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Nature Communications - 10 October 2018

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10 October 2018 
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Focal Point on Kobe A seismic shift

How Kobe rebuilt itself after a devastating earthquake and turned into a biotechnology hub
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Singular sublimation of ice and snow crystals OPEN
Etienne Jambon-Puillet, Noushine Shahidzadeh & Daniel Bonn

Ice sublimation is a common, yet little-studied, heat and mass transfer problem with climatic and industrial implications. Here, the authors show that the sublimation of ice crystals is purely diffusive and is unaffected by the underlying crystalline lattice.

10 October 2018 | doi: 10.1038/s41467-018-06689-x
Applied physics  Fluid dynamics 

MiR-34 inhibits polycomb repressive complex 2 to modulate chaperone expression and promote healthy brain aging OPEN
Jason R. Kennerdell, Nan Liu & Nancy M. Bonini

miR-34 is known to regulate age-related gene expression in the Drosophila brain, and miR-34 overexpression can attenuate neurodegeneration induced by polyQ-expanded proteins. Here, Kennerdell and colleagues show that miR-34 confers longevity and neuroprotection via an epigenetic regulator Polycomb Repressive Complex 2 and molecular chaperone expression.

10 October 2018 | doi: 10.1038/s41467-018-06592-5
Epigenetics  Neural ageing  Neurodegeneration 

Structural basis for PtdInsP2-mediated human TRPML1 regulation OPEN
Michael Fine, Philip Schmiege & Xiaochun Li

Transient receptor potential mucolipin 1 (TRPML1) is a lysosomal channel which maintains the low pH and calcium levels for lysosomal function. Here authors use structural biology and electrophysiology to show how lipids bind and allosterically activate TRPML1.

10 October 2018 | doi: 10.1038/s41467-018-06493-7
Physiology  Structural biology  Transient receptor potential channels 

Prevention of pancreatic acinar cell carcinoma by Roux-en-Y Gastric Bypass Surgery OPEN
Rui He, Yue Yin, Wenzhen Yin, Yin Li, Jing Zhao & Weizhen Zhang

Pancreatic cancer risk increases in obese and diabetic people. In this manuscript, the authors show that Roux-en-Y gastric bypass surgery (RYGB) decreases the impact of pancreatic cancer in a mouse model; this effect seems independent of weight loss or decreased hyperglycemia pointing to an involvement of mTOR pathway.

10 October 2018 | doi: 10.1038/s41467-018-06571-w
Cancer prevention 

Electrically reconfigurable terahertz signal processing devices using liquid metal components OPEN
Kimberly S. Reichel, Nicolas Lozada-Smith, Ishan D. Joshipura, Jianjun Ma, Rabi Shrestha, Rajind Mendis, Michael D. Dickey & Daniel M. Mittleman

Although there are many reports on the development of devices for terahertz signal processing, the possibility of electrical control of the functionality remains elusive. Here, the authors use electrically actuated liquid metal components incorporated into terahertz waveguides for controlling power flow and for frequency filtering.

10 October 2018 | doi: 10.1038/s41467-018-06463-z
Optoelectronic devices and components  Terahertz optics 

Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages OPEN
Stefan Schoenfelder, Borbala Mifsud, Claire E. Senner, Christopher D. Todd, Stephanie Chrysanthou, Elodie Darbo, Myriam Hemberger & Miguel R. Branco

The role of the genome structure in the establishment of the embryonic and trophoblast lineages is still not well understood. Here the authors perform promoter capture Hi-C in mouse trophoblast and embryonic stem cells and find divergent networks of repressive and active chromatin interactions between the two lineages.

10 October 2018 | doi: 10.1038/s41467-018-06666-4
Chromatin structure  Epigenetics  Transcriptional regulatory elements 

Host-associated niche metabolism controls enteric infection through fine-tuning the regulation of type 3 secretion OPEN
James P. R. Connolly, Sabrina L. Slater, Nicky O'Boyle, Robert J. Goldstone, Valerie F. Crepin, David R. Gallego, Pawel Herzyk, David G. E. Smith, Gillian R. Douce, Gad Frankel & Andrew J. Roe

Infection of mice with Citrobacter rodentium is a common model of infection with attaching-and-effacing pathogens. Here, Connolly et al. analyse the transcriptome of C. rodentium during mouse infection, showing host-induced coordinated upregulation of virulence factors and 1,2-propanediol metabolism.

10 October 2018 | doi: 10.1038/s41467-018-06701-4
Bacterial genes  Bacteriology  Pathogens 

GABAergic signaling linked to autophagy enhances host protection against intracellular bacterial infections OPEN
Jin Kyung Kim, Yi Sak Kim, Hye-Mi Lee, Hyo Sun Jin, Chiranjivi Neupane, Sup Kim, Sang-Hee Lee, Jung-Joon Min, Miwa Sasai, Jae-Ho Jeong, Seong-Kyu Choe, Jin-Man Kim, Masahiro Yamamoto, Hyon E. Choy, Jin Bong Park & Eun-Kyeong Jo

Gamma-aminobutyric acid (GABA) is a major inhibitory neurotransmitter in neuronal systems, but the potential role for such neurotransmitters on the immune system are emerging. Here the authors show GABA signaling is linked to autophagy, enhancing the host response against intracellular bacteria.

10 October 2018 | doi: 10.1038/s41467-018-06487-5
Antimicrobial responses  Autophagy  Bacterial infection  Neuroimmunology 

Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia OPEN
Mary L. McMaster, Sonja I. Berndt, Jianqing Zhang, Susan L. Slager, Shengchao Alfred Li, Claire M. Vajdic, Karin E. Smedby, Huihuang Yan, Brenda M. Birmann, Elizabeth E. Brown, Alex Smith, Geffen Kleinstern, Mervin M. Fansler, Christine Mayr, Bin Zhu, Charles C. Chung, Ju-Hyun Park, Laurie Burdette, Belynda D. Hicks, Amy Hutchinson et al.

Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a non-Hodgkin-type B cell lymphoma. Here, the authors identify two risk loci for WM/LPL in a two-stage GWAS involving a family-oversampling approach and provide evidence for a functional role of the non-coding SNP rs116446171.

10 October 2018 | doi: 10.1038/s41467-018-06541-2
B-cell lymphoma  Cancer epidemiology  Genome-wide association studies  miRNAs 

Structural insights on TRPV5 gating by endogenous modulators OPEN
Taylor E. T. Hughes, Ruth A. Pumroy, Aysenur Torun Yazici, Marina A. Kasimova, Edwin C. Fluck, Kevin W. Huynh, Amrita Samanta, Sudheer K. Molugu, Z. Hong Zhou, Vincenzo Carnevale, Tibor Rohacs & Vera Y. Moiseenkova-Bell

TRPV5 is a kidney specific transient receptor potential (TRP) channel with an important role in calcium reabsorption. Here the authors provide mechanistic insights into TRPV5 modulation by determining the phosphatidylinositol 4,5-bisphosphate and calmodulin bound TRPV5 cryo-EM structures.

10 October 2018 | doi: 10.1038/s41467-018-06753-6
Cryoelectron microscopy  Ion transport 

Complement receptor CD46 co-stimulates optimal human CD8+ T cell effector function via fatty acid metabolism OPEN
Giuseppina Arbore, Erin E. West, Jubayer Rahman, Gaelle Le Friec, Nathalie Niyonzima, Mehdi Pirooznia, Ilker Tunc, Polychronis Pavlidis, Nicholas Powell, Yuesheng Li, Poching Liu, Aude Servais, Lionel Couzi, Veronique Fremeaux-Bacchi, Leo Placais, Alastair Ferraro, Patrick R. Walsh, David Kavanagh, Behdad Afzali, Paul Lavender et al.

Complement, while serving to remove pathogens in the circulation, is also important for synergizing with inflammasomes to modulate CD4 T cell activation. Here the authors show that CD46, a complement receptor expressed only in humans, is essential for inducing optimal activation and effector functions of human CD8 T cells.

10 October 2018 | doi: 10.1038/s41467-018-06706-z
CD8-positive T cells  Complement cascade  Inflammasome  Innate immunity 

Quantum machine learning for electronic structure calculations OPEN
Rongxin Xia & Sabre Kais

With the rapid development of quantum computers, quantum machine learning approaches are emerging as powerful tools to perform electronic structure calculations. Here, the authors develop a quantum machine learning algorithm, which demonstrates significant improvements in solving quantum many-body problems.

10 October 2018 | doi: 10.1038/s41467-018-06598-z
Computational science  Information theory and computation  Quantum chemistry 

SIRT1 mediates obesity- and nutrient-dependent perturbation of pubertal timing by epigenetically controlling Kiss1 expression OPEN
M. J. Vazquez, C. A. Toro, J. M. Castellano, F. Ruiz-Pino, J. Roa, D. Beiroa, V. Heras, I. Velasco, C. Dieguez, L. Pinilla, F. Gaytan, R. Nogueiras, M. A. Bosch, O. K. Rønnekleiv, A. Lomniczi, S. R. Ojeda & M. Tena-Sempere

The onset of mammalian puberty is sensitive to metabolic changes and nutritional status, but the mechanisms underlying this phenomenon are poorly understood. Here the authors show that the epigenetic regulator of transcription, SIRT1, mediates the effects of under and overnutrition on pubertal timing by controlling the expression of Kiss1 in hypothalamic neurons.

10 October 2018 | doi: 10.1038/s41467-018-06459-9
Endocrine reproductive disorders  Neuroendocrine diseases 

Low threshold and efficient multiple exciton generation in halide perovskite nanocrystals OPEN
Mingjie Li, Raihana Begum, Jianhui Fu, Qiang Xu, Teck Ming Koh, Sjoerd A. Veldhuis, Michael Grätzel, Nripan Mathews, Subodh Mhaisalkar & Tze Chien Sum

The hot carriers in halide perovskite nanocrystals cool much slower than those in conventional semiconductor nanocrystals due to the phonon bottleneck. Here, Li et al. demonstrate enhanced multiple exciton generation with lower threshold in intermediate-confined perovskite nanocrystals based on this effect.

10 October 2018 | doi: 10.1038/s41467-018-06596-1
Electronic properties and materials  Organic–inorganic nanostructures  Quantum dots  Solar cells 

Contact angle measurement of free-standing square-millimeter single-layer graphene OPEN
Anna V. Prydatko, Liubov A. Belyaeva, Lin Jiang, Lia M. C. Lima & Grégory F. Schneider

Experimental determination of the contact angle of a two-dimensional film is crucial to understand its wettability characteristics. Here, the authors use the captive bubble method to estimate a contact angle value of 42° ± 3° for a monolayer graphene film.

10 October 2018 | doi: 10.1038/s41467-018-06608-0
Graphene  Physical chemistry  Surface chemistry  Two-dimensional materials  Wetting 

A guanine-flipping and sequestration mechanism for G-quadruplex unwinding by RecQ helicases OPEN
Andrew F. Voter, Yupeng Qiu, Ramreddy Tippana, Sua Myong & James L. Keck

How G-quadruplexes (G4s) are resolved by helicases is still a matter of investigation. Here the authors provide mechanistic insight into G4s unwinding by presenting a crystal structure of resolved G4 DNA and the G4 binding domain of RecQ helicase from the bacterium Cronobacter sakazakii.

10 October 2018 | doi: 10.1038/s41467-018-06751-8
Enzyme mechanisms  Molecular biophysics  Single-molecule biophysics  X-ray crystallography 

Shu complex SWS1-SWSAP1 promotes early steps in mouse meiotic recombination OPEN
Carla M. Abreu, Rohit Prakash, Peter J. Romanienko, Ignasi Roig, Scott Keeney & Maria Jasin

Homologous recombination ensures genome integrity during meiotic recombination. Here the authors reveal that factors SWS1 and SWSAP1 are critical for meiotic homologues recombination, particularly in promoting assembly of RAD51 and DMC1 on early recombination intermediates.

