Meinrad Gawaz, Cor de Wit & Robert Feil

Nitric oxide (NO) inhibits thrombosis in part by stimulating cyclic guanosine monophosphate (cGMP) production and cGMP-dependent protein kinase I (cGKI) activity in platelets. Here, Wen et al. develop a cGMP sensor mouse to follow cGMP dynamics in platelets, and find that shear stress activates NO-cGMP-cGKI signaling during platelet aggregation to limit thrombosis.

16 October 2018 | doi: 10.1038/s41467-018-06638-8
Calcium signalling  Fluorescence imaging  Platelets  Thrombosis 

A luminous blue kilonova and an off-axis jet from a compact binary merger at z = 0.1341 OPEN
E. Troja, G. Ryan, L. Piro, H. van Eerten, S. B. Cenko, Y. Yoon, S.-K. Lee, M. Im, T. Sakamoto, P. Gatkine, A. Kutyrev & S. Veilleux

A faint gamma-ray burst (GRB 170817A) has been recently detected in coincidence with the gravitational wave (GW) event GW 170817. Here, the authors report that another faint short GRB at a cosmological distance (GRB150101B) and its late time emission are analogous to the neutron star merger event GRB 170817A.

16 October 2018 | doi: 10.1038/s41467-018-06558-7
Compact astrophysical objects  High-energy astrophysics  Time-domain astronomy  Transient astrophysical phenomena 

Mediterranean UNESCO World Heritage at risk from coastal flooding and erosion due to sea-level rise OPEN
Lena Reimann, Athanasios T. Vafeidis, Sally Brown, Jochen Hinkel & Richard S. J. Tol

UNESCO World Heritage located in low-lying coastal areas is increasingly at risk from flooding and erosion due to sea-level rise. This study shows that up to 82% of cultural World Heritage sites located in the Mediterranean will be at risk from coastal flooding and over 93% from coastal erosion by 2100 under high-end sea-level rise.

16 October 2018 | doi: 10.1038/s41467-018-06645-9
Climate-change impacts  Environmental impact  Environmental sciences  Natural hazards 

A selenium-catalysed para-amination of phenols OPEN
Dingyuan Yan, Guoqiang Wang, Feng Xiong, Wei-Yin Sun, Zhuangzhi Shi, Yi Lu, Shuhua Li & Jing Zhao

Selenium has emerged as a metalloid for the catalytic construction of C–N bonds; however no functionalisation of aromatic compounds has been developed yet. Here, the authors report the para-amination of phenols via two successive sigmatropic rearrangements of a redox versatile Se–N bond.

16 October 2018 | doi: 10.1038/s41467-018-06763-4
Homogeneous catalysis  Synthetic chemistry methodology  Organocatalysis 

Haploinsufficiency of autism spectrum disorder candidate gene NUAK1 impairs cortical development and behavior in mice OPEN
Virginie Courchet, Amanda J. Roberts, Géraldine Meyer-Dilhet, Peggy Del Carmine, Tommy L. Lewis Jr, Franck Polleux & Julien Courchet

Nuak1 is an autism spectrum disorder candidate gene. Here the authors report behavioral and cortical development in mice heterozygous for Nuak1, suggesting loss of function mutations in one copy of Nuak1 may contribute to neurodevelopmental disorders.

16 October 2018 | doi: 10.1038/s41467-018-06584-5
Autism spectrum disorders  Development of the nervous system  Neural circuits  Social behaviour 

Cationic nanoparticle as an inhibitor of cell-free DNA-induced inflammation OPEN
Huiyi Liang, Bo Peng, Cong Dong, Lixin Liu, Jiaji Mao, Song Wei, Xinlu Wang, Hanshi Xu, Jun Shen, Hai-Quan Mao, Xiaohu Gao, Kam W. Leong & Yongming Chen

Cell-free DNA (cfDNA) released from damaged or dead cells can activate DNA sensors that exacerbate the pathogenesis of rheumatoid arthritis (RA). Here the authors use ~40 nm cationic nanoparticles to scavenge cfDNA, and demonstrate the potential for nanomedicine to relieve debilitating RA symptoms.

16 October 2018 | doi: 10.1038/s41467-018-06603-5
Inflammatory diseases  Nanomedicine  Nanoparticles  Rheumatoid arthritis 

Dopamine-dependent prefrontal reactivations explain long-term benefit of fear extinction OPEN
A. M. V. Gerlicher, O. Tüscher & R. Kalisch

The success of extinction learning is not predictive of long-term retrieval of an extinction memory. Using fMRI to study consolidation of fear extinction in human subjects, the authors show that reactivation in the ventromedial prefrontal cortex during memory retrieval predicts extinction memory retrieval, and that increasing dopaminergic signaling increases the number of these activations.

16 October 2018 | doi: 10.1038/s41467-018-06785-y
Consolidation  Cortex  Extinction  Fear conditioning  Long-term memory 

PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex OPEN
Stephanie Link, Ramona M. M. Spitzer, Maryam Sana, Mario Torrado, Moritz C. Völker-Albert, Eva C. Keilhauer, Thomas Burgold, Sebastian Pünzeler, Jason K. K. Low, Ida Lindström, Andrea Nist, Catherine Regnard, Thorsten Stiewe, Brian Hendrich, Axel Imhof, Matthias Mann, Joel P. Mackay, Marek Bartkuhn & Sandra B. Hake

PWWP2A is a chromatin-binding transcriptional regulator that mediates mitosis-progression. Here, the authors provide evidence that PWWP2A directly interacts with H2A.Z nucleosomes, DNA and H3K36me3, binds to an MTA1-specific subcomplex of the NuRD complex (M1HR) and promotes changes to histone acetylation.

16 October 2018 | doi: 10.1038/s41467-018-06665-5
Biochemistry  DNA  Epigenetics  Gene expression  Genetics 

Lipopolysaccharide-affinity copolymer senses the rapid motility of swarmer bacteria to trigger antimicrobial drug release OPEN
Shengtao Lu, Wuguo Bi, Quanchao Du, Sheetal Sinha, Xiangyang Wu, Arnold Subrata, Surajit Bhattacharjya, Bengang Xing & Edwin K. L. Yeow

Urinary tract infections are a common side effect of urethral catheters. Here, the authors report on the development of antibiotic loaded NPs with functional polymer coatings which attach too and are removed by motile bacteria to trigger the release of antibiotic.

15 October 2018 | doi: 10.1038/s41467-018-06729-6
Antibiotics  Drug delivery  Nanoscale materials 

The olfactory epithelium as a port of entry in neonatal neurolisteriosis OPEN
Dennis Pägelow, Chintan Chhatbar, Andreas Beineke, Xiaokun Liu, Andreas Nerlich, Kira van Vorst, Manfred Rohde, Ulrich Kalinke, Reinhold Förster, Stephan Halle, Peter Valentin-Weigand, Mathias W. Hornef & Marcus Fulde

Listeria monocytogenes causes meningitis in newborns. Here, Pägelow et al. present a mouse model of neonatal cerebral listeriosis, and show that nasal inoculation, but not intragastric administration, leads to early brain infection in the absence of bacteraemia during the neonatal period.

15 October 2018 | doi: 10.1038/s41467-018-06668-2
Infection  Pathogens 

Uncovering the heterogeneity and temporal complexity of neurodegenerative diseases with Subtype and Stage Inference OPEN
Alexandra L Young, Razvan V Marinescu, Neil P Oxtoby, Martina Bocchetta, Keir Yong, Nicholas C Firth, David M Cash, David L Thomas, Katrina M Dick, Jorge Cardoso, John van Swieten, Barbara Borroni, Daniela Galimberti, Mario Masellis, Maria Carmela Tartaglia, James B Rowe, Caroline Graff, Fabrizio Tagliavini, Giovanni B Frisoni, Robert Laforce Jr et al.

Progressive diseases tend to be heterogeneous in their underlying aetiology mechanism, disease manifestation, and disease time course. Here, Young and colleagues devise a computational method to account for both phenotypic heterogeneity and temporal heterogeneity, and demonstrate it using two neurodegenerative disease cohorts.