10 October 2018 | doi: 10.1038/s41467-018-06384-x
Double-strand DNA breaks  Homologous recombination  Meiosis 

Efficient carrier multiplication in CsPbI3 perovskite nanocrystals OPEN
Chris de Weerd, Leyre Gomez, Antonio Capretti, Delphine M. Lebrun, Eiichi Matsubara, Junhao Lin, Masaaki Ashida, Frank C. M. Spoor, Laurens D. A. Siebbeles, Arjan J. Houtepen, Kazutomo Suenaga, Yasufumi Fujiwara & Tom Gregorkiewicz

In semiconductor nanocrystals, efficient carrier multiplication counteracts hot carrier thermalization, increasing the overall carrier generation yield. Here, de Weerd et al. observe a quantum yield of up to 98% in CsPbI3 nanocrystals as a result of efficient carrier multiplication.

10 October 2018 | doi: 10.1038/s41467-018-06721-0
Electronic properties and materials  Nanoparticles 

Compact folded metasurface spectrometer OPEN
MohammadSadegh Faraji-Dana, Ehsan Arbabi, Amir Arbabi, Seyedeh Mahsa Kamali, Hyounghan Kwon & Andrei Faraon

Here, the authors introduce the folded metasurface optics architecture by demonstrating a compact high-resolution optical spectrometer made from a 1-mm-thick glass slab. The spectrometer has a resolution of 1.2 nm, resolving more than 80 spectral points in a 100-nm bandwidth centered at 810 nm.

10 October 2018 | doi: 10.1038/s41467-018-06495-5
Integrated optics  Metamaterials 

LRH-1 mitigates intestinal inflammatory disease by maintaining epithelial homeostasis and cell survival OPEN
James R. Bayrer, Hongtao Wang, Roy Nattiv, Miyuki Suzawa, Hazel S. Escusa, Robert J. Fletterick, Ophir D. Klein, David D. Moore & Holly A. Ingraham

Inflammatory bowel disease is characterised by epithelial dysfunction. Here the authors show that loss of the nuclear receptor LRH-1 leads to epithelial disruption by altering Notch signaling in mouse intestinal organoids, and that LRH-1 overexpression ameliorates immune-mediated colitis in a mouse model.

10 October 2018 | doi: 10.1038/s41467-018-06137-w
Crohn's disease  Gastrointestinal system  Mechanisms of disease 

Nanoporous aramid nanofibre separators for nonaqueous redox flow batteries OPEN
Siu on Tung, Sydney L. Fisher, Nicholas A. Kotov & Levi T. Thompson

Nonaqueous redox flow batteries may offer high energy and power densities, but development of separators is key for optimization. Here the authors achieve high coulombic efficiency with a nanoporous aramid nanofibres-based separator with low permeability, high ion conductivity, and exceptional stability.

10 October 2018 | doi: 10.1038/s41467-018-05752-x
Batteries  Electrochemistry 

A growing bacterial colony in two dimensions as an active nematic OPEN
D. Dell'Arciprete, M. L. Blow, A. T. Brown, F. D. C. Farrell, J. S. Lintuvuori, A. F. McVey, D. Marenduzzo & W. C. K. Poon

Rod-shaped bacteria are an example of active matter. Here the authors find that a growing bacterial colony harbours internal cellular flows affecting orientational ordering in its interior and at the boundary. Results suggest this system may belong to a new active matter universality class.

10 October 2018 | doi: 10.1038/s41467-018-06370-3
Biological physics  Biophysics  Liquid crystals 

Relativistic and resonant effects in the ionization of heavy atoms by ultra-intense hard X-rays OPEN
Benedikt Rudek, Koudai Toyota, Lutz Foucar, Benjamin Erk, Rebecca Boll, Cédric Bomme, Jonathan Correa, Sebastian Carron, Sébastien Boutet, Garth J. Williams, Ken R. Ferguson, Roberto Alonso-Mori, Jason E. Koglin, Tais Gorkhover, Maximilian Bucher, Carl Stefan Lehmann, Bertold Krässig, Stephen H. Southworth, Linda Young, Christoph Bostedt et al.

Availability of intense hard X-ray pulses allows exploration of multiple ionization effects in heavier elements. Here, the authors measure the complex charge state distributions of xenon and found a reasonable agreement by comparing with the model including the relativistic and resonance effects.

10 October 2018 | doi: 10.1038/s41467-018-06745-6
Atomic and molecular interactions with photons  Electronic structure of atoms and molecules  Free-electron lasers 

Genetic signature to provide robust risk assessment of psoriatic arthritis development in psoriasis patients OPEN
Matthew T. Patrick, Philip E. Stuart, Kalpana Raja, Johann E. Gudjonsson, Trilokraj Tejasvi, Jingjing Yang, Vinod Chandran, Sayantan Das, Kristina Callis-Duffin, Eva Ellinghaus, Charlotta Enerbäck, Tõnu Esko, Andre Franke, Hyun M. Kang, Gerald G. Krueger, Henry W. Lim, Proton Rahman, Cheryl F. Rosen, Stephan Weidinger, Michael Weichenthal et al.

Approximately 30% of psoriasis patients develop psoriatic arthritis (PsA) and early diagnosis is crucial for the management of PsA. Here, Patrick et al. develop a computational pipeline involving statistical and machine-learning methods that can assess the risk of progression to PsA based on genetic markers.

09 October 2018 | doi: 10.1038/s41467-018-06672-6
Genome-wide association studies  Machine learning  Predictive medicine  Psoriatic arthritis 

Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism OPEN
Rasmus Kock Flygaard, Niels Boegholm, Marat Yusupov & Lasse B. Jenner

During stress conditions bacterial ribosomes dimerize and form inactive but stable hibernating 100S particles, a process that is facilitated by the hibernation-promoting factor (HPF). Here the authors analyze 100S dimer formation as a function of HPF protein concentration and present the Thermus thermophilus 100S ribosome cryo-EM structure.

09 October 2018 | doi: 10.1038/s41467-018-06724-x
Cryoelectron microscopy  Ribosome 

Stabilizing black phosphorus nanosheets via edge-selective bonding of sacrificial C60 molecules OPEN
Xianjun Zhu, Taiming Zhang, Daochuan Jiang, Hengli Duan, Zijun Sun, Mengmeng Zhang, Hongchang Jin, Runnan Guan, Yajuan Liu, Muqing Chen, Hengxing Ji, Pingwu Du, Wensheng Yan, Shiqiang Wei, Yalin Lu & Shangfeng Yang

Few-layered black phosphorus has unique and appealing electronic properties but is easily oxidized in air. Here, the authors covalently functionalize black phosphorus nanosheets with C60 at their edges, providing improved stability and enhanced photoelectrochemical and photocatalytic activities.

09 October 2018 | doi: 10.1038/s41467-018-06437-1
Materials chemistry  Photocatalysis  Two-dimensional materials 

Metastatic adrenocortical carcinoma displays higher mutation rate and tumor heterogeneity than primary tumors OPEN
Sudheer Kumar Gara, Justin Lack, Lisa Zhang, Emerson Harris, Margaret Cam & Electron Kebebew

Adrenocortical cancer (ACC) is a rarely diagnosed and aggressive cancer whose metastatic form has been scarcely studied. Here, the authors study primary and metastatic ACC to investigate genomic heterogeneity, discovering higher mutation rates in metastatic lesions and novel recurrent mutations.

09 October 2018 | doi: 10.1038/s41467-018-06366-z
Cancer  Endocrinology  Genetics  Oncology 

A genetic network mediating the control of bud break in hybrid aspen OPEN
Rajesh Kumar Singh, Jay P. Maurya, Abdul Azeez, Pal Miskolczi, Szymon Tylewicz, Katja Stojkovič, Nicolas Delhomme, Victor Busov & Rishikesh P. Bhalerao

Molecular mechanism of how temperature-mediated control of bud break in perennial plants remains unclear. Here, the author show that transcriptional factor SHORT VEGETATIVE PHASE-LIKE and its downstream target TCP18 are negative regulators of hybrid aspen bud break.

09 October 2018 | doi: 10.1038/s41467-018-06696-y
Plant molecular biology  Plant physiology  Plant signalling 

Loss of pyruvate kinase M2 limits growth and triggers innate immune signaling in endothelial cells OPEN
Oliver A. Stone, Mohamed El-Brolosy, Kerstin Wilhelm, Xiaojing Liu, Ana M. Romão, Elisabetta Grillo, Jason K. H. Lai, Stefan Günther, Sylvia Jeratsch, Carsten Kuenne, I-Ching Lee, Thomas Braun, Massimo M. Santoro, Jason W. Locasale, Michael Potente & Didier Y. R. Stainier

The glycolytic enzyme pyruvate kinase M2 (PKM2) is required for nucleotide synthesis and cell proliferation. Using gene expression and metabolomics analyses, the authors here show that PKM2 regulates methionine metabolism and DNA methylation in endothelial cells.

09 October 2018 | doi: 10.1038/s41467-018-06406-8
Angiogenesis  Cell growth  Energy metabolism 

Highly selective transition-metal-free transamidation of amides and amidation of esters at room temperature OPEN
Guangchen Li & Michal Szostak

Transamidation reactions usually require transition metal catalysts and/or harsh conditions. Here, the authors show a general and operationally-simple protocol for the transamidation of amides and amidation of esters by highly selective acyl cleavage with non-nucleophilic amines under mild conditions.

09 October 2018 | doi: 10.1038/s41467-018-06623-1
Chemistry  Organic chemistry 

Long non-coding RNA CCRR controls cardiac conduction via regulating intercellular coupling OPEN
Yong Zhang, Lihua Sun, Lina Xuan, Zhenwei Pan, Xueling Hu, Hongyu Liu, Yunlong Bai, Lei Jiao, Zhange Li, Lina Cui, Xiaoxue Wang, Siqi Wang, Tingting Yu, Bingbing Feng, Ying Guo, Zonghong Liu, Weixin Meng, Hequn Ren, Jiyuan Zhu, Xuyun Zhao et al.

Long noncoding RNAs have been shown to play a role in cardiovascular disease. Here, the authors identify a lncRNA named CCRR, whose downregulation in failing hearts causes cardiac conduction disturbances by altering the endocytic trafficking of Cx43.

09 October 2018 | doi: 10.1038/s41467-018-06637-9
Arrhythmias  Heart failure  Long non-coding RNAs 

Physical descriptor for the Gibbs energy of inorganic crystalline solids and temperature-dependent materials chemistry OPEN
Christopher J. Bartel, Samantha L. Millican, Ann M. Deml, John R. Rumptz, William Tumas, Alan W. Weimer, Stephan Lany, Vladan Stevanović, Charles B. Musgrave & Aaron M. Holder

Materials databases currently neglect the temperature effect on compound thermodynamics. Here the authors introduce a Gibbs energy descriptor enabling the high-throughput prediction of temperature-dependent thermodynamics across a wide range of compositions and temperatures for inorganic solids.

09 October 2018 | doi: 10.1038/s41467-018-06682-4
Statistics  Theory and computation 

A mechanoelectrical mechanism for detection of sound envelopes in the hearing organ OPEN
Alfred L. Nuttall, Anthony J. Ricci, George Burwood, James M. Harte, Stefan Stenfelt, Per Cayé-Thomasen, Tianying Ren, Sripriya Ramamoorthy, Yuan Zhang, Teresa Wilson, Thomas Lunner, Brian C. J. Moore & Anders Fridberger

The sound envelope is important for speech perception. Here, the authors look at mechanisms by which the sound envelope is encoded, finding that it arises from distortion produced by mechanoelectrical transduction channels. Surprisingly, the envelope is not present in basilar membrane vibrations.

09 October 2018 | doi: 10.1038/s41467-018-06725-w
Cochlea  Ion channels in the nervous system  Sensory processing 

A hippocampal circuit linking dorsal CA2 to ventral CA1 critical for social memory dynamics OPEN
Torcato Meira, Felix Leroy, Eric W. Buss, Azahara Oliva, Jung Park & Steven A. Siegelbaum

Although the CA2 region of the hippocampus has been implicated in social memory, its precise role has been unclear. Here, the authors show that the dorsal subregion of CA2 is required for the encoding, consolidation and recall of social memory through a circuit linking it to ventral CA1.

09 October 2018 | doi: 10.1038/s41467-018-06501-w
Hippocampus  Neural circuits  Social behaviour  Social neuroscience 

Interface-mediated hygroelectric generator with an output voltage approaching 1.5 volts OPEN
Yaxin Huang, Huhu Cheng, Ce Yang, Panpan Zhang, Qihua Liao, Houze Yao, Gaoquan Shi & Liangti Qu

Hygroelectric generators comprised of electrodes and a hygroscopic material with a chemical-gradient structure can produce electricity by absorbing water vapor. Here, the authors achieve a high output voltage by employing hygroscopic heterogeneous graphene oxide and materials with Schottky junctions.

09 October 2018 | doi: 10.1038/s41467-018-06633-z
Electronic devices  Electronic materials 

Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations OPEN
Nhan T. Ho, Fan Li, Kathleen A. Lee-Sarwar, Hein M. Tun, Bryan P. Brown, Pia S. Pannaraj, Jeffrey M. Bender, Meghan B. Azad, Amanda L. Thompson, Scott T. Weiss, M. Andrea Azcarate-Peril, Augusto A. Litonjua, Anita L. Kozyrskyj, Heather B. Jaspan, Grace M. Aldrovandi & Louise Kuhn

Studies on the effects of breastfeeding on the infant gut microbiota have provided inconsistent results. Here, Ho et al. perform a meta-analysis of seven studies across different populations, supporting that exclusive breastfeeding is associated with short-term and long-term alterations in the infant gut microbiota.

09 October 2018 | doi: 10.1038/s41467-018-06473-x
Clinical microbiology  Gastroenterology  Microbiome  Paediatric research 

Two-site H2O2 photo-oxidation on haematite photoanodes OPEN
Yotam Y. Avital, Hen Dotan, Dino Klotz, Daniel A. Grave, Anton Tsyganok, Bhavana Gupta, Sofia Kolusheva, Iris Visoly-Fisher, Avner Rothschild & Arik Yochelis

Understanding fundamental processes that occur using solar-to-fuel conversion materials is crucial for constructing effective renewable energy collection. Here, authors find the hydrogen peroxide light-driven hole-scavenging mechanism over haematite to proceed with two active sites rather than one

09 October 2018 | doi: 10.1038/s41467-018-06141-0
Nonlinear phenomena  Photocatalysis  Reaction mechanisms 

Patchwork of contrasting medication cultures across the USA OPEN
Rachel D. Melamed & Andrey Rzhetsky

Health care in the United States is heterogeneous with respect to factors like disease incidence, treatment choices and health care spending. Here, the authors use insurance claims data from over 150 million patients to compare prescription rates of over 600 drugs, and uncover patterns of geographical variation that suggest an influence of race, health care laws and wealth.

09 October 2018 | doi: 10.1038/s41467-018-06205-1
Data mining  Health care 

Exceptional catalytic effects of black phosphorus quantum dots in shuttling-free lithium sulfur batteries OPEN
Zheng-Long Xu, Shenghuang Lin, Nicolas Onofrio, Limin Zhou, Fangyi Shi, Wei Lu, Kisuk Kang, Qiang Zhang & Shu Ping Lau

Lithium sulfur batteries are promising for next-generation energy storage, but are hindered by polysulfide shuttle effects. Here the authors use black phosphorus quantum dots to adsorb and catalyze the conversion of lithium polysulfides to lithium sulfide, achieving low capacity fade and high sulfur loading.

09 October 2018 | doi: 10.1038/s41467-018-06629-9
Batteries  Quantum dots 

Transformation of amorphous calcium phosphate to bone-like apatite OPEN
Antiope Lotsari, Anand K. Rajasekharan, Mats Halvarsson & Martin Andersson

The growth of apatite crystals from amorphous calcium phosphate is an area of intense study. Here, the authors report on the use of high resolution TEM imaging to provide evidence of nucleation clusters in the transformation process

09 October 2018 | doi: 10.1038/s41467-018-06570-x
Bioinspired materials  Biomineralization  Nanoparticles  Organic–inorganic nanostructures 

A missense variant in SLC39A8 is associated with severe idiopathic scoliosis OPEN
Gabe Haller, Kevin McCall, Supak Jenkitkasemwong, Brooke Sadler, Lilian Antunes, Momchil Nikolov, Julia Whittle, Zachary Upshaw, Jimann Shin, Erin Baschal, Carlos Cruchaga, Matthew Harms, Cathleen Raggio, Jose A. Morcuende, Philip Giampietro, Nancy H. Miller, Carol Wise, Ryan S. Gray, Lila Solnica-Krezel, Mitchell Knutson et al.

The majority of scoliosis is considered idiopathic with onset in adolescence (AIS) and has a genetic contribution. Here, the authors perform an exome wide association study of data from 457 severe AIS cases and 987 controls, and find a missense variant in SLC39A8 is associated with AIS.

09 October 2018 | doi: 10.1038/s41467-018-06705-0
Development  Genome-wide association studies  Skeleton 

LEM4 confers tamoxifen resistance to breast cancer cells by activating cyclin D-CDK4/6-Rb and ERα pathway OPEN
Ang Gao, Tonghua Sun, Gui Ma, Jiangran Cao, Qingxia Hu, Ling Chen, Yanxin Wang, Qianying Wang, Jiafu Sun, Rui Wu, Qiao Wu, Jiaxi Zhou, Lin Liu, Junjie Hu, Jin-Tang Dong & Zhengmao Zhu

Tamoxifen resistance is a major problem in the treatment of ERa positive breast cancer. Here, the authors show that LEM4 confers tamoxifen resistance by activating the cyclin D-CDK4/6-Rb axis and ERa signaling in endocrine-resistant breast cancer.

09 October 2018 | doi: 10.1038/s41467-018-06309-8
Breast cancer  Cell-cycle exit  Oncogenes 

Unravelling the structure of glycosyl cations via cold-ion infrared spectroscopy OPEN
Eike Mucha, Mateusz Marianski, Fei-Fei Xu, Daniel A. Thomas, Gerard Meijer, Gert von Helden, Peter H. Seeberger & Kevin Pagel

Glycosyl cations are key intermediates in glycosylation reactions, but their structure has remained elusive due to their transient nature. Here, the authors perform an in-depth structural analysis and report that C2-participating protective groups induce acetoxonium cations with distinct ring conformations.

09 October 2018 | doi: 10.1038/s41467-018-06764-3
Carbohydrate chemistry  Infrared spectroscopy  Mass spectrometry 

Microglia innately develop within cerebral organoids OPEN
Paul R. Ormel, Renata Vieira de Sá, Emma J. van Bodegraven, Henk Karst, Oliver Harschnitz, Marjolein A. M. Sneeboer, Lill Eva Johansen, Roland E. van Dijk, Nicky Scheefhals, Amber Berdenis van Berlekom, Eduardo Ribes Martínez, Sandra Kling, Harold D. MacGillavry, Leonard H. van den Berg, René S. Kahn, Elly M. Hol, Lot D. de Witte & R. Jeroen Pasterkamp

Brain organoid models reported to date lack cells of mesodermal origin, such as microglia. Here, the authors demonstrate that mature microglia-like cells are generated within their cerebral organoid model, providing new avenues for studying human microglia in a three-dimensional brain environment.

09 October 2018 | doi: 10.1038/s41467-018-06684-2
Induced pluripotent stem cells  Microglia  Molecular neuroscience 

Blood meal-induced inhibition of vector-borne disease by transgenic microbiota OPEN
Jackie L. Shane, Christina L. Grogan, Caroline Cwalina & David J. Lampe

Vector alteration strategies are emerging as attractive tools for malaria transmission control. Here, Shane et al. engineer a bacterial strain, isolated from mosquitoes, to produce an antiplasmodial protein in the presence of blood meal, causing the mosquitoes to become refractory to Plasmodium infection.

08 October 2018 | doi: 10.1038/s41467-018-06580-9
Gene regulation  Genetic engineering  Microbiology techniques 

Fractionalized excitations in the partially magnetized spin liquid candidate YbMgGaO4 OPEN
Yao Shen, Yao-Dong Li, H. C. Walker, P. Steffens, M. Boehm, Xiaowen Zhang, Shoudong Shen, Hongliang Wo, Gang Chen & Jun Zhao

Recent experiments have indicated that YbMgGaO4 may be a quantum spin liquid with spinon Fermi surfaces but additional evidence is needed to support this interpretation. Shen et al. show weak magnetic fields cause changes in the excitation continuum that are consistent with spin liquid predictions.

08 October 2018 | doi: 10.1038/s41467-018-06588-1
Magnetic properties and materials 

Modulation of proteoglycan receptor PTPσ enhances MMP-2 activity to promote recovery from multiple sclerosis OPEN
Fucheng Luo, Amanda Phuong Tran, Li Xin, Chandrika Sanapala, Bradley T. Lang, Jerry Silver & Yan Yang

Demyelination failure in multiple sclerosis (MS) may contribute to the disease progression. This study shows that chondroitin sulfate proteoglycans (CSPGs) can inhibit remyelination in an animal model of MS via CSPG binding with the receptor PTPσ on oligodendrocyte progenitor cells, and disruption of this interaction can promote recovery in the animal models of MS.

08 October 2018 | doi: 10.1038/s41467-018-06505-6
Demyelinating diseases  Multiple sclerosis  Neuroscience  Regeneration and repair in the nervous system 

SWI/SNF catalytic subunits' switch drives resistance to EZH2 inhibitors in ARID1A-mutated cells OPEN
Shuai Wu, Nail Fatkhutdinov, Takeshi Fukumoto, Benjamin G. Bitler, Pyoung Hwa Park, Andrew V. Kossenkov, Marco Trizzino, Hsin-Yao Tang, Lin Zhang, Alessandro Gardini, David W. Speicher & Rugang Zhang

The mechanism of resistance to EZH2 inhibitors in cancers with inactivating SWI/SNF mutations is unknown. Here, the authors demonstrate that the switch of the SWI/SNF catalytic subunits from SMARCA4 to SMARCA2 drives resistance to EZH2 inhibitors in ARID1A-mutated ovarian cancer cells.

08 October 2018 | doi: 10.1038/s41467-018-06656-6
Chromatin remodelling  Ovarian cancer 

Bacterial coinfection restrains antiviral CD8 T-cell response via LPS-induced inhibitory NK cells OPEN
Tobias Straub, Marina A. Freudenberg, Ulrike Schleicher, Christian Bogdan, Georg Gasteiger & Hanspeter Pircher

Exposure to multiple pathogens is common in nature, yet interactions between the immune components targeting bacterial and viral pathogens during co-infection are poorly understood. Here the authors show that bacteria-derived LPS induces cytotoxic NK cells that suppress antiviral CD8 T cell response.

08 October 2018 | doi: 10.1038/s41467-018-06609-z
Bacterial infection  Infection  Lymphocyte activation  Viral infection 

Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control OPEN
Mario Brosch, Kathrin Kattler, Alexander Herrmann, Witigo von Schönfels, Karl Nordström, Daniel Seehofer, Georg Damm, Thomas Becker, Sebastian Zeissig, Sophie Nehring, Fabian Reichel, Vincent Moser, Raghavan Veera Thangapandi, Felix Stickel, Gustavo Baretton, Christoph Röcken, Michael Muders, Madlen Matz-Soja, Michael Krawczak, Gilles Gasparoni et al.

Spatial mapping of genomic programs in tissue cells is an important step in the understanding of organ function and disease. Here, the authors provide a spatially resolved epigenomic and transcriptomic map of human liver and show porto-central gradients in metabolic and morphogen networks and transcription factor binding sites as a basis to better understand liver regeneration and function.