15 October 2018 | doi: 10.1038/s41467-018-05892-0
Computer science  Neurodegenerative diseases 

Synthetic lethality between HER2 and transaldolase in intrinsically resistant HER2-positive breast cancers OPEN
Yi Ding, Chang Gong, De Huang, Rui Chen, Pinpin Sui, Kevin H. Lin, Gehao Liang, Lifeng Yuan, Handan Xiang, Junying Chen, Tao Yin, Peter B. Alexander, Qian-Fei Wang, Er-Wei Song, Qi-Jing Li, Kris C. Wood & Xiao-Fan Wang

Resistance to anti-HER2 therapy in breast cancer remains a major obstacle in the clinic. Here the authors performed a CRISPR-selective vulnerability screen to identify transaldoloase as a target that is synthetically lethal with HER2 inhibition in breast cancer cells.

15 October 2018 | doi: 10.1038/s41467-018-06651-x
Breast cancer  Cancer  Cell biology 

Modulation of AMPA receptor surface diffusion restores hippocampal plasticity and memory in Huntington's disease models OPEN
Hongyu Zhang, Chunlei Zhang, Jean Vincent, Diana Zala, Caroline Benstaali, Matthieu Sainlos, Dolors Grillo-Bosch, Sophie Daburon, Françoise Coussen, Yoon Cho, Denis J. David, Frederic Saudou, Yann Humeau & Daniel Choquet

Cognitive decline in Huntington's disease (HD) may be due to impaired hippocampal synaptic plasticity. In this study the authors show that AMPA receptor surface diffusion, a key player in synaptic plasticity, is deregulated in multiple HD mouse models as a result of impaired BDNF signalling that underlies the memory deficits, and can be pharmacologically rescued.

15 October 2018 | doi: 10.1038/s41467-018-06675-3
Cellular neuroscience  Huntington's disease  Synaptic plasticity 

Single Particle Automated Raman Trapping Analysis OPEN
Jelle Penders, Isaac J. Pence, Conor C. Horgan, Mads S. Bergholt, Christopher S. Wood, Adrian Najer, Ulrike Kauscher, Anika Nagelkerke & Molly M. Stevens

Enabling concurrent, high throughput analysis of single nano particles would greatly increase the capacity to study size, composition and inter and intra particle population variance. Here, the authors present a comprehensive platform for single particle automated Raman trapping analysis without any target modification.

15 October 2018 | doi: 10.1038/s41467-018-06397-6
Characterization and analytical techniques  Optical manipulation and tweezers  Raman spectroscopy 

The fungal peptide toxin Candidalysin activates the NLRP3 inflammasome and causes cytolysis in mononuclear phagocytes OPEN
Lydia Kasper, Annika König, Paul-Albert Koenig, Mark S. Gresnigt, Johannes Westman, Rebecca A. Drummond, Michail S. Lionakis, Olaf Groß, Jürgen Ruland, Julian R. Naglik & Bernhard Hube

Phagocytic cells of the innate immune system play critical roles in defence against invading pathogens including the opportunistic pathogen Candida albicans. Here the authors show that C. albicans derived Candidalysin in addition to being a cell-damaging toxin to mononuclear phagocytes is a trigger of NLRP3 inflammasome activation in these cells.

15 October 2018 | doi: 10.1038/s41467-018-06607-1
Cell death and immune response  Fungal host response  Fungal infection  Inflammasome 

Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin OPEN
Pierrick Moreau, Axel Cournac, Gianna Aurora Palumbo, Martial Marbouty, Shogofa Mortaza, Agnes Thierry, Stefano Cairo, Marc Lavigne, Romain Koszul & Christine Neuveut

Whether DNA viruses contact specific regions of host genomes or make random contacts is unclear. Here, the authors use Hi-C and show that HBV cccDNA and Ad5 DNA contact preferentially active chromatin at CpG islands for the former and at transcription start sites and enhancers for the latter.

15 October 2018 | doi: 10.1038/s41467-018-06739-4
Adenovirus  Chromatin  Hepatitis B virus  Virus–host interactions 

High prevalence of focal and multi-focal somatic genetic variants in the human brain OPEN
Michael J. Keogh, Wei Wei, Juvid Aryaman, Lauren Walker, Jelle van den Ameele, Jon Coxhead, Ian Wilson, Matthew Bashton, Jon Beck, John West, Richard Chen, Christian Haudenschild, Gabor Bartha, Shujun Luo, Chris M. Morris, Nick S. Jones, Johannes Attems & Patrick F. Chinnery

Similar to cancers, somatic mutations might lead to neurodegenerative diseases. Here, the authors perform ultra-deep sequencing of 102 genes in 173 adult human brains, detect somatic mutations in 54 brains, and develop a mathematical model to estimate the frequency of mutated foci in human brains.

15 October 2018 | doi: 10.1038/s41467-018-06331-w
Genetic markers  Genetics  Neurodegeneration  Neuroscience 

Fuelling conditions at staging sites can mitigate Arctic warming effects in a migratory bird OPEN
Eldar Rakhimberdiev, Sjoerd Duijns, Julia Karagicheva, Cornelis J. Camphuysen, Anne Dekinga, Rob Dekker, Anatoly Gavrilov, Job ten Horn, Joop Jukema, Anatoly Saveliev, Mikhail Soloviev, T. Lee Tibbitts, Jan A. van Gils, Theunis Piersma, Andre van Loon, Arnold Wijker, Guido Keijl, Henk Levering, Jan Visser, Leo Heemskerk et al.

Advancing phenological timing is a risk for migratory birds, particularly in the Arctic where change is most rapid. Here, the authors show that bar-tailed godwits can adjust for phenological shifts by fuelling faster at staging areas to arrive at breeding sites in time.

15 October 2018 | doi: 10.1038/s41467-018-06673-5
Animal migration  Climate-change ecology  Phenology  Population dynamics 

The dimensionality of niche space allows bounded and unbounded processes to jointly influence diversification OPEN
Matthew J. Larcombe, Gregory J. Jordan, David Bryant & Steven I. Higgins

The degree to which species diversity is bounded by limited niche space is under debate. Here, Larcombe and colleagues show that bounded and unbounded processes contribute more-or-less equally to conifer diversification, and that it may be niche dimensionality that facilitates these opposing forces.

15 October 2018 | doi: 10.1038/s41467-018-06732-x
Biodiversity  Evolutionary ecology  Evolutionary theory  Plant evolution 

Definite photon deflections of topological defects in metasurfaces and symmetry-breaking phase transitions with material loss OPEN
Chong Sheng, Hui Liu, Huanyang Chen & Shining Zhu

Photonic structures can be used to simulate fundamental physical phenomena like the optical analog of gravity. Here, the authors use metasurface-engineered waveguides to emulate the optical effects of a topological defect on space-time.

15 October 2018 | doi: 10.1038/s41467-018-06718-9
Metamaterials  Physics 

CRISPR knockout screening identifies combinatorial drug targets in pancreatic cancer and models cellular drug response OPEN
Karol Szlachta, Cem Kuscu, Turan Tufan, Sara J. Adair, Stephen Shang, Alex D. Michaels, Matthew G. Mullen, Natasha Lopes Fischer, Jiekun Yang, Limin Liu, Prasad Trivedi, Edward B. Stelow, P. Todd Stukenberg, J. Thomas Parsons, Todd W. Bauer & Mazhar Adli

Predicting the response to chemotherapy is a major goal of cancer research. Here the authors use CRISPR knockout screens in pancreatic ductal adenocarcinoma cells to identify deletions synergistic with MEK inhibitors.