08 October 2018 | doi: 10.1038/s41467-018-06611-5
Epigenomics  Hepatocytes  Regeneration 

Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma OPEN
Suzana A. Kahn, Xin Wang, Ryan T. Nitta, Sharareh Gholamin, Johanna Theruvath, Gregor Hutter, Tej D. Azad, Lina Wadi, Sara Bolin, Vijay Ramaswamy, Rogelio Esparza, Kun-Wei Liu, Michael Edwards, Fredrik J. Swartling, Debashis Sahoo, Gordon Li, Robert J. Wechsler-Reya, Jüri Reimand, Yoon-Jae Cho, Michael D. Taylor et al.

Group 3 medulloblastoma is an aggressive pediatric brain tumour that disseminates through the leptomeningeal cerebral spinal fluid. Here, the authors show that in Group 3 medulloblastoma NOTCH1 activates BMI1 through the activation of TWIST1, driving metastasis and self-renewal, and in mouse models a NOTCH1 blocking antibody decreased spinal metastases.

08 October 2018 | doi: 10.1038/s41467-018-06564-9
Cancer in the nervous system  Cell invasion  CNS cancer  Self-renewal 

Seasonal modulation of deep slow-slip and earthquakes on the Main Himalayan Thrust OPEN
Dibyashakti Panda, Bhaskar Kundu, Vineet K. Gahalaut, Roland Bürgmann, Birendra Jha, Renuhaa Asaithambi, Rajeev Kumar Yadav, Naresh Krishna Vissa & Amit Kumar Bansal

The interaction between seasonally-induced non-tectonic and tectonic deformation along the Himalayan plate boundary is still debated. Here, the authors propose that seasonal hydrological loading can influence tectonic deformation along this plate boundary using continuous GPS measurements and satellite data.

08 October 2018 | doi: 10.1038/s41467-018-06371-2
Climate sciences  Hydrology  Seismology 

Dopamine–endocannabinoid interactions mediate spike-timing-dependent potentiation in the striatum OPEN
Hao Xu, Sylvie Perez, Amandine Cornil, Bérangère Detraux, Ilya Prokin, Yihui Cui, Bertrand Degos, Hugues Berry, Alban de Kerchove d'Exaerde & Laurent Venance

Dopamine tightly regulates plasticity at corticostriatal synapses. Here, the authors report that endocannabinoid dependent LTP induced with few spikes in the striatum is impaired in a rodent model of Parkinson's disease, requires dopamine through presynaptic D2 receptors located on corticostriatal inputs.

08 October 2018 | doi: 10.1038/s41467-018-06409-5
Neuroscience  Parkinson's disease  Spike-timing-dependent plasticity  Synaptic plasticity 

Galanin neurons in the ventrolateral preoptic area promote sleep and heat loss in mice OPEN
Daniel Kroeger, Gianna Absi, Celia Gagliardi, Sathyajit S. Bandaru, Joseph C. Madara, Loris L. Ferrari, Elda Arrigoni, Heike Münzberg, Thomas E. Scammell, Clifford B. Saper & Ramalingam Vetrivelan

Anatomical lesions of the preoptic area (POA) can cause sleep loss while electrical, chemical, or thermal stimulation of POA can induce sleep. To better understand the exact neural function of the POA, this study shows that galanin and GABA+ inhibitory neurons in the ventrolateral POA that project to the wake-promoting tuberomammillary nucleus promote sleep in a stimulation frequency dependent manner.

08 October 2018 | doi: 10.1038/s41467-018-06590-7
Circadian rhythms and sleep  Neural circuits  Neuroscience 

Enhanced validation of antibodies for research applications OPEN
Fredrik Edfors, Andreas Hober, Klas Linderbäck, Gianluca Maddalo, Alireza Azimi, Åsa Sivertsson, Hanna Tegel, Sophia Hober, Cristina Al-Khalili Szigyarto, Linn Fagerberg, Kalle von Feilitzen, Per Oksvold, Cecilia Lindskog, Björn Forsström & Mathias Uhlen

Five validation pillars have been proposed to verify the specificity of research antibodies. Here the authors screen 6,000 antibodies from the Human Protein Atlas with these methods to provide an antibody validation resource for providers and users.

08 October 2018 | doi: 10.1038/s41467-018-06642-y
Assay systems  Proteomics 

Simple ruthenium-catalyzed reductive amination enables the synthesis of a broad range of primary amines OPEN
Thirusangumurugan Senthamarai, Kathiravan Murugesan, Jacob Schneidewind, Narayana V. Kalevaru, Wolfgang Baumann, Helfried Neumann, Paul C. J. Kamer, Matthias Beller & Rajenahally V. Jagadeesh

Synthesis of primary amines via operationally simple, inexpensive and environmentally friendly methodologies has high impact in industrial settings. Here, the authors show a reductive amination process involving a ruthenium catalyst, aldehydes/ketones, ammonia, and hydrogen that displays a remarkable scope of primary amine products.

08 October 2018 | doi: 10.1038/s41467-018-06416-6
Homogeneous catalysis  Synthetic chemistry methodology  Sustainability 

Reconfigurable photoactuator through synergistic use of photochemical and photothermal effects OPEN
Markus Lahikainen, Hao Zeng & Arri Priimagi

Despite recent advances in light-active soft actuators, demonstrating reconfigurable actuation under the same stimuli remains a challenge. Here, the authors realize reconfigurable photoactuation in liquid crystal polymer networks based on a synergistic use of photochemical and photothermal effects.

08 October 2018 | doi: 10.1038/s41467-018-06647-7
Actuators  Polymers 

ROS-induced R loops trigger a transcription-coupled but BRCA1/2-independent homologous recombination pathway through CSB OPEN
Yaqun Teng, Tribhuwan Yadav, Meihan Duan, Jun Tan, Yufei Xiang, Boya Gao, Jianquan Xu, Zhuobin Liang, Yang Liu, Satoshi Nakajima, Yi Shi, Arthur S. Levine, Lee Zou & Li Lan

Transcription-coupled homologous recombination (TC-HR) is activated by reactive oxygen species-induced DNA damage to maintain transcribed genome stability. The authors demonstrate that R loops are induced by ROS at the transcribed genome, triggering a CSB-RAD52- dependent but BRCA1/2-independent RAD51 loading for repair.

08 October 2018 | doi: 10.1038/s41467-018-06586-3
DNA recombination  Double-strand DNA breaks 

Biosynthetic energy cost for amino acids decreases in cancer evolution OPEN
Hong Zhang, Yirong Wang, Jun Li, Han Chen, Xionglei He, Huiwen Zhang, Han Liang & Jian Lu

Proliferating cancer cells have a high demand for amino acids. Here, Zhang et al. show that cancer cells evolve towards gene expression profiles that use amino acids with lower biosynthetic energy costs, and demonstrate the potential prognostic utility of quantifying the extent of this adaptation.

08 October 2018 | doi: 10.1038/s41467-018-06461-1
Cancer genomics  Cancer metabolism  Computational biology and bioinformatics 

A global strategy to mitigate the environmental impact of China's ruminant consumption boom OPEN
Yuanyuan Du, Ying Ge, Yuan Ren, Xing Fan, Kaixuan Pan, Linshan Lin, Xu Wu, Yong Min, Laura A. Meyerson, Mikko Heino, Scott X. Chang, Xiaozi Liu, Feng Mao, Guofu Yang, Changhui Peng, Zelong Qu, Jie Chang & Raphael K. Didham

Rising demand for ruminant meat and dairy products in developing nations drives increasing GHG and ammonia emissions from livestock. Authors show here that only long-term adoption of global best-practice in sustainable intensification buffered by a short-term coping strategy of green-source trading can offer a way forward.

08 October 2018 | doi: 10.1038/s41467-018-06381-0
Agriculture  Climate-change mitigation  Environmental impact  Sustainability 

Formation of the β-barrel assembly machinery complex in lipid bilayers as seen by solid-state NMR OPEN
Cecilia Pinto, Deni Mance, Tessa Sinnige, Mark Daniëls, Markus Weingarth & Marc Baldus

The β-barrel assembly machinery (BAM) catalyzes β-barrel protein insertion into the outer membrane of E.coli. Here authors employ high-sensitivity solid-state NMR to reveal how the lipid environment and formation of the BamA-BamCDE complex affect BamA structure and dynamics with regards to the lateral gate and the β-barrel associated domains.

08 October 2018 | doi: 10.1038/s41467-018-06466-w
Biophysics  Chemistry  Microbiology  Molecular biology  Structural biology 

Quasiparticle interference and nonsymmorphic effect on a floating band surface state of ZrSiSe OPEN
Zhen Zhu, Tay-Rong Chang, Cheng-Yi Huang, Haiyang Pan, Xiao-Ang Nie, Xin-Zhe Wang, Zhe-Ting Jin, Su-Yang Xu, Shin-Ming Huang, Dan-Dan Guan, Shiyong Wang, Yao-Yi Li, Canhua Liu, Dong Qian, Wei Ku, Fengqi Song, Hsin Lin, Hao Zheng & Jin-Feng Jia

A new type of surface state has recently been reported in ZrSiSe but its physical properties remain unclear. Here, Zhu, Chang, Huang, et al. report rotational symmetry breaking, healing effect and anomalous Umklapp scattering arising from the nonsymmorphic effect of the floating band state on ZrSiSe (001) surface.

08 October 2018 | doi: 10.1038/s41467-018-06661-9
Surfaces, interfaces and thin films  Topological insulators 

The H3K9 methyltransferase SETDB1 maintains female identity in Drosophila germ cells OPEN
Anne E. Smolko, Laura Shapiro-Kulnane & Helen K. Salz

Epigenetic regulation is critical for the maintenance of germ cell identity. Here the authors show that H3K9me3-mediated gene silencing is critical for repression of testis-specific transcription in Drosophila female germ cells, indicating H3K9me3 maintains female germ cell sexual identity.

08 October 2018 | doi: 10.1038/s41467-018-06697-x
Gene silencing  Germline development  Oogenesis 

Direct protein-lipid interactions shape the conformational landscape of secondary transporters OPEN
Chloe Martens, Mrinal Shekhar, Antoni J. Borysik, Andy M. Lau, Eamonn Reading, Emad Tajkhorshid, Paula J. Booth & Argyris Politis

Secondary transporters catalyse substrate translocation across the cell membrane but the role of lipids during the transport cycle remains unclear. Here authors used hydrogen-deuterium exchange mass spectrometry and molecular dynamics simulations to understand how lipids regulate the conformational dynamics of secondary transporters.

08 October 2018 | doi: 10.1038/s41467-018-06704-1
Lipids  Mass spectrometry  Membrane proteins  Structural biology  Transporters 

A sulfotransferase dosage-dependently regulates mouthpart polyphenism in the nematode Pristionchus pacificus OPEN
Linh T. Bui, Nicholas A. Ivers & Erik J. Ragsdale

Certain genotypes define developmental plasticity and discrete morphologies, but a mechanism as to how this arises is unclear. Here, the authors show that dosage-specific sulfotransferase (SEUD-1) expression specifies which mouthparts are expressed in the nematode Pristionchus pacificus, dependent on the environment.

08 October 2018 | doi: 10.1038/s41467-018-05612-8
Evolutionary developmental biology  Evolutionary genetics 

Subtomogram averaging of COPII assemblies reveals how coat organization dictates membrane shape OPEN
Joshua Hutchings, Viktoriya Stancheva, Elizabeth A. Miller & Giulia Zanetti

The COPII coat assembles in two concentric layers and mediates protein export from the endoplasmic reticulum. Here the authors present the 4.9 Å resolution cryo-tomography and subtomogram averaging structure of the membrane bound COPII inner coat that was obtained by in vitro reconstitution and discuss mechanistic implications.

08 October 2018 | doi: 10.1038/s41467-018-06577-4
Coat complexes  Cryoelectron tomography  Membrane curvature  Small GTPases 

Salt concentration and charging velocity determine ion charge storage mechanism in nanoporous supercapacitors OPEN
C. Prehal, C. Koczwara, H. Amenitsch, V. Presser & O. Paris

To improve supercapacitor performance, mechanisms of operation should be understood. Here the authors identify parameters controlling ion charge storage mechanisms and show that charging initially implies a non-equilibrium ion configuration followed by charge-neutral equilibration.

08 October 2018 | doi: 10.1038/s41467-018-06612-4
Electrochemistry  Supercapacitors 

Ice rule fragility via topological charge transfer in artificial colloidal ice OPEN
András Libál, Dong Yun Lee, Antonio Ortiz-Ambriz, Charles Reichhardt, Cynthia J. O. Reichhardt, Pietro Tierno & Cristiano Nisoli

Spin ice materials are defined by ice rules, local constraints that lead to frustrated interactions and macroscopic numbers of degenerate configurations. Here the authors show that the ice rule in colloidal ice is emergent, limited to certain geometries, and demonstrate how it can break down under changes of the lattice structure.

08 October 2018 | doi: 10.1038/s41467-018-06631-1
Colloids  Magnetic properties and materials  Statistical physics 

Synergy between intrinsically disordered domains and structured proteins amplifies membrane curvature sensing OPEN
Wade F. Zeno, Upayan Baul, Wilton T. Snead, Andre C. M. DeGroot, Liping Wang, Eileen M. Lafer, D. Thirumalai & Jeanne C. Stachowiak

Many proteins which sense membrane curvature contain intrinsically disordered domains. Here the authors use Monte Carlo simulations combined with experimental approaches and report that disordered domains are potent sensors of membrane curvature.

08 October 2018 | doi: 10.1038/s41467-018-06532-3
Endocytosis  Intrinsically disordered proteins 

Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice OPEN
Yongzhen Wu, Shuangshuang Zhao, Xianran Li, Bosen Zhang, Liyun Jiang, Yanyan Tang, Jie Zhao, Xin Ma, Hongwei Cai, Chuanqing Sun & Lubin Tan

Plant architecture transition is one of the great consequences during rice domestication. Here, the authors find that chromosomal deletions linked to the previously known PROG1 gene also participate in plant architecture domestication in both Asian and African cultivated rice.

08 October 2018 | doi: 10.1038/s41467-018-06509-2
Agricultural genetics  Plant breeding  Plant domestication  Plant genetics 

An efficient and multiple target transgenic RNAi technique with low toxicity in Drosophila OPEN
Huan-Huan Qiao, Fang Wang, Rong-Gang Xu, Jin Sun, Ruibao Zhu, Decai Mao, Xingjie Ren, Xia Wang, Yu Jia, Ping Peng, Da Shen, Lu-Ping Liu, Zhijie Chang, Guirong Wang, Shao Li, Jun-Yuan Ji, Qingfei Liu & Jian-Quan Ni

Drosophila transgenic RNAi can have drawbacks such as false positives and negative results. Here the authors develop a next generation RNAi system with reduced leakiness of expression and simultaneous knockdown.

08 October 2018 | doi: 10.1038/s41467-018-06537-y
Gene regulation  Genetic techniques 

Pressure tuning of charge ordering in iron oxide OPEN
Sergey V. Ovsyannikov, Maxim Bykov, Elena Bykova, Konstantin Glazyrin, Rudra Sekhar Manna, Alexander A. Tsirlin, Valerio Cerantola, Ilya Kupenko, Alexander V. Kurnosov, Innokenty Kantor, Anna S. Pakhomova, Irina Chuvashova, Aleksandr I. Chumakov, Rudolf Rüffer, Catherine McCammon & Leonid S. Dubrovinsky

The charge order transition of commonly known magnetite has only recently been unraveled. Here, the measurement of the low-temperature high-pressure phase diagram of a related material (Fe4O5) elucidates the interplay of average oxidation state and charge-ordering phenomena in the iron oxide family.

08 October 2018 | doi: 10.1038/s41467-018-06457-x
Electronic properties and materials  Ferromagnetism  Phase transitions and critical phenomena  Semiconductors  Structure of solids and liquids 

Time units for learning involving maintenance of system-wide cFos expression in neuronal assemblies OPEN
Ananya Chowdhury & Pico Caroni

Learning often involves multiple exposures and trials, but it is not known whether those are treated independently, or integrated during dedicated time windows. Here, Chowdhury and Caroni show mice learn new associations during 5 h time windows, where related experiences are integrated in a process requiring coordinated cFos-activated neuronal assemblies.

08 October 2018 | doi: 10.1038/s41467-018-06516-3
Cellular neuroscience  Consolidation 

Typing tumors using pathways selected by somatic evolution OPEN
Sheng Wang, Jianzhu Ma, Wei Zhang, John Paul Shen, Justin Huang, Jian Peng & Trey Ideker

Informative pathways driving cancer pathogenesis and subtypes can be difficult to identify in the presence of many gene interactions irrelevant to cancer. Here, the authors describe an approach for cancer gene pathway analysis based on key molecular interactions that drive cancer in relevant tissue types, and they assemble a focused map of Evolutionarily Selected Pathways (ESP) with interactions supported by both protein–protein binding and genetic epistasis during somatic tumor evolution.

08 October 2018 | doi: 10.1038/s41467-018-06464-y
Cancer  Classification and taxonomy  Computational biology and bioinformatics 

Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism OPEN
James Peek, Mirjana Lilic, Daniel Montiel, Aleksandr Milshteyn, Ian Woodworth, John B. Biggins, Melinda A. Ternei, Paula Y. Calle, Michael Danziger, Thulasi Warrier, Kohta Saito, Nathaniel Braffman, Allison Fay, Michael S. Glickman, Seth A. Darst, Elizabeth A. Campbell & Sean F. Brady

Resistance to rifamycin antibiotics, which target bacterial RNA polymerases, is a growing problem. Here, the authors identify gene clusters from soil metagenomes encoding production of rifamycin analogues that are active against rifampicin-resistant bacteria through a distinct mechanism.

08 October 2018 | doi: 10.1038/s41467-018-06587-2
Bacterial transcription  Metagenomics  Natural products  X-ray crystallography 

C16-ceramide is a natural regulatory ligand of p53 in cellular stress response OPEN
Baharan Fekry, Kristen A. Jeffries, Amin Esmaeilniakooshkghazi, Zdzislaw M. Szulc, Kevin J. Knagge, David R. Kirchner, David A. Horita, Sergey A. Krupenko & Natalia I. Krupenko

Ceramides are important participants of signal transduction, regulating fundamental cellular processes. Here authors show that C16-ceramide binds to the tumor suppressor p53, disrupts its interaction with MDM2 and facilitates p53 accumulation and activation of its downstream targets.

08 October 2018 | doi: 10.1038/s41467-018-06650-y
Lipid signalling  Sphingolipids 

Sequencing HIV-neutralizing antibody exons and introns reveals detailed aspects of lineage maturation OPEN
Erik L. Johnson, Nicole A. Doria-Rose, Jason Gorman, Jinal N. Bhiman, Chaim A. Schramm, Ashley Q. Vu, William H. Law, Baoshan Zhang, Valerie Bekker, Salim S. Abdool Karim, Gregory C. Ippolito, Lynn Morris, Penny L. Moore, Peter D. Kwong, John R. Mascola & George Georgiou

Knowledge on how antibody responses have evolved is critical for the induction of protective immunity. Here the authors analyse, using high-throughput sequencing of both exon and intron regions, the mutation and lineage development of an HIV-neutralizing antibody to find an unexpected early emergence of broadly neutralizing species.

08 October 2018 | doi: 10.1038/s41467-018-06424-6
Antibodies  HIV infections  Immunogenetics  Somatic hypermutation 

Haplosaurus computes protein haplotypes for use in precision drug design OPEN
William Spooner, William McLaren, Timothy Slidel, Donna K. Finch, Robin Butler, Jamie Campbell, Laura Eghobamien, David Rider, Christine Mione Kiefer, Matthew J. Robinson, Colin Hardman, Fiona Cunningham, Tristan Vaughan, Paul Flicek & Catherine Chaillan Huntington

Proteoforms arise as protein isoforms or as protein haplotypes, which are the result of genetic variation. Here, the authors develop Haplosaurus, a database that computes protein haplotypes genome-wide from existing genotype data and analyse protein haplotype variability in the 1000 Genomes dataset.

08 October 2018 | doi: 10.1038/s41467-018-06542-1
Haplotypes  Personalized medicine  Protein analysis  Protein databases 

ATR/Chk1 signaling induces autophagy through sumoylated RhoB-mediated lysosomal translocation of TSC2 after DNA damage OPEN
Mingdong Liu, Taoling Zeng, Xin Zhang, Chunyan Liu, Zhihui Wu, Luming Yao, Changchuan Xie, Hui Xia, Qi Lin, Liping Xie, Dawang Zhou, Xianming Deng, Hong-Lin Chan, Tong-Jin Zhao & Hong-Rui Wang

DNA damage can lead to autophagy. Here the authors reveal a molecular mechanism for ATR/Chk1 signaling-induced autophagy in response to DNA damage, through an ATR/Chk1/RhoB-mediated lysosomal recruitment of TSC complex and subsequent mTORC1 inhibition.

08 October 2018 | doi: 10.1038/s41467-018-06556-9
Autophagy  DNA damage response  Sumoylation 

Ultra-long-acting removable drug delivery system for HIV treatment and prevention OPEN
Martina Kovarova, S. Rahima Benhabbour, Ivana Massud, Rae Ann Spagnuolo, Brianna Skinner, Caroline E. Baker, Craig Sykes, Katie R. Mollan, Angela D. M. Kashuba, J. Gerardo García-Lerma, Russell J. Mumper & J. Victor Garcia

Long-acting (LA) formulations of antiretroviral (ARV) drugs are an alternative approach to improve adherence for HIV treatment and prevention. Here the authors show a removable biodegradable ultra-LA-ARV drug system that effectively delivers drug, controls viremia and prevents infection in animal models of HIV infection.

08 October 2018 | doi: 10.1038/s41467-018-06490-w
Antivirals  Drug delivery  Experimental models of disease  HIV infections 

Maintaining and breaking symmetry in homomeric coiled-coil assemblies OPEN
Guto G. Rhys, Christopher W. Wood, Eric J. M. Lang, Adrian J. Mulholland, R. Leo Brady, Andrew R. Thomson & Derek N. Woolfson

Higher order coiled coils with five or more helices can form α-helical barrels. Here the authors show that placing β-branched aliphatic residues along the lumen yields stable and open α-helical barrels, which is of interest for the rational design of functional proteins; whereas, the absence of β-branched side chains leads to unusual low-symmetry α-helical bundles.

08 October 2018 | doi: 10.1038/s41467-018-06391-y
Protein design  X-ray crystallography 

Genetic and mechanistic basis for APOBEC3H alternative splicing, retrovirus restriction, and counteraction by HIV-1 protease OPEN
Diako Ebrahimi, Christopher M. Richards, Michael A. Carpenter, Jiayi Wang, Terumasa Ikeda, Jordan T. Becker, Adam Z. Cheng, Jennifer L. McCann, Nadine M. Shaban, Daniel J. Salamango, Gabriel J. Starrett, Jairam R. Lingappa, Jeongsik Yong, William L. Brown & Reuben S. Harris

Human APOBEC3H has several haplotypes and splice variants with distinct anti-HIV-1 activities, but the genetics underlying the expression of these variants are unclear. Here, the authors identify an intronic deletion in A3H haplotype II resulting in production of the most active splice variant, which is counteracted by HIV-1 protease.

08 October 2018 | doi: 10.1038/s41467-018-06594-3
Haplotypes  HIV infections  RNA splicing  Virus–host interactions 

High-efficiency optogenetic silencing with soma-targeted anion-conducting channelrhodopsins OPEN
Mathias Mahn, Lihi Gibor, Pritish Patil, Katayun Cohen-Kashi Malina, Shir Oring, Yoav Printz, Rivka Levy, Ilan Lampl & Ofer Yizhar

Current optogenetic inhibition methods like light-controlled ion pumps require high-intensity light and disrupt physiological ion gradients. Here, the authors somatically target the anion-conducting opsin GtACR to eliminate spiking in distal axons and improve photocurrents, thus enhancing its utility.