15 October 2018 | doi: 10.1038/s41467-018-06676-2
Cancer  Computational biology and bioinformatics 

A phosphatidylinositol 4,5-bisphosphate redistribution-based sensing mechanism initiates a phagocytosis programing OPEN
Libing Mu, Zhongyuan Tu, Lin Miao, Hefei Ruan, Ning Kang, Yongzhen Hei, Jiahuan Chen, Wei Wei, Fangling Gong, Bingjie Wang, Yanan Du, Guanghui Ma, Matthias W. Amerein, Tie Xia & Yan Shi

The origin of Fc receptor-based phagocytosis is unknown, although plasma lipid redistribution after solid structure binding induces similar phagocytic signaling. Here, Mu et al. show that PIP2 accumulation from plasma membrane deformation recruits Moesin to trigger receptor-independent phagocytosis.

15 October 2018 | doi: 10.1038/s41467-018-06744-7
Lipid signalling  Membrane biophysics  Phagocytosis  Signal transduction 

Single cell RNA-seq reveals profound transcriptional similarity between Barrett's oesophagus and oesophageal submucosal glands OPEN
Richard Peter Owen, Michael Joseph White, David Tyler Severson, Barbara Braden, Adam Bailey, Robert Goldin, Lai Mun Wang, Carlos Ruiz-Puig, Nicholas David Maynard, Angie Green, Paolo Piazza, David Buck, Mark Ross Middleton, Chris Paul Ponting, Benjamin Schuster-Böckler & Xin Lu

Barrett's oesophagus is associated with an increased risk of oseophageal cancer, but its cell of origin is unclear. Here the authors show, using single-cell RNA sequencing of biopsies from six patients and two unaffected subjects, that cells in Barrett's oesophagus show a transcriptional profile that is similar to that of cells in oesophageal submucosal glands.

15 October 2018 | doi: 10.1038/s41467-018-06796-9
Barrett oesophagus  Functional clustering  Gene expression 

Skin-touch-actuated textile-based triboelectric nanogenerator with black phosphorus for durable biomechanical energy harvesting OPEN
Jiaqing Xiong, Peng Cui, Xiaoliang Chen, Jiangxin Wang, Kaushik Parida, Meng-Fang Lin & Pooi See Lee

Incorporation of triboelectric nanogenerators into textiles is attractive for self-powered wearable electronics. Here the authors employ black phosphorus with a hydrophobic coating in a durable, washable, and air permeable textile-based device that converts biomechanical motion into electricity.

15 October 2018 | doi: 10.1038/s41467-018-06759-0
Electronic devices  Two-dimensional materials 

HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry OPEN
Vincent V. Pham, Carolina Salguero, Shamsun Nahar Khan, Jennifer L. Meagher, W. Clay Brown, Nicolas Humbert, Hugues de Rocquigny, Janet L. Smith & Victoria M. D'Souza

The HIV Tat protein recruits a host elongation factor from the cellular 7SK complex to the viral TAR RNA to ensure transcriptional elongation. Here, Pham et al. solve the structures of both 7SK and TAR RNAs in complex with Tat's RNA binding domain and gain mechanistic insights into the process.

15 October 2018 | doi: 10.1038/s41467-018-06591-6
HIV infections  Solution-state NMR  Transcription  Virus–host interactions 

SHQ1 regulation of RNA splicing is required for T-lymphoblastic leukemia cell survival OPEN
Hexiu Su, Juncheng Hu, Liang Huang, Yang Yang, Morgan Thenoz, Anna Kuchmiy, Yufeng Hu, Peng Li, Hui Feng, Yu Zhou, Tom Taghon, Pieter Van Vlierberghe, Guoliang Qing, Zhichao Chen & Hudan Liu

T-acute lymphoblastic leukemia is an aggressive cancer. Here the authors provide insights into the functional role of SHQ1, an H/ACA snoRNP assembly factor involved in snRNA pseudouridylation, in T-lymphoblastic leukemia cell survival through regulating the maturation of MYC mRNA.

15 October 2018 | doi: 10.1038/s41467-018-06523-4
Mechanisms of disease  Oncogenes  RNA splicing 

Automated quantification of bioluminescence images OPEN
Alexander D. Klose & Neal Paragas

Analysis of bioluminescence images of bacterial distributions in living animals is mostly manual and semiquantitative. Here, the authors present an analysis platform featuring an animal mold, a probabilistic organ atlas, and a mirror gantry to perform automatic in vivo bioluminescence quantification.

15 October 2018 | doi: 10.1038/s41467-018-06288-w
Hardware and infrastructure  Image processing  Imaging and sensing 

Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria OPEN
Oriana S. Fisher, Grace E. Kenney, Matthew O. Ross, Soo Y. Ro, Betelehem E. Lemma, Sharon Batelu, Paul M. Thomas, Victoria C. Sosnowski, Caroline J. DeHart, Neil L. Kelleher, Timothy L. Stemmler, Brian M. Hoffman & Amy C. Rosenzweig

Methane- and ammonia-oxidizing bacteria use the integral membrane, copper-dependent enzymes particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO) to oxidize methane and ammonia. Here the authors structurally characterize the copper-binding protein PmoD, which contains an unusual CuA site and their genetic analyses strongly support a pMMO and AMO related function of PmoD.

15 October 2018 | doi: 10.1038/s41467-018-06681-5
Metalloproteins  X-ray crystallography 

Gene expression imputation identifies candidate genes and susceptibility loci associated with cutaneous squamous cell carcinoma OPEN
Nilah M. Ioannidis, Wei Wang, Nicholas A. Furlotte, David A. Hinds, Michelle Agee, Babak Alipanahi, Adam Auton, Robert K. Bell, Katarzyna Bryc, Sarah L. Elson, Pierre Fontanillas, Karen E. Huber, Aaron Kleinman, Nadia K. Litterman, Jennifer C. McCreight, Matthew H. McIntyre, Joanna L. Mountain, Elizabeth S. Noblin, Carrie A. M. Northover, Steven J. Pitts et al.

Genetic loci linked to susceptibility for the common skin cancer cutaneous squamous cell carcinoma (cSCC) have been identified by genome wide association studies (GWAS). Here, the authors impute gene expression levels from GWAS data to perform a transcriptome wide association study (TWAS), identifying five novel genetic loci linked to cSCC susceptibility.

15 October 2018 | doi: 10.1038/s41467-018-06149-6
Cancer genomics  Gene expression  Genome-wide association studies  Squamous cell carcinoma 

Energy level tuned indium arsenide colloidal quantum dot films for efficient photovoltaics OPEN
Jung Hoon Song, Hyekyoung Choi, Hien Thu Pham & Sohee Jeong

Existing n-type colloidal quantum dot materials easily lose their doping polarity in air. Here Song et al. passivate the reactive covalent surface of indium arsenide quantum dots to gain the energy-level tunability and show p–n junction type solar cells with 7.92% certified efficiency.

15 October 2018 | doi: 10.1038/s41467-018-06399-4
Chemical engineering  Materials for energy and catalysis 

Mrp1 is involved in lipid presentation and iNKT cell activation by Streptococcus pneumoniae OPEN
Shilpi Chandra, James Gray, William B. Kiosses, Archana Khurana, Kaori Hitomi, Catherine M. Crosby, Ashu Chawla, Zheng Fu, Meng Zhao, Natacha Veerapen, Stewart K. Richardson, Steven A. Porcelli, Gurdyal Besra, Amy R. Howell, Sonia Sharma, Bjoern Peters & Mitchell Kronenberg

The CD1d pathway present lipid antigens resulting in the activation of iNKT cells but the complete pathway remains to be fully elucidated. Here, Chandra et al. use an siRNA screen and identify Mrp1 as crucial for CD1d lipid presentation and activation of iNKT in the context of Streptococcus pneumoniae infection.

15 October 2018 | doi: 10.1038/s41467-018-06646-8
Bacterial host response  Bacterial infection  Cellular immunity  NKT cells 

Rats adopt the optimal timescale for evidence integration in a dynamic environment OPEN
Alex T. Piet, Ahmed El Hady & Carlos D. Brody

In a dynamic environment old evidence could be outdated. Here, the authors investigate the ability of rats to integrate and discount evidence provided by auditory clicks to infer a hidden, dynamic, state of the world and model the consequence of sensory noise to explain the source of errors.

15 October 2018 | doi: 10.1038/s41467-018-06561-y
Computational neuroscience  Decision 

Complex virome in feces from Amerindian children in isolated Amazonian villages OPEN
Juliana D. Siqueira, Maria Gloria Dominguez-Bello, Monica Contreras, Orlana Lander, Hortensia Caballero-Arias, Deng Xutao, Oscar Noya-Alarcon & Eric Delwart

The authors compare human fecal viromes from three isolated villages of the Amazon rain forest with those from city dwellers. They report that the diversity of human viruses is not reduced in isolated villages, suggesting frequent viral introductions or increased susceptibility to enteric infections.

15 October 2018 | doi: 10.1038/s41467-018-06502-9
Metagenomics  Microbiome  Virology 

Cramming versus threading of long amphiphilic oligomers into a polyaromatic capsule OPEN
Masahiro Yamashina, Shunsuke Kusaba, Munetaka Akita, Takashi Kikuchi & Michito Yoshizawa

Molecular capsules typically bind only guests with volumes smaller than their cavities. Here, the authors find that a polyaromatic capsule accommodates linear amphiphilic oligomers in a length-dependent manner, whereas short chains are fully crammed into the cavity, long chains can be incorporated into the capsule in a threaded fashion.

12 October 2018 | doi: 10.1038/s41467-018-06458-w
Interlocked molecules  Molecular capsules  Supramolecular chemistry 

Astrocytes detect and upregulate transmission at inhibitory synapses of somatostatin interneurons onto pyramidal cells OPEN
Marco Matos, Anthony Bosson, Ilse Riebe, Clare Reynell, Joanne Vallée, Isabel Laplante, Aude Panatier, Richard Robitaille & Jean-Claude Lacaille

Astrocytes have been shown to regulate glutamatergic transmission in the brain. Here, the authors show that astrocytes also detect and modulate GABAergic transmission from somatostatin but not parvalbumin-positive interneurons, thus regulating dendritic inhibition via a feedback loop.

12 October 2018 | doi: 10.1038/s41467-018-06731-y
Astrocyte  Neurotransmitters 

Harnessing copper-palladium alloy tetrapod nanoparticle-induced pro-survival autophagy for optimized photothermal therapy of drug-resistant cancer OPEN
Yunjiao Zhang, Rui Sha, Lan Zhang, Wenbin Zhang, Peipei Jin, Weiguo Xu, Jianxun Ding, Jun Lin, Jing Qian, Guangyu Yao, Rui Zhang, Fanchen Luo, Jie Zeng, Jie Cao & Long-ping Wen

"Conventional chemotherapy-photothermal therapy combination has limited efficacy in drug resistant cancers. Here they develop Copper-palladium tetrapod nanoparticles to overcome these challenges and show them to work in synergy with autophagy inhibitors to treat drug resistant cancers"

12 October 2018 | doi: 10.1038/s41467-018-06529-y
Autophagy  Nanoparticles  Nanotechnology in cancer 

Local generation of hydrogen for enhanced photothermal therapy OPEN
Penghe Zhao, Zhaokui Jin, Qian Chen, Tian Yang, Danyang Chen, Jin Meng, Xifeng Lu, Zhen Gu & Qianjun He

The tracking and targeted release of multi-agents to cooperatively treat cancer is a developing and evolving field. Here, the authors demonstrate the anticancer effects of cubic Pd hydride nanocrystals with photoacoustic imaging properties that can release hydrogen under an NIR trigger and have photothermal effects.

12 October 2018 | doi: 10.1038/s41467-018-06630-2
Biological techniques  Cancer  Nanotechnology in cancer 

Influence of Tibetan Plateau snow cover on East Asian atmospheric circulation at medium-range time scales OPEN
Wenkai Li, Weidong Guo, Bo Qiu, Yongkang Xue, Pang-Chi Hsu & Jiangfeng Wei

The atmospheric response to subseasonal variability of Tibetan Plateau snow cover has been largely ignored. Here the authors show that the fast subseasonal variability of Tibetan Plateau snow cover is closely related to the subsequent East Asian atmospheric circulation at medium-range time scales.

12 October 2018 | doi: 10.1038/s41467-018-06762-5
Atmospheric dynamics  Atmospheric science  Climate sciences  Cryospheric science  Hydrology 

Myogenin promotes myocyte fusion to balance fibre number and size OPEN
Massimo Ganassi, Sara Badodi, Huascar Pedro Ortuste Quiroga, Peter S. Zammit, Yaniv Hinits & Simon M. Hughes

Loss of the transcription factor Myogenin in mice reduces skeletal myogenesis and leads to perinatal death but how Myogenin regulates muscle formation is unclear. Here, the authors show that zebrafish Myogenin enhances Myomaker expression, muscle cell fusion and myotome size, yet decreases fast muscle fibre number.

12 October 2018 | doi: 10.1038/s41467-018-06583-6
Differentiation  Morphogenesis 

Variants in exons 5 and 6 of ACTB cause syndromic thrombocytopenia OPEN
Sharissa L. Latham, Nadja Ehmke, Patrick Y. A. Reinke, Manuel H. Taft, Dorothee Eicke, Theresia Reindl, Werner Stenzel, Michael J. Lyons, Michael J. Friez, Jennifer A. Lee, Ramona Hecker, Michael C. Frühwald, Kerstin Becker, Teresa M. Neuhann, Denise Horn, Evelin Schrock, Indra Niehaus, Katharina Sarnow, Konrad Grützmann, Luzie Gawehn et al.

Genetic variants in ACTB and ACTG1 have been associated with Baraitser-Winter Cerebrofrontofacial syndrome. Here, the authors report of a syndromic thrombocytopenia caused by variants in ACTB exons 5 or 6 that compromise the organization and coupling of the cytoskeleton, leading to impaired platelet maturation.

12 October 2018 | doi: 10.1038/s41467-018-06713-0
Disease genetics  Haematological diseases  Microtubules  Platelets 

Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements OPEN
Jesper Svedberg, Sara Hosseini, Jun Chen, Aaron A. Vogan, Iva Mozgova, Lars Hennig, Pennapa Manitchotpisit, Anna Abusharekh, Thomas M. Hammond, Martin Lascoux & Hanna Johannesson

Meiotic drive elements are selfish genetic elements that mediate a skew in their sexual transmission from parent to offspring. Here, the authors sequence and analyze large and complex genomic regions associated with meiotic drive elements in the fungus Neurospora intermedia.

12 October 2018 | doi: 10.1038/s41467-018-06562-x
Evolutionary genetics  Genomics  Microbial genetics  Molecular evolution 

DUSP10 constrains innate IL-33-mediated cytokine production in ST2hi memory-type pathogenic Th2 cells OPEN
Takeshi Yamamoto, Yusuke Endo, Atsushi Onodera, Kiyoshi Hirahara, Hikari K. Asou, Takahiro Nakajima, Toshio Kanno, Yasuo Ouchi, Satoshi Uematsu, Hiroshi Nishimasu, Osamu Nureki, Damon J. Tumes, Naoki Shimojo & Toshinori Nakayama

T helper 2 (Th2) cells and type 2 innate lymphoid cells (ILC2) respond differently to interleukin-33 (IL-33) stimulation. Here the authors show that a phosphatase, Dusp10, is expressed in Th2, but not ILC2, to dephosphorylate p38 kinase, reduce GATA3 transcription factor activity, and suppress the induction of IL-5 in response to IL-33.

12 October 2018 | doi: 10.1038/s41467-018-06468-8
Innate lymphoid cells  Interleukins  Signal transduction  T-helper 2 cells 

Chemical and structural studies provide a mechanistic basis for recognition of the MYC G-quadruplex OPEN
David R. Calabrese, Xiang Chen, Elena C. Leon, Snehal M. Gaikwad, Zaw Phyo, William M. Hewitt, Stephanie Alden, Thomas A. Hilimire, Fahu He, Aleksandra M. Michalowski, John K. Simmons, Lindsey B. Saunders, Shuling Zhang, Daniel Connors, Kylie J. Walters, Beverly A. Mock & John S. Schneekloth Jr.