08 October 2018 | doi: 10.1038/s41467-018-06511-8
Excitability  Ion channels in the nervous system 

Ultrasmall targeted nanoparticles with engineered antibody fragments for imaging detection of HER2-overexpressing breast cancer OPEN
Feng Chen, Kai Ma, Brian Madajewski, Li Zhuang, Li Zhang, Keith Rickert, Marcello Marelli, Barney Yoo, Melik Z. Turker, Michael Overholtzer, Thomas P. Quinn, Mithat Gonen, Pat Zanzonico, Anthony Tuesca, Michael A. Bowen, Larry Norton, J. Anand Subramony, Ulrich Wiesner & Michelle S. Bradbury

One of the major obstacles in nanoparticle-based therapy is to achieve tumour targeting, limiting non-specific accumulation of the nanoparticles. Here the authors propose the conjugation of anti-HER2 scFv fragments to the silica nanoparticles, increasing specificity and limiting the final size of the immunoconjugates below the renal clearance threshold.

08 October 2018 | doi: 10.1038/s41467-018-06271-5
Nanomedicine  Nanoscale materials 

Designed synthesis of stable light-emitting two-dimensional sp2 carbon-conjugated covalent organic frameworks OPEN
Enquan Jin, Juan Li, Keyu Geng, Qiuhong Jiang, Hong Xu, Qing Xu & Donglin Jiang

Topological connection of organic chromophores is an attractive way to design light-emitting covalent organic frameworks but the synthesis of stable light-emitting frameworks remains challenging. Here the authors report the designed synthesis of sp2 carbon conjugated frameworks that combine stability with light-emitting activity

08 October 2018 | doi: 10.1038/s41467-018-06719-8
Optical materials  Polymer synthesis  Two-dimensional materials 

Matrix mechanical plasticity regulates cancer cell migration through confining microenvironments OPEN
Katrina M. Wisdom, Kolade Adebowale, Julie Chang, Joanna Y. Lee, Sungmin Nam, Rajiv Desai, Ninna Struck Rossen, Marjan Rafat, Robert B. West, Louis Hodgson & Ovijit Chaudhuri

In order to metastasize, cancer cells must migrate through basement membranes and dense stroma, and proteases are thought to be required due to the confining nature of these matrices. Here the authors use synthetic matrices to show that cells can migrate through confining matrices using force generation alone, rather than protease degradation, if the matrices exhibit mechanical plasticity.

08 October 2018 | doi: 10.1038/s41467-018-06641-z
Biomaterials – cells  Breast cancer  Cancer microenvironment  Cell invasion  Invadopodia 

A comprehensive overview of genomic imprinting in breast and its deregulation in cancer OPEN
Tine Goovaerts, Sandra Steyaert, Chari A. Vandenbussche, Jeroen Galle, Olivier Thas, Wim Van Criekinge & Tim De Meyer

In growth and development genomic imprinting is important in regulating gene expression. Here, the authors study loss of imprinting (LOI) in cancer, developing a mixture model to detect monoallelically expressed loci without genotyping data - applying this novel methodology to TCGA breast cancer data they find massive deregulation of imprinting.

08 October 2018 | doi: 10.1038/s41467-018-06566-7
Breast cancer  Cancer genomics  Genetics research 

A rapid rate of sex-chromosome turnover and non-random transitions in true frogs OPEN
Daniel L. Jeffries, Guillaume Lavanchy, Roberto Sermier, Michael J. Sredl, Ikuo Miura, Amaël Borzée, Lisa N. Barrow, Daniele Canestrelli, Pierre-André Crochet, Christophe Dufresnes, Jinzhong Fu, Wen-Juan Ma, Constantino Macías Garcia, Karim Ghali, Alfredo G. Nicieza, Ryan P. O'Donnell, Nicolas Rodrigues, Antonio Romano, Íñigo Martínez-Solano, Ilona Stepanyan et al.

The evolutionary forces that favour transitions in sex chromosomes are not well understood. Here, Jeffries and colleagues show a very high rate of sex chromosome turnover in true frogs, which may be driven by rapid mutation-load accumulation due to the low recombination rate in males.

05 October 2018 | doi: 10.1038/s41467-018-06517-2
Comparative genomics  Evolutionary genetics 

Evidence for magmatic carbon bias in 14C dating of the Taupo and other major eruptions OPEN
Richard N. Holdaway, Brendan Duffy & Ben Kennedy

Correlations between prehistoric eruptions and other phenomena depend on accurate dating of the eruption. Here the authors show that magmatic CO2 in groundwater can bias radiocarbon ages for eruptions and that plateaux of carbon isotopic values in tree ring sequences biased by magmatic CO2 foreshadow major eruptions.

05 October 2018 | doi: 10.1038/s41467-018-06357-0
Environmental impact  Geochemistry  Natural hazards  Volcanology 

Graphene-enabled and directed nanomaterial placement from solution for large-scale device integration OPEN
Michael Engel, Damon B. Farmer, Jaione Tirapu Azpiroz, Jung-Woo T. Seo, Joohoon Kang, Phaedon Avouris, Mark C. Hersam, Ralph Krupke & Mathias Steiner

The placement of nanomaterials at predefined locations is a key requirement for their integration in nanoelectronic devices. Here, the authors devise a method allowing placement of solution-based nanomaterials by using structured graphene layers as deposition sites with the aid of an electric field.

05 October 2018 | doi: 10.1038/s41467-018-06604-4
Graphene  Nanoscale devices  Nanoscale materials 

Self-induced mechanical stress can trigger biofilm formation in uropathogenic Escherichia coli OPEN
Eric K. Chu, Onur Kilic, Hojung Cho, Alex Groisman & Andre Levchenko

Bacterial biofilms are an increasingly important medical problem but the mechanisms by which they develop remain largely unknown. Here, using a high-throughput approach, the authors show that biofilm formation is linked to self-imposed mechanical stress.

05 October 2018 | doi: 10.1038/s41467-018-06552-z
Biofilms  Computer modelling  Lab-on-a-chip 

High-performance nanomaterials formed by rigid yet extensible cyclic β-peptide polymers OPEN
Kenan P. Fears, Manoj K. Kolel-Veetil, Daniel E. Barlow, Noam Bernstein, Christopher R. So, Kathryn J. Wahl, Xianfeng Li, John L. Kulp III, Robert A. Latour & Thomas D. Clark

Synthetic materials tend to excel in either stiffness or extensibility, whereas a combination of the two is necessary to exceed the performance of natural biomaterials. Here the authors present a bioinspired polymer consisting of cyclic β-peptide rings that is capable of transitioning between rigid and unfolded conformations on demand.

05 October 2018 | doi: 10.1038/s41467-018-06576-5
Bioinspired materials  Molecular self-assembly  Synthesis and processing 

Lateral inhibition by Martinotti interneurons is facilitated by cholinergic inputs in human and mouse neocortex OPEN
Joshua Obermayer, Tim S. Heistek, Amber Kerkhofs, Natalia A. Goriounova, Tim Kroon, Johannes C. Baayen, Sander Idema, Guilherme Testa-Silva, Jonathan J. Couey & Huibert D. Mansvelder

Parvalbumin and somatostatin expressing interneurons mediate lateral inhibition between cortical neurons. Here the authors report the mechanisms by which acetylcholine from the basal forebrain selectively augments lateral inhibition via Martinotti cells and show that this is conserved in humans.

05 October 2018 | doi: 10.1038/s41467-018-06628-w
Attention  Cognitive neuroscience  Neural circuits  Neuroscience 

Structural properties of a haemophore facilitate targeted elimination of the pathogen Porphyromonas gingivalis OPEN
Jin-Long Gao, Ann H. Kwan, Anthony Yammine, Xiaoyan Zhou, Jill Trewhella, Barbara M. Hugrass, Daniel A. T. Collins, James Horne, Ping Ye, Derek Harty, Ky-Anh Nguyen, David A. Gell & Neil Hunter

The pathogenic bacterium Porphyromonas gingivalis causes periodontal disease and depends on porphyrin from host sources. Here the authors show that the P. gingivalis haem uptake system protein A (HusA) mediates the uptake of exogenous porphyrin, present its solution NMR structure and show how HusA can be exploited as a drug target.

05 October 2018 | doi: 10.1038/s41467-018-06470-0
Antimicrobials  Pathogens  Solution-state NMR 

Latitude-dependent finescale turbulent shear generations in the Pacific tropical-extratropical upper ocean OPEN
Zhiwei Zhang, Bo Qiu, Jiwei Tian, Wei Zhao & Xiaodong Huang

Turbulent mixing is critically important for ocean circulation, but their latitudinal distribution are poorly known. Here, the authors show that the generation mechanism of the W-shaped distribution of turbulent mixing in the tropical-extratropical Pacific is latitude dependent.

05 October 2018 | doi: 10.1038/s41467-018-06260-8
Physical oceanography 

Genome mining of cyclodipeptide synthases unravels unusual tRNA-dependent diketopiperazine-terpene biosynthetic machinery OPEN
Tingting Yao, Jing Liu, Zengzhi Liu, Tong Li, Huayue Li, Qian Che, Tianjiao Zhu, Dehai Li, Qianqun Gu & Wenli Li

Diketopiperazine derivatives are bioactive molecules with scaffold formed by the condensation of two amino acids. Here, Yao et al. mine the genomes of Streptomyces strains and identify new biosynthetic machinery for drimentines biosynthesis, which includes cyclodipeptide synthase, prenyltransferase, and terpene cyclase.

05 October 2018 | doi: 10.1038/s41467-018-06411-x
Applied microbiology  Biosynthesis  Metabolic engineering 

Direct electrical quantification of glucose and asparagine from bodily fluids using nanopores OPEN
Nicole Stéphanie Galenkamp, Misha Soskine, Jos Hermans, Carsten Wloka & Giovanni Maglia

Protein nanopores are emerging as sensors for a variety of biomolecules. Here the authors develop a nanopore based on the bacterial toxin ClyA, in conjunction with binding proteins for glucose and asparagine, to detect these biomolecules simultaneously from a variety of unprocessed, diluted body fluids.

05 October 2018 | doi: 10.1038/s41467-018-06534-1
Biosensors  Nanopores  Single-molecule biophysics 

Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy OPEN
Dominiek Smeets, Ian S. Miller, Darran P. O'Connor, Sudipto Das, Bruce Moran, Bram Boeckx, Timo Gaiser, Johannes Betge, Ana Barat, Rut Klinger, Nicole C. T. van Grieken, Chiara Cremolini, Hans Prenen, Massimiliano Mazzone, Jeroen Depreeuw, Orna Bacon, Bozena Fender, Joseph Brady, Bryan T. Hennessy, Deborah A. McNamara et al.

Increased copy number alterations, indicative of chromosomal instability, is associated with poor cancer outcome. Here, metastatic colorectal cancer patients displaying intermediate-high CIN associate with improved outcome following chemotherapy and bevacizumab treatment, suggesting CIN as a predictive biomarker.

05 October 2018 | doi: 10.1038/s41467-018-06567-6
Cancer  Colon cancer  Gastrointestinal cancer  Tumour angiogenesis  Tumour biomarkers 

Orthogonal programming of heterogeneous micro-mechano-environments and geometries in three-dimensional bio-stereolithography OPEN
Hang Yin, Yonghui Ding, Yao Zhai, Wei Tan & Xiaobo Yin

Tuning the mechanical properties of extracellular matrix is of great interest in tissue engineering but spatial control over stiffness in hydrogels has been demonstrated in two dimensions only. Here the authors developed a layer-by-layer printing technique which uses oxygen inhibition to control the heterogeneous stiffness in 3D printed structures.

05 October 2018 | doi: 10.1038/s41467-018-06685-1
Biomaterials – cells  Gels and hydrogels  Mechanical properties 

Antigen-selective modulation of AAV immunogenicity with tolerogenic rapamycin nanoparticles enables successful vector re-administration OPEN

Immunogenicity of AAV vectors renders repeated AAV dosing ineffective. Here the authors show that coadministration of nanoparticle-encapsulated rapamycin overcomes AAV immunogenicity through Treg induction, enabling efficient AAV redosing in mice and nonhuman primates.