Targeting noncoding nucleic acids with small molecules represents an important and significant challenge in chemical biology and drug discovery. Here the authors characterize DC-34, a small molecule that exhibits selective binding to specific G4 structures, and provide a structural basis for its selectivity

12 October 2018 | doi: 10.1038/s41467-018-06315-w
NMR spectroscopy  Nucleic acids  Small molecules 

Hub-organized parallel circuits of central circadian pacemaker neurons for visual photoentrainment in Drosophila OPEN
Meng-Tong Li, Li-Hui Cao, Na Xiao, Min Tang, Bowen Deng, Tian Yang, Taishi Yoshii & Dong-Gen Luo

The central circadian clock in Drosophila is made up of ~ 150 anatomically distributed neurons; the circuits underlying photoentrainment is unclear. This study describes ex vivo patch-clamp recording of the eye-mediated light response of all known circadian clock neurons, and shows that they are organized in parallel circuits centered around a hub.

12 October 2018 | doi: 10.1038/s41467-018-06506-5
Circadian mechanisms  Neural circuits 

Diverging importance of drought stress for maize and winter wheat in Europe OPEN
Heidi Webber, Frank Ewert, Jørgen E. Olesen, Christoph Müller, Stefan Fronzek, Alex C. Ruane, Maryse Bourgault, Pierre Martre, Behnam Ababaei, Marco Bindi, Roberto Ferrise, Robert Finger, Nándor Fodor, Clara Gabaldón-Leal, Thomas Gaiser, Mohamed Jabloun, Kurt-Christian Kersebaum, Jon I. Lizaso, Ignacio J. Lorite, Loic Manceau et al.

Drivers of crop yield variability require quantification, and historical records can help in improving understanding. Here, Webber et al. report that drought stress will remain a key driver of yield losses in wheat and maize across Europe, and benefits from CO2 will be limited in low-yielding years.

12 October 2018 | doi: 10.1038/s41467-018-06525-2
Agriculture  Environmental impact 

Cortical population activity within a preserved neural manifold underlies multiple motor behaviors OPEN
Juan A. Gallego, Matthew G. Perich, Stephanie N. Naufel, Christian Ethier, Sara A. Solla & Lee E. Miller

Motor cortical neurons enable performance of a wide range of movements. Here, the authors report that dominant population activity patterns, the neural modes, are largely preserved across various tasks, with many displaying consistent temporal dynamics and reliably mapping onto muscle activity.

12 October 2018 | doi: 10.1038/s41467-018-06560-z
Computational neuroscience  Motor control  Motor cortex 

A conserved HH-Gli1-Mycn network regulates heart regeneration from newt to human OPEN
Bhairab N. Singh, Naoko Koyano-Nakagawa, Wuming Gong, Ivan P. Moskowitz, Cyprian V. Weaver, Elizabeth Braunlin, Satyabrata Das, Jop H. van Berlo, Mary G. Garry & Daniel J. Garry

Due to the limited proliferation capacity of adult mammalian cardiomyocytes, the human heart has negligible regenerative capacity after injury. Here the authors show that a Hedgehog-Gli1-Mycn signaling cascade regulates cardiomyocyte proliferation and cardiac regeneration from amphibians to mammals.

12 October 2018 | doi: 10.1038/s41467-018-06617-z
Cardiac regeneration  Cell proliferation  Cell signalling  Developmental biology 

Enhanced climate instability in the North Atlantic and southern Europe during the Last Interglacial OPEN
P. C. Tzedakis, R. N. Drysdale, V. Margari, L. C. Skinner, L. Menviel, R. H. Rhodes, A. S. Taschetto, D. A. Hodell, S. J. Crowhurst, J. C. Hellstrom, A. E. Fallick, J. O. Grimalt, J. F. McManus, B. Martrat, Z. Mokeddem, F. Parrenin, E. Regattieri, K. Roe & G. Zanchetta

It is important to establish a baseline for natural climate variability under relatively warm conditions. Here we show that the Last Interglacial in the North Atlantic and southern Europe was characterized by enhanced climate instability relative to the pre-industrial Holocene.

12 October 2018 | doi: 10.1038/s41467-018-06683-3
Palaeoceanography  Palaeoclimate 

Photonic thermal management of coloured objects OPEN
Wei Li, Yu Shi, Zhen Chen & Shanhui Fan

Understanding the tunable range of radiative thermal load for a given colour is important for thermal management of outdoor structures. Here, the authors theoretically and experimentally highlighted all mechanisms through which one can control the radiative thermal load of coloured objects.

12 October 2018 | doi: 10.1038/s41467-018-06535-0
Applied optics  Energy science and technology  Optical materials and structures 

Fine-tuning the efficiency of para-hydrogen-induced hyperpolarization by rational N-heterocyclic carbene design OPEN
Peter J. Rayner, Philip Norcott, Kate M. Appleby, Wissam Iali, Richard O. John, Sam J. Hart, Adrian C. Whitwood & Simon B. Duckett

Hyperpolarization methods play a crucial role in the in vivo observation of molecular metabolism by MRI techniques. Here, the authors develop NHC-containing iridium complexes which improve the NMR detectability of 1H, 13C and 15N nuclei via transfer of latent magnetism of para-hydrogen into a substrate.

12 October 2018 | doi: 10.1038/s41467-018-06766-1
Homogeneous catalysis  Ligands  NMR spectroscopy 

REV-ERBα integrates colon clock with experimental colitis through regulation of NF-κB/NLRP3 axis OPEN
Shuai Wang, Yanke Lin, Xue Yuan, Feng Li, Lianxia Guo & Baojian Wu

REV-ERBα is a nuclear receptor that links the circadian pathways with those of metabolism. Here the authors show REV-ERBα is also involved with linking the circadian system with the inflammatory pathways of an experimental model of colitis through regulation of the NF-κB/NLRP3 axis.

12 October 2018 | doi: 10.1038/s41467-018-06568-5
Circadian rhythms  Inflammasome  Inflammation  Inflammatory bowel disease 

An engineered thermal-shift screen reveals specific lipid preferences of eukaryotic and prokaryotic membrane proteins OPEN
Emmanuel Nji, Yurie Chatzikyriakidou, Michael Landreh & David Drew

Membrane bilayers are made up of a myriad of different lipids that affect membrane proteins, but identifying those specific lipid requirements remains a challenge. Here authors present an engineered thermal-shift screen which reveals specific lipid preferences of eukaryotic and prokaryotic membrane proteins.

12 October 2018 | doi: 10.1038/s41467-018-06702-3
Assay systems  Membrane lipids  Membrane proteins 

Probing aggrephagy using chemically-induced protein aggregates OPEN
Anne F. J. Janssen, Eugene A. Katrukha, Wendy van Straaten, Pauline Verlhac, Fulvio Reggiori & Lukas C. Kapitein

Autophagic clearance of aggregates, aggrephagy, is essential for cellular homeostasis but tools to induce and monitor it are limited. Here the authors present a fluorescence-based aggrephagy induction assay to study spatiotemporal dynamics and control mechanisms driving protein aggregate clearance.

12 October 2018 | doi: 10.1038/s41467-018-06674-4
Autophagy  Cytological techniques 

Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions OPEN
Eugenio F. Fornasiero, Sunit Mandad, Hanna Wildhagen, Mihai Alevra, Burkhard Rammner, Sarva Keihani, Felipe Opazo, Inga Urban, Till Ischebeck, M. Sadman Sakib, Maryam K. Fard, Koray Kirli, Tonatiuh Pena Centeno, Ramon O. Vidal, Raza-Ur Rahman, Eva Benito, André Fischer, Sven Dennerlein, Peter Rehling, Ivo Feussner et al.