05 October 2018 | doi: 10.1038/s41467-018-06621-3
Adaptive immunity  Applied immunology  Gene delivery  Gene therapy 

Targeting of NLRP3 inflammasome with gene editing for the amelioration of inflammatory diseases OPEN
Congfei Xu, Zidong Lu, Yingli Luo, Yang Liu, Zhiting Cao, Song Shen, Hongjun Li, Jing Liu, Kaige Chen, Zhiyao Chen, Xianzhu Yang, Zhen Gu & Jun Wang

Activation of the NLRP3 inflammasome triggers the production of inflammatory cytokines. Here, the authors inactivate NLRP3 in macrophages using CRISPR/Cas9 encapsulated in nanoparticles, and show that administration in mice is effective in preventing septic shock and peritonitis, and in improving diabetes-associated inflammation and insulin resistance.

05 October 2018 | doi: 10.1038/s41467-018-06522-5
Gene delivery  Inflammatory diseases  Nanoparticles 

Myelo-lymphoid lineage restriction occurs in the human haematopoietic stem cell compartment before lymphoid-primed multipotent progenitors OPEN
Serena Belluschi, Emily F. Calderbank, Valerio Ciaurro, Blanca Pijuan-Sala, Antonella Santoro, Nicole Mende, Evangelia Diamanti, Kendig Yen Chi Sham, Xiaonan Wang, Winnie W. Y. Lau, Wajid Jawaid, Berthold Göttgens & Elisa Laurenti

Human blood cells all develop from haematopoietic stem cells (HSCs), classically thought to be multipotent. Here the authors show, using single-cell RNA-seq and functional assays, that loss of erythroid potential and commitment to the myelo-lymphoid lineage occurs within the purest HSC compartment to date.

05 October 2018 | doi: 10.1038/s41467-018-06442-4
Bone marrow  Gene regulation in immune cells  Haematopoietic stem cells  Lymphopoiesis 

Bright room temperature single photon source at telecom range in cubic silicon carbide OPEN
Junfeng Wang, Yu Zhou, Ziyu Wang, Abdullah Rasmita, Jianqun Yang, Xingji Li, Hans Jürgen von Bardeleben & Weibo Gao

Room-temperature solid-state single photon emitters in the telecom range are suitable for quantum communication. Here, the authors observe defects in high-purity 3C-SiC epitaxy layers grown on a silicon substrate, with good characteristics in terms of brightness, emission's polarization and photostability.

05 October 2018 | doi: 10.1038/s41467-018-06605-3
Quantum information  Single photons and quantum effects 

Electrophysiological mechanisms of human memory consolidation OPEN
Hui Zhang, Juergen Fell & Nikolai Axmacher

It is believed that fast "ripple" oscillations in the hippocampus play a role in consolidation, a process by which memory traces are stabilized. Here, the authors show that ripples occuring during non-REM sleep trigger "replay" of brain activity associated with previously experienced stimuli.

05 October 2018 | doi: 10.1038/s41467-018-06553-y
Cognitive neuroscience  Consolidation  Neural circuits  Psychology 

Powerful turbidity currents driven by dense basal layers OPEN
Charles K. Paull, Peter J. Talling, Katherine L. Maier, Daniel Parsons, Jingping Xu, David W. Caress, Roberto Gwiazda, Eve M. Lundsten, Krystle Anderson, James P. Barry, Mark Chaffey, Tom O'Reilly, Kurt J. Rosenberger, Jenny A. Gales, Brian Kieft, Mary McGann, Steve M. Simmons, Mike McCann, Esther J. Sumner, Michael A. Clare et al.

The structure of turbidity currents has remained unresolved mainly due to lack of observations. Here the authors present data from a high-resolution monitoring array deployed for 18 months over Monterey Bay, that suggests turbidity currents are driven by dense near-bed layers.

05 October 2018 | doi: 10.1038/s41467-018-06254-6
Natural hazards  Ocean sciences 

Thermal and electrical signatures of a hydrodynamic electron fluid in tungsten diphosphide OPEN
J. Gooth, F. Menges, N. Kumar, V. Süβ, C. Shekhar, Y. Sun, U. Drechsler, R. Zierold, C. Felser & B. Gotsmann

Advances in the fabrication of low-disorder metallic materials have made it possible to reach the hydrodynamic regime of electronic transport. Here the authors investigate a hydrodynamic electron fluid in tungsten diphosphide and find that both electrical and thermal transport are limited by the quantum indeterminacy.

05 October 2018 | doi: 10.1038/s41467-018-06688-y
Electronic properties and materials  Quantum fluids and solids  Topological matter 

Nickel nanoparticles set a new record of strength OPEN
A. Sharma, J. Hickman, N. Gazit, E. Rabkin & Y. Mishin

While metallic nanosized objects are stronger than their macroscopic counterparts, they rarely reach the metal's maximum theoretical strength. Here, the authors produce faceted nickel nanoparticles and show that their strength under compression matches the theoretically predicted strength in the literature.

05 October 2018 | doi: 10.1038/s41467-018-06575-6
Metals and alloys  Nanoparticles  Structural properties 

Dynamic intercellular transport modulates the spatial patterning of differentiation during early neural commitment OPEN
Chad M. Glen, Todd C. McDevitt & Melissa L. Kemp

How heterogeneities arise in stem cell populations remains unclear. Here, Glen et al. find that in ESC colonies cell cycle asynchronies modulate gap junctions, causing variation in intracellular signalling molecule diffusion between cells, and ultimately in spatial heterogeneity in differentiation.

05 October 2018 | doi: 10.1038/s41467-018-06693-1
Computational models  Dynamic networks  Multicellular systems  Pattern formation  Stem-cell differentiation 

Aberrant expression of CITED2 promotes prostate cancer metastasis by activating the nucleolin-AKT pathway OPEN
Seung-Hyun Shin, Ga Young Lee, Mingyu Lee, Jengmin Kang, Hyun-Woo Shin, Yang-Sook Chun & Jong-Wan Park

More effective strategies are needed to prevent prostate cancer metastasis. Here they report CBP/p300-interacting transactivator with E/D-rich carboxy-terminal domain-2 (CITED2) to interact with nucleolin, p300, and PRMT5 subunits, and reveal a role of CITED2-nucleolin axis in prostate cancer metastasis.

05 October 2018 | doi: 10.1038/s41467-018-06606-2
Biochemistry  Cancer  Cell biology 

Bone protection by inhibition of microRNA-182 OPEN
Kazuki Inoue, Zhonghao Deng, Yufan Chen, Eugenia Giannopoulou, Ren Xu, Shiaoching Gong, Matthew B. Greenblatt, Lingegowda S. Mangala, Gabriel Lopez-Berestein, David G. Kirsch, Anil K. Sood, Liang Zhao & Baohong Zhao

Osteoclasts mediate bone disruption in a number of degenerative bone diseases. Here, the authors show that miR-182 regulates osteoclastogenesis via PKR and IFN-beta signaling, is correlated with rheumatoid arthritis, and that its ablation or inhibition is protective against bone erosion in mouse models of osteoporosis or inflammatory arthritis.

05 October 2018 | doi: 10.1038/s41467-018-06446-0
Interferons  Osteoimmunology  Osteoporosis  Rheumatoid arthritis 

Intestinal microbiome adjusts the innate immune setpoint during colonization through negative regulation of MyD88 OPEN
Bjørn E. V. Koch, Shuxing Yang, Gerda Lamers, Jens Stougaard & Herman P. Spaink

It remains unclear how microbial sensing during early-life colonization results in immune homeostasis rather than acute inflammation. Here the authors show that zebrafish larvae colonization suppresses intestinal MyD88, accounting for a considerable proportion of microbiota-induced alterations in immune setpoint.

05 October 2018 | doi: 10.1038/s41467-018-06658-4
Biological techniques  Immunology  Microbiology  Molecular biology 

Suppressor mutations in Rpf2–Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation OPEN
Matthias Thoms, Valentin Mitterer, Lukas Kater, Laurent Falquet, Roland Beckmann, Dieter Kressler & Ed Hurt

During biogenesis of the eukaryotic 60S ribosome, a large rotational movement of the 5S RNP is required to achieve its mature position. By analyzing extragenic suppressors of crg1—a key factor required for rotation—the authors provide mechanistic insight into a key step of ribosome biogenesis.

05 October 2018 | doi: 10.1038/s41467-018-06660-w
Ribosomal proteins  Ribosome  Structural biology 

A ballistic graphene superconducting microwave circuit OPEN
Felix E. Schmidt, Mark D. Jenkins, Kenji Watanabe, Takashi Taniguchi & Gary A. Steele

Encapsulated graphene Josephson junctions are promising for microwave quantum circuits but so far haven't been explored. Here, Schmidt and Jenkins et al. observe a gate-tunable Josephson inductance in a microwave circuit based on a ballistic graphene Josephson junction embedded in a superconducting cavity.

04 October 2018 | doi: 10.1038/s41467-018-06595-2
Electronic properties and devices  Superconducting devices  Superconducting properties and materials 

Observation of Coulomb gap in the quantum spin Hall candidate single-layer 1T'-WTe2 OPEN
Ye-Heng Song, Zhen-Yu Jia, Dongqin Zhang, Xin-Yang Zhu, Zhi-Qiang Shi, Huaiqiang Wang, Li Zhu, Qian-Qian Yuan, Haijun Zhang, Ding-Yu Xing & Shao-Chun Li

The conductance from bulk bands in a topological insulator usually blurs effects arising from edge states. Here, Song et al. report a Coulomb gap opened by electron–electron interactions, which effectively suppress the bulk conductance and promote observation of topological edge states in the single-layer 1T'-WTe2.

04 October 2018 | doi: 10.1038/s41467-018-06635-x
Electronic properties and materials  Surfaces, interfaces and thin films  Topological insulators 

Prolonged bacterial lag time results in small colony variants that represent a sub-population of persisters OPEN
Clément Vulin, Nadja Leimer, Markus Huemer, Martin Ackermann & Annelies S. Zinkernagel

Persisters are bacterial subpopulations that are not killed by antibiotics even though they lack genetic resistance. Here, the authors show that persisters can manifest as small colony variants in clinical infections, and arise as a result of a long lag time in stress conditions including antibiotic exposure.

04 October 2018 | doi: 10.1038/s41467-018-06527-0
Bacteriology  Clinical microbiology  Infectious-disease diagnostics  Microbiology  Pathogens 

Twist angle-dependent conductivities across MoS2/graphene heterojunctions OPEN
Mengzhou Liao, Ze-Wen Wu, Luojun Du, Tingting Zhang, Zheng Wei, Jianqi Zhu, Hua Yu, Jian Tang, Lin Gu, Yanxia Xing, Rong Yang, Dongxia Shi, Yugui Yao & Guangyu Zhang

Twisting vertically stacked individual layers of two-dimensional materials can trigger exciting fundamental physics and advanced electronic device applications. Here, the authors report five times enhancement in vertical heterojunction conductivity on rotating MoS2 over graphene.

04 October 2018 | doi: 10.1038/s41467-018-06555-w
Two-dimensional materials 

Stepwise oxygenation of the Paleozoic atmosphere OPEN
Alexander J. Krause, Benjamin J. W. Mills, Shuang Zhang, Noah J. Planavsky, Timothy M. Lenton & Simon W. Poulton

The GEOCARBSULF model provides the most detailed reconstructions of Phanerozoic O2, but its predictions are not supported by geochemical data. Here, a GEOCARBSULF model rebuilt from first principles, with the addition of an amended sulphur cycle and the latest isotope records, supports a Paleozoic Oxygenation Event.

04 October 2018 | doi: 10.1038/s41467-018-06383-y
Biogeochemistry  Carbon cycle  Element cycles  Palaeoclimate 

Improvement and extension of anti-EGFR targeting in breast cancer therapy by integration with the Avidin-Nucleic-Acid-Nano-Assemblies OPEN
Francesco Roncato, Fatlum Rruga, Elena Porcù, Elisabetta Casarin, Roberto Ronca, Federica Maccarinelli, Nicola Realdon, Giuseppe Basso, Ronen Alon, Giampietro Viola & Margherita Morpurgo

The nature of the linker is known to affect the efficacy of antibody–drug conjugate (ADC). Here the authors show cetuximab-guided Avidin-Nucleic-Acid-Nanoassemblies to be superior to cetuximab-doxorubicin conjugate, and show its efficacy in KRAS mutant breast cancer, allowing for therapeutic expansion of anti-EGFR therapy.

04 October 2018 | doi: 10.1038/s41467-018-06602-6
Breast cancer  Drug delivery  Transport carrier 

Genome-wide association study identifies two risk loci for tuberculosis in Han Chinese OPEN
Ruijuan Zheng, Zhiqiang Li, Fusheng He, Haipeng Liu, Jianhua Chen, Jiayu Chen, Xuefeng Xie, Juan Zhou, Hao Chen, Xiangyang Wu, Juehui Wu, Boyu Chen, Yahui Liu, Haiyan Cui, Lin Fan, Wei Sha, Yin Liu, Jiqiang Wang, Xiaochen Huang, Linfeng Zhang et al.

Genetic risk loci for tuberculosis (TB) have so far been identified in African and Russian populations. Here, the authors perform a three-stage GWAS for TB in Han Chinese populations and find two risk loci near ESRRB and TGM6 and further demonstrate that tgm6 protects mice from Mtb infection.

04 October 2018 | doi: 10.1038/s41467-018-06539-w
Genome-wide association studies  Immunogenetics  Infection  Tuberculosis 

Ultra-low-field magneto-elastocaloric cooling in a multiferroic composite device OPEN
Huilong Hou, Peter Finkel, Margo Staruch, Jun Cui & Ichiro Takeuchi

The broad use of elastocaloric materials in cooling applications is hindered by the need to exert large forces onto the material. Compressing a magnetostrictive-elastocaloric composite using a low magnetic field of 0.16 T, temperature changes up to 4 K are achieved without applying external forces.

04 October 2018 | doi: 10.1038/s41467-018-06626-y
Ferroelectrics and multiferroics  Materials for energy and catalysis  Phase transitions and critical phenomena 

DNA damage sensitivity of SWI/SNF-deficient cells depends on TFIIH subunit p62/GTF2H1 OPEN
Cristina Ribeiro-Silva, Özge Z. Aydin, Raquel Mesquita-Ribeiro, Jana Slyskova, Angela Helfricht, Jurgen A. Marteijn, Jan H. J. Hoeijmakers, Hannes Lans & Wim Vermeulen

SWI/SNF genes are commonly found to be mutated in different cancers. Here the authors report that the remodelers BRM and BRG1 are necessary for efficient nucleotide excision repair by promoting the expression of TFIIH subunit GTF2H1.

04 October 2018 | doi: 10.1038/s41467-018-06402-y
DNA damage response  Nucleotide excision repair 

Germline pathogenic variants of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls OPEN
Yukihide Momozawa, Yusuke Iwasaki, Michael T. Parsons, Yoichiro Kamatani, Atsushi Takahashi, Chieko Tamura, Toyomasa Katagiri, Teruhiko Yoshida, Seigo Nakamura, Kokichi Sugano, Yoshio Miki, Makoto Hirata, Koichi Matsuda, Amanda B. Spurdle & Michiaki Kubo

Association between variants in 11 different genes and breast cancer risk has been established and sequencing of these genes is recommended to provide personalized diagnosis, therapy, and surveillance for the high-risk patients and their relatives. Here the authors analyse the frequency of germline pathogenic mutations in these genes specifically in a Japanese population.

04 October 2018 | doi: 10.1038/s41467-018-06581-8
Breast cancer  Genetic predisposition to disease  Genetic testing  Genetics  Sequence annotation 

Selective prebiotic conversion of pyrimidine and purine anhydronucleosides into Watson-Crick base-pairing arabino-furanosyl nucleosides in water OPEN
Samuel J. Roberts, Rafał Szabla, Zoe R. Todd, Shaun Stairs, Dejan-Krešimir Bučar, Jiří Šponer, Dimitar D. Sasselov & Matthew W. Powner

Arabinonucleic acid (ANA) Watson-Crick base-pair with RNA/DNA and can evolve to display enzyme-like function. Here, the authors now identify a prebiotic pathway that yields the complete set of Watson-Crick base-pairing purine and pyrimidine ANA nucleosides.

04 October 2018 | doi: 10.1038/s41467-018-06374-z
Excited states  Chemical origin of life 

High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites OPEN
Mia K. Mihailovic, Jorge Vazquez-Anderson, Yan Li, Victoria Fry, Praveen Vimalathas, Daniel Herrera, Richard A. Lease, Warren B. Powell & Lydia M. Contreras

Mapping RNA accessibility is valuable for identifying functional/regulatory RNA regions. Here the authors introduce INTERFACE, an intracellular method that quantifies antisense hybridization efficacy of any number of RNA regions simultaneously via a transcriptional elongation output, measurable via RNA-seq

04 October 2018 | doi: 10.1038/s41467-018-06207-z
Biochemistry  Biological techniques  Biotechnology  Computational biology and bioinformatics  Microbiology 

Repurposing of promoters and enhancers during mammalian evolution OPEN
Francesco N. Carelli, Angélica Liechti, Jean Halbert, Maria Warnefors & Henrik Kaessmann

Enhancers and promoters are different types of regulatory elements with shared architectural and functional features. Here the authors perform integrated cross-mammalian analyses of DNase hypersensitivity, chromatin modification and transcriptional data, to provide evidence of regulatory repurposing during evolution.

04 October 2018 | doi: 10.1038/s41467-018-06544-z
Computational biology and bioinformatics  Evolution  Genetics  Transcriptional regulatory elements 

Sustainable scalable synthesis of sulfide nanocrystals at low cost with an ionic liquid sulfur precursor OPEN
Bin Yuan, Timothy Karl Egner, Vincenzo Venditti & Ludovico Cademartiri

Developing sustainable and scalable nanocrystal syntheses is challenging but necessary for future technologies and the environment. Here, the authors show that using an ionic liquid to stabilize a highly reactive precursor can fulfill the major aims of sustainable nanocrystal synthesis, including high yields, energy efficiency, atom economy, and recyclability.

04 October 2018 | doi: 10.1038/s41467-018-06549-8
Ionic liquids  Materials chemistry  Nanoparticles  Sustainability 

Androgen deprivation promotes neuroendocrine differentiation and angiogenesis through CREB-EZH2-TSP1 pathway in prostate cancers OPEN
Yan Zhang, Dayong Zheng, Ting Zhou, Haiping Song, Mohit Hulsurkar, Ning Su, Ying Liu, Zheng Wang, Long Shao, Michael Ittmann, Martin Gleave, Huanxing Han, Feng Xu, Wangjun Liao, Hongbo Wang & Wenliang Li

Neuroendocrine prostate cancers are very difficult to treat and often arise after androgen-deprivation therapy. Here the authors show that ADT activates CREB that acts by increasing EZH2 activity to promote neuroendocrine differentiation in prostate cancer, providing alternative avenues for therapy.

04 October 2018 | doi: 10.1038/s41467-018-06177-2
Mechanisms of disease  Prostate cancer 

Resolving the mechanisms of hygroscopic growth and cloud condensation nuclei activity for organic particulate matter OPEN
Pengfei Liu, Mijung Song, Tianning Zhao, Sachin S. Gunthe, Suhan Ham, Yipeng He, Yi Ming Qin, Zhaoheng Gong, Juliana C. Amorim, Allan K. Bertram & Scot T. Martin

The interactions between organic particulate matter and water vapour affect climate predictions, yet the mechanisms of these interactions remain unresolved. Here, the authors propose a phase separation mechanism that reconciles the observed hygroscopicity and cloud condensation nuclei activity.

04 October 2018 | doi: 10.1038/s41467-018-06622-2
Atmospheric science  Environmental chemistry  Physical chemistry 

Atomic cobalt as an efficient electrocatalyst in sulfur cathodes for superior room-temperature sodium-sulfur batteries OPEN
Bin-Wei Zhang, Tian Sheng, Yun-Dan Liu, Yun-Xiao Wang, Lei Zhang, Wei-Hong Lai, Li Wang, Jianping Yang, Qin-Fen Gu, Shu-Lei Chou, Hua-Kun Liu & Shi-Xue Dou

Room-temperature sodium-sulfur batteries hold promise, but are hindered by low reversible capacity and fast capacity fade. Here the authors construct a multifunctional sulfur host comprised of cobalt-decorated carbon nanospheres that impart attractive performance as a cathode in a sodium sulfide battery.

04 October 2018 | doi: 10.1038/s41467-018-06144-x
Electrocatalysis  Electrochemistry  Energy  Materials chemistry 

Large-scale transcriptome-wide association study identifies new prostate cancer risk regions OPEN
Nicholas Mancuso, Simon Gayther, Alexander Gusev, Wei Zheng, Kathryn L. Penney, Zsofia Kote-Jarai, Rosalind Eeles, Matthew Freedman, Christopher Haiman, Bogdan Pasaniuc, Brian E. Henderson, Sara Benlloch, Fredrick R. Schumacher, Ali Amin Al Olama, Kenneth Muir, Sonja I. Berndt, David V. Conti, Fredrik Wiklund, Stephen Chanock, Victoria L. Stevens et al.

Genome-wide association studies (GWAS) have identified hundreds of genomic risk regions for prostate cancer. Here, the authors perform a transcriptome wide association study (TWAS) by incorporating prostate cancer GWAS with gene expression data to identify potential novel prostate cancer risk loci and possible risk mechanisms.

04 October 2018 | doi: 10.1038/s41467-018-06302-1
Cancer genetics  Gene expression  Genome-wide association studies 
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  Latest Addendum  
Addendum: TGF-β signaling alters H4K20me3 status via miR-29 and contributes to cellular senescence and cardiac aging OPEN
Guoliang Lyu, Yiting Guan, Chao Zhang, Le Zong, Lei Sun, Xiaoke Huang, Li Huang, Lijun Zhang, Xiao-Li Tian, Zhongjun Zhou & Wei Tao
08 October 2018 | doi: 10.1038/s41467-018-06710-3
Cell biology  Senescence 
  Latest Author Corrections  
Author Correction: Clopidogrel as a donor probe and thioenol derivatives as flexible promoieties for enabling H2S biomedicine OPEN
Yaoqiu Zhu, Elkin L. Romero, Xiaodong Ren, Angel J. Sanca, Congkuo Du, Cai Liu, Zubair A. Karim, Fatima Z. Alshbool, Fadi T. Khasawneh, Jiang Zhou, Dafang Zhong & Bin Geng
10 October 2018 | doi: 10.1038/s41467-018-06832-8
Drug discovery and development  Small molecules 

Author Correction: 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
08 October 2018 | doi: 10.1038/s41467-018-06671-7
Computational models  Morphogenesis 

Author Correction: Large intrinsic anomalous Hall effect in half-metallic ferromagnet Co3Sn2S2 with magnetic Weyl fermions OPEN
Qi Wang, Yuanfeng Xu, Rui Lou, Zhonghao Liu, Man Li, Yaobo Huang, Dawei Shen, Hongming Weng, Shancai Wang & Hechang Lei
08 October 2018 | doi: 10.1038/s41467-018-06643-x
Electronic properties and materials  Ferromagnetism  Topological insulators 
  Latest Publisher Correction  
Publisher Correction: Exosomes maintain cellular homeostasis by excreting harmful DNA from cells OPEN
Akiko Takahashi, Ryo Okada, Koji Nagao, Yuka Kawamata, Aki Hanyu, Shin Yoshimoto, Masaki Takasugi, Sugiko Watanabe, Masato T. Kanemaki, Chikashi Obuse & Eiji Hara
08 October 2018 | doi: 10.1038/s41467-018-06613-3

Nature Outlook: Brain cancer

The uncontrolled growth of a tumour inside the brain creates an extraordinarily potent threat to our being. A diagnosis of brain cancer still carries the high likelihood of death within five years. But efforts to prolong survival are advancing on several fronts.

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