Measuring precise protein turnover rates in animals is technically challenging at the proteomic level. Here, Fornasiero and colleagues use isotopic labeling with mass spectrometry and mathematical modeling to accurately determine protein lifetimes in the mouse brain

12 October 2018 | doi: 10.1038/s41467-018-06519-0
Homeostasis  Molecular medicine  Molecular neuroscience  Proteomics 

Disrupted alternative splicing for genes implicated in splicing and ciliogenesis causes PRPF31 retinitis pigmentosa OPEN
Adriana Buskin, Lili Zhu, Valeria Chichagova, Basudha Basu, Sina Mozaffari-Jovin, David Dolan, Alastair Droop, Joseph Collin, Revital Bronstein, Sudeep Mehrotra, Michael Farkas, Gerrit Hilgen, Kathryn White, Kuan-Ting Pan, Achim Treumann, Dean Hallam, Katarzyna Bialas, Git Chung, Carla Mellough, Yuchun Ding et al.

Mutations in pre-mRNA processing factors cause autosomal dominant retinitis pigmentosa. Here the authors provide insights into the pathophysiological mechanisms underlying non-syndromic retinal disease caused by heterozygous mutations in genes encoding ubiquitously expressed splicing factors.

12 October 2018 | doi: 10.1038/s41467-018-06448-y
Differentiation  Induced pluripotent stem cells 

Perceptual learning of fine contrast discrimination changes neuronal tuning and population coding in macaque V4 OPEN
Mehdi Sanayei, Xing Chen, Daniel Chicharro, Claudia Distler, Stefano Panzeri & Alexander Thiele

Perceptual learning, the improvement in perceptual abilities with training, is thought to involve changes in neuronal 'tuning'. Here, the authors show that perceptual learning works by making neurons increasingly sensitive to task-relevant differences in stimuli, and by improving population coding mechanisms.

12 October 2018 | doi: 10.1038/s41467-018-06698-w
Cortex  Extrastriate cortex  Neural encoding  Sensory processing 

Epistasis studies reveal redundancy among calcium-dependent protein kinases in motility and invasion of malaria parasites OPEN
Hanwei Fang, Ana Rita Gomes, Natacha Klages, Paco Pino, Bohumil Maco, Eloise M. Walker, Zenon A. Zenonos, Fiona Angrisano, Jake Baum, Christian Doerig, David A. Baker, Oliver Billker & Mathieu Brochet

Despite functional optimisation during evolution of parasitism, most members of a calcium dependent protein kinase (CDPK) family show genetic redundancy in Plasmodium. Here, the authors screen 294 genetic interactions among protein kinases in Plasmodium and show how some CDPKs functionally interact to control motility and host cell invasion.

12 October 2018 | doi: 10.1038/s41467-018-06733-w
Kinases  Malaria  Parasite biology 

POH1 deubiquitinates pro-interleukin-1β and restricts inflammasome activity OPEN
Li Zhang, Yun Liu, Boshi Wang, Guiqin Xu, Zhaojuan Yang, Ming Tang, Aihui Ma, Tiantian Jing, Xiaoli Xu, Xiaoren Zhang & Yongzhong Liu

The inflammasomes are important for activating the pro-inflammatory cytokine interleukin-β (IL-1β) for protection against pathogens. Here the authors show that a deubiquitinase, POH1, reduces the conversion of pro-IL-1β into its active form, with in vivo data further implicating a role of POH1 for maintaining immune homeostasis.

12 October 2018 | doi: 10.1038/s41467-018-06455-z
Inflammasome  Inflammation  Monocytes and macrophages  Mucosal immunology 

S-nitrosylation of the zinc finger protein SRG1 regulates plant immunity OPEN
Beimi Cui, Qiaona Pan, David Clarke, Marisol Ochoa Villarreal, Saima Umbreen, Bo Yuan, Weixing Shan, Jihong Jiang & Gary J. Loake

Upon pathogen infection plants accumulate nitric oxide which subsequently regulates defence gene expression. Here, the authors show that S-nitrosylation of the zinc finger transcription factor SRG1 affects transcriptional suppression and contributes to activation of defence responses.

12 October 2018 | doi: 10.1038/s41467-018-06578-3
Plant immunity  Plant sciences 

ATRX, DAXX or MEN1 mutant pancreatic neuroendocrine tumors are a distinct alpha-cell signature subgroup OPEN
Chang S. Chan, Saurabh V. Laddha, Peter W. Lewis, Matthew S. Koletsky, Kenneth Robzyk, Edaise Da Silva, Paula J. Torres, Brian R. Untch, Janet Li, Promita Bose, Timothy A. Chan, David S. Klimstra, C. David Allis & Laura H. Tang

In pancreatic neuroendocrine tumors (PanNETs) ATRX, DAXX, and MEN1 are commonly mutated (A-D-M mutant PanNETs). Here, the authors find in a cohort of PanNETS 58% are A-D-M mutant PanNETs, with a worse clinical outcome and differences in gene expression and methylation compared to A-D-M wild type cases- these gene expression differences suggest that A-D-M mutant PanNETs potentially originate from a cell type similar to alpha cells.

12 October 2018 | doi: 10.1038/s41467-018-06498-2
Cancer genetics  Molecular medicine 

An expression atlas of variant ionotropic glutamate receptors identifies a molecular basis of carbonation sensing OPEN
Juan Antonio Sánchez-Alcañiz, Ana Florencia Silbering, Vincent Croset, Giovanna Zappia, Anantha Krishna Sivasubramaniam, Liliane Abuin, Saumya Yashmohini Sahai, Daniel Münch, Kathrin Steck, Thomas O. Auer, Steeve Cruchet, G. Larisa Neagu-Maier, Simon G. Sprecher, Carlos Ribeiro, Nilay Yapici & Richard Benton

Little is known about the role of variant ionotropic glutamate receptors (IRs) in insect taste. Here the authors characterise the expression pattern of IRs in the Drosophila gustatory system and highlight the role of one receptor, IR56d, in the detection of carbonation

12 October 2018 | doi: 10.1038/s41467-018-06453-1
Genetics  Neuroscience 

Steering is an essential feature of non-locality in quantum theory OPEN
Ravishankar Ramanathan, Dardo Goyeneche, Sadiq Muhammad, Piotr Mironowicz, Marcus Grünfeld, Mohamed Bourennane & Paweł Horodecki

Quantum nonlocality is known to be reducible to quantum uncertainty and steering, but it is unclear whether steering is actually as essential as uncertainty. Here, the authors show that both steering and uncertainty play a role in determining optimal strategies in nonlocal games.

12 October 2018 | doi: 10.1038/s41467-018-06255-5
Quantum information  Quantum mechanics  Qubits  Single photons and quantum effects 

EVI1 overexpression reprograms hematopoiesis via upregulation of Spi1 transcription OPEN
Edward Ayoub, Michael P. Wilson, Kathleen E. McGrath, Allison J. Li, Benjamin J. Frisch, James Palis, Laura M. Calvi, Yi Zhang & Archibald S. Perkins

Chr3q26 rearrangements cause overexpression of EVI1 and associate with myeloid neoplasms, but the mechanism behind this association is unclear. Here, using a novel mouse model they show that EVI1 causes premalignant myeloid expansion with suppression of other lineages through upregulation of Spi1/PU.1.

12 October 2018 | doi: 10.1038/s41467-018-06208-y
Cancer models  Oncogenes  Oncogenesis  Transcriptional regulatory elements 

Large-scale whole-exome sequencing association studies identify rare functional variants influencing serum urate levels OPEN
Adrienne Tin, Yong Li, Jennifer A. Brody, Teresa Nutile, Audrey Y. Chu, Jennifer E. Huffman, Qiong Yang, Ming-Huei Chen, Cassianne Robinson-Cohen, Aurélien Macé, Jun Liu, Ayşe Demirkan, Rossella Sorice, Sanaz Sedaghat, Melody Swen, Bing Yu, Sahar Ghasemi, Alexanda Teumer, Peter Vollenweider, Marina Ciullo et al.

Elevated serum urate levels are a risk factor for gout. Here, Tin et al. perform whole-exome sequencing in 19,517 individuals and detect low-frequency genetic variants in urate transporter genes, SLC22A12 and SLC2A9, associated with serum urate levels and confirm their damaging nature in vitro and in silico.

12 October 2018 | doi: 10.1038/s41467-018-06620-4
Genetic association study  Kidney  Permeation and transport  Risk factors 

Charging dynamics of an individual nanopore OPEN
Ran Tivony, Sam Safran, Philip Pincus, Gilad Silbert & Jacob Klein

Modern energy-storage technologies are based on porous electrodes that store charge within nanometrically-narrow pores or slits. Here the authors show an approach to probe and measure, for the first time, the charging dynamics within an individual nano-slit – the basic element of a porous electrode.

11 October 2018 | doi: 10.1038/s41467-018-06364-1
Materials for energy and catalysis  Physical chemistry 

A cysteine-based molecular code informs collagen C-propeptide assembly OPEN
Andrew S. DiChiara, Rasia C. Li, Patreece H. Suen, Azade S. Hosseini, Rebecca J. Taylor, Alexander F. Weickhardt, Diya Malhotra, Darrell R. McCaslin & Matthew D. Shoulders

Collagen proteins assemble into trimers from distinct monomers with high specificity, yet the molecular basis for this specificity remains unclear. Here the authors demonstrate the crucial role of conserved C-terminal domain cysteine residues and calcium in homotrimeric procollagen assembly.

11 October 2018 | doi: 10.1038/s41467-018-06185-2
Biophysics  Cytoskeletal proteins  Protein folding 

Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters OPEN
Julien de Lorgeril, Aude Lucasson, Bruno Petton, Eve Toulza, Caroline Montagnani, Camille Clerissi, Jeremie Vidal-Dupiol, Cristian Chaparro, Richard Galinier, Jean-Michel Escoubas, Philippe Haffner, Lionel Dégremont, Guillaume M. Charrière, Maxime Lafont, Abigaïl Delort, Agnès Vergnes, Marlène Chiarello, Nicole Faury, Tristan Rubio, Marc A. Leroy et al.

Pacific oyster mortality syndrome is a poorly understood cause of mortality in commercially important oyster species. Here, the authors use multiple infection experiments to show that the syndrome is caused by sequential infection by herpesvirus and opportunistic bacteria.

11 October 2018 | doi: 10.1038/s41467-018-06659-3
Infectious diseases  Marine biology  Microbial ecology  Pathogens 

Unbiased biocatalytic solar-to-chemical conversion by FeOOH/BiVO4/perovskite tandem structure OPEN
Yang Woo Lee, Passarut Boonmongkolras, Eun Jin Son, Jinhyun Kim, Sahng Ha Lee, Su Keun Kuk, Jong Wan Ko, Byungha Shin & Chan Beum Park

Photoelectrochemical (PEC) cell platforms typically need an electrical bias that drives the electron transfer from the photoanode to the photocathode. Here, the authors report a bias-free PEC tandem device for solar-driven redox biocatalysis.

11 October 2018 | doi: 10.1038/s41467-018-06687-z
Biocatalysis  Bioenergetics 

Non-neutralizing antibodies elicited by recombinant Lassa–Rabies vaccine are critical for protection against Lassa fever OPEN
Tiago Abreu-Mota, Katie R. Hagen, Kurt Cooper, Peter B. Jahrling, Gene Tan, Christoph Wirblich, Reed F. Johnson & Matthias J. Schnell

There is currently no approved vaccine for Lassa fever virus (LASV). Here, Abreu-Mota et al. develop an inactivated, adjuvanted vaccine candidate expressing LASV glycoprotein (GPC) in a rabies virus vector, and show that non-neutralizing LASV GPC-specific antibodies are a major mechanism of protection.

11 October 2018 | doi: 10.1038/s41467-018-06741-w
Antibodies  Inactivated vaccines  Viral infection 

The quantum-confined Stark effect in layered hybrid perovskites mediated by orientational polarizability of confined dipoles OPEN
G. Walters, M. Wei, O. Voznyy, R. Quintero-Bermudez, A. Kiani, D.-M. Smilgies, R. Munir, A. Amassian, S. Hoogland & E. Sargent

The quantum-confined Stark effect is conventionally observed in inorganic semiconductor multilayer quantum well structures that are expensive to make. Here Walters et al. report large Stark effects in easily made layered hybrid perovskites and exploit the orientational polarizability of dipolar cations.

11 October 2018 | doi: 10.1038/s41467-018-06746-5
Applied optics  Nanoparticles  Nanoscale materials  Nonlinear optics  Photonic devices 

Patient-derived frontotemporal lobar degeneration brain extracts induce formation and spreading of TDP-43 pathology in vivo OPEN
Sílvia Porta, Yan Xu, Clark R. Restrepo, Linda K. Kwong, Bin Zhang, Hannah J. Brown, Edward B. Lee, John Q. Trojanowski & Virginia M.-Y. Lee

Cell-to-cell transmission of TDP43 occurs in cell cultures and may contribute to pathological TDP43 propagation in FTLD-TDP. In this study, the authors demonstrate using mouse models that a single intracerebral injection of human brain-derived pathological TDP43 from FTLD-TDP cases initiates the process of seeding and spreading of TDP43 pathology in a spatio-temporal dependent manner in the brain.

11 October 2018 | doi: 10.1038/s41467-018-06548-9
Amyotrophic lateral sclerosis  Dementia 

Spatially-resolved fluorescence-detected two-dimensional electronic spectroscopy probes varying excitonic structure in photosynthetic bacteria OPEN
Vivek Tiwari, Yassel Acosta Matutes, Alastair T. Gardiner, Thomas L. C. Jansen, Richard J. Cogdell & Jennifer P. Ogilvie

2D electronic spectroscopy enables a spatially-averaged view of the electronic structure of a heterogeneous system. Here, the authors extend it to sub-micron resolution and ~106 times better sensitivity, to resolve spatially varying excitonic structure in a heterogeneous mixture of photosynthetic cells.

11 October 2018 | doi: 10.1038/s41467-018-06619-x
Biophysics  Electronic properties and materials  Energy transfer  Fluorescence spectroscopy 

Space- and time-resolved small angle X-ray scattering to probe assembly of silver nanocrystal superlattices OPEN
Yixuan Yu, Dian Yu, Babak Sadigh & Christine A. Orme

How nanocrystals assemble into superlattices is poorly understood, given the difficulty of probing these processes in real time, in a controlled environment. Here, the authors use space- and time-resolved in situ small angle X-ray scattering to monitor the ordering of nanocrystal superlattices by electric field, which allows them to extract quantitative information about the assembly process.

11 October 2018 | doi: 10.1038/s41467-018-06734-9
Nanoscale materials  Synthesis and processing  Techniques and instrumentation 

Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features OPEN
Yan Kai, Jaclyn Andricovich, Zhouhao Zeng, Jun Zhu, Alexandros Tzatsos & Weiqun Peng

CTCF mediates long-range chromatin interactions which are important for genome organization and function. Here, the authors demonstrate that CTCF-mediated interactome exhibits extensive plasticity and present Lollipop, a machine-learning framework which predicts CTCF-mediated long-range interactions using genomic and epigenomic features.

11 October 2018 | doi: 10.1038/s41467-018-06664-6
Computational biology and bioinformatics  Functional genomics  Genome informatics 

Broad phylogenetic analysis of cation/proton antiporters reveals transport determinants OPEN
Gal Masrati, Manish Dwivedi, Abraham Rimon, Yael Gluck-Margolin, Amit Kessel, Haim Ashkenazy, Itay Mayrose, Etana Padan & Nir Ben-Tal

Cation/proton antiporters (CPAs) play a major role in maintaining living cells' homeostasis and are divided in two main groups: CPA1 and CPA2. Here authors use a comprehensive evolutionary analysis of 6537 representative CPAs and reveal a sequence motif that determines central phenotypic characteristics.

11 October 2018 | doi: 10.1038/s41467-018-06770-5
Carrier proteins  Classification and taxonomy  Functional clustering  Membrane proteins  Phylogeny 

Spectral field mapping in plasmonic nanostructures with nanometer resolution OPEN
J. Krehl, G. Guzzinati, J. Schultz, P. Potapov, D. Pohl, Jérôme Martin, J. Verbeeck, A. Fery, B. Büchner & A. Lubk

Characterizing plasmonic coupling has proven elusive. Here, the authors obtain a spectrally resolved deflection map related to a focused electron beam, which has excited a surface plasmon resonance, and relate this deflection to the spectral component of the induced electric and magnetic fields pertaining to the mode.

11 October 2018 | doi: 10.1038/s41467-018-06572-9
Characterization and analytical techniques  Nanophotonics and plasmonics  Optical materials and structures 

State-recycling and time-resolved imaging in topological photonic lattices OPEN
Sebabrata Mukherjee, Harikumar K. Chandrasekharan, Patrik Öhberg, Nathan Goldman & Robert R. Thomson

Topological effects can be emulated using photonic lattices where the length of a waveguide represents time, which is often limited by fabrication constraints. Here, Mukherjee et al. exploit a single-photon detector array enabled state-recycling scheme to increase the accessible time scale.

11 October 2018 | doi: 10.1038/s41467-018-06723-y
Single photons and quantum effects  Topological matter 

Rifampicin can induce antibiotic tolerance in mycobacteria via paradoxical changes in rpoB transcription OPEN
Jun-Hao Zhu, Bi-Wei Wang, Miaomiao Pan, Yu-Na Zeng, Hesper Rego & Babak Javid

The antibiotic rifampicin inhibits transcription by targeting RpoB, a bacterial RNA polymerase subunit. Here, Zhu et al. show that certain cells in mycobacterial populations can continue to grow and divide in the presence of rifampicin due, paradoxically, to rifampicin-induced upregulation of the rpoB gene.

11 October 2018 | doi: 10.1038/s41467-018-06667-3
Antibacterial drug resistance  Antibiotics 

Generation of orthotopically functional salivary gland from embryonic stem cells OPEN
Junichi Tanaka, Miho Ogawa, Hironori Hojo, Yusuke Kawashima, Yo Mabuchi, Kenji Hata, Shiro Nakamura, Rika Yasuhara, Koki Takamatsu, Tarou Irié, Toshiyuki Fukada, Takayoshi Sakai, Tomio Inoue, Riko Nishimura, Osamu Ohara, Ichiro Saito, Shinsuke Ohba, Takashi Tsuji & Kenji Mishima

Functional salivary glands have not been generated from embryonic stem cells (mESCs) to date. Here the authors demonstrate directed in vitro differentiation of mESCs to oral ectoderm and salivary gland rudiments that form mature, functional salivary glands after orthotopic transplantation.

11 October 2018 | doi: 10.1038/s41467-018-06469-7
Organogenesis  Stem-cell biotechnology 

Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole OPEN
Dazhi Liu, Yifeng Wei, Xuyang Liu, Yan Zhou, Li Jiang, Jinyu Yin, Feifei Wang, Yiling Hu, Ankanahalli N. Nanjaraj Urs, Yanhong Liu, Ee Lui Ang, Suwen Zhao, Huimin Zhao & Yan Zhang

Skatole is a bacterial metabolite responsible for boar taint and the objectionable smell of manure. Here, the authors elucidate the final step of skatole biosynthesis, describing the discovery and biochemical characterization of the enzyme catalysing the conversion of indoleacetate into skatole.

11 October 2018 | doi: 10.1038/s41467-018-06627-x
Biochemistry  Computational biology and bioinformatics 

Mechanochemical feedback control of dynamin independent endocytosis modulates membrane tension in adherent cells OPEN
Joseph Jose Thottacherry, Anita Joanna Kosmalska, Amit Kumar, Amit Singh Vishen, Alberto Elosegui-Artola, Susav Pradhan, Sumit Sharma, Parvinder P. Singh, Marta C. Guadamillas, Natasha Chaudhary, Ram Vishwakarma, Xavier Trepat, Miguel A. del Pozo, Robert G. Parton, Madan Rao, Pramod Pullarkat, Pere Roca-Cusachs & Satyajit Mayor

Plasma membrane tension is an important factor that regulates many key cellular processes. Here authors show that a specific dynamin-independent endocytic pathway is modulated by changes in tension via the mechano-transducer vinculin.

11 October 2018 | doi: 10.1038/s41467-018-06738-5
Endocytosis  Fluorescence imaging  Optical tweezers  Total internal reflection microscopy  Wide-field fluorescence microscopy 

A transportome-scale amiRNA-based screen identifies redundant roles of Arabidopsis ABCB6 and ABCB20 in auxin transport OPEN
Yuqin Zhang, Victoria Nasser, Odelia Pisanty, Moutasem Omary, Nikolai Wulff, Martin Di Donato, Iris Tal, Felix Hauser, Pengchao Hao, Ohad Roth, Hillel Fromm, Julian I. Schroeder, Markus Geisler, Hussam Hassan Nour-Eldin & Eilon Shani

Characterizing plant membrane transporters via genetic methods is complicated by functional redundancy among multi-gene transporter families. Here Zhang et al. use an artificial microRNA-based screen to overcome this issue and show that ABCB6 and ABCB20 act redundantly to regulate auxin transport.

11 October 2018 | doi: 10.1038/s41467-018-06410-y
Auxin  Plant development  Plant genetics 

Identifying triplet pathways in dilute pentacene films OPEN
Daphné Lubert-Perquel, Enrico Salvadori, Matthew Dyson, Paul N. Stavrinou, Riccardo Montis, Hiroki Nagashima, Yasuhiro Kobori, Sandrine Heutz & Christopher W. M. Kay

Singlet fission results in the formation of a pair of triplets, known as a quintet. Here, the authors identify long-lived quintets in dilute pentacene films at room temperature, with lifetimes influenced by intermolecular geometry having implications for the design of triplet-harvesting films.

11 October 2018 | doi: 10.1038/s41467-018-06330-x
Electronic devices  Molecular electronics 

Pol μ dGTP mismatch insertion opposite T coupled with ligation reveals promutagenic DNA repair intermediate OPEN
Melike Çağlayan & Samuel H. Wilson

Incorporation of mismatched nucleotides during DNA replication or repair can lead to mutagenesis. Here the authors reveal that DNA ligase can ligate NHEJ intermediates following incorporation of 8-oxodGTP or dGTP opposite T by DNA Polymerase mu (Pol mu) in vitro, which suggests that Pol mu could cause promutagenic mismatches during DSB repair.

11 October 2018 | doi: 10.1038/s41467-018-06700-5
DNA  DNA repair enzymes  Non-homologous-end joining 
 
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  Latest Author Corrections  
 
Author Correction: Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria OPEN
Chen Dong, Jason Fontana, Anika Patel, James M. Carothers & Jesse G. Zalatan
15 October 2018 | doi: 10.1038/s41467-018-06909-4
CRISPR-Cas systems  Metabolic engineering  Synthetic biology 

Author Correction: Topographic precision in sensory and motor corticostriatal projections varies across cell type and cortical area OPEN
Bryan M. Hooks, Andrew E. Papale, Ronald F. Paletzki, Muhammad W. Feroze, Brian S. Eastwood, Jonathan J. Couey, Johan Winnubst, Jayaram Chandrashekar & Charles R. Gerfen
12 October 2018 | doi: 10.1038/s41467-018-06928-1
Barrel cortex  Basal ganglia  Motor cortex  Neural circuits  Sensorimotor processing 
 
  Latest Publisher Corrections  
 
Publisher Correction: Deubiquitinase Usp12 functions noncatalytically to induce autophagy and confer neuroprotection in models of Huntington's disease OPEN
Rebecca Aron, Pasquale Pellegrini, Edward W. Green, Daniel C. Maddison, Kwadwo Opoku-Nsiah, Jinny S. Wong, Aaron C. Daub, Flaviano Giorgini & Steven Finkbeiner
15 October 2018 | doi: 10.1038/s41467-018-06888-6
Enzyme mechanisms  Huntington's disease 

Publisher Correction: 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
12 October 2018 | doi: 10.1038/s41467-018-06852-4
Natural hazards  Ocean sciences  Physical oceanography 
 
 

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