Wednesday, August 9, 2017

Nature Communications - 09 August 2017

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Measuring inter-protein pairwise interaction energies from a single native mass spectrum by double-mutant cycle analysis OPEN
Miri Sokolovski, Jelena Cveticanin, Déborah Hayoun, Ilia Korobko, Michal Sharon & Amnon Horovitz

Double mutant cycle (DMC) analyses can provide the interaction energies between amino acids at the interface of protein complexes. Here, the authors determine pairwise interaction energies using high-resolution native mass spectroscopy, offering a straightforward route for the DMC methodology.

09 August 2017 | doi: 10.1038/s41467-017-00285-1
Biophysical chemistry  Thermodynamics 

Annotating pathogenic non-coding variants in genic regions OPEN
Sahar Gelfman, Quanli Wang, K. Melodi McSweeney, Zhong Ren, Francesca La Carpia, Matt Halvorsen, Kelly Schoch, Fanni Ratzon, Erin L. Heinzen, Michael J. Boland, Slavé Petrovski & David B. Goldstein

While non-coding synonymous and intronic variants are often not under strong selective constraint, they can be pathogenic through affecting splicing or transcription. Here, the authors develop a score that uses sequence context alterations to predict pathogenicity of synonymous and non-coding genetic variants, and provide a web server of pre-computed scores.

09 August 2017 | doi: 10.1038/s41467-017-00141-2
Genome informatics  Personalized medicine  Sequence annotation 

Endocrine disruptors induce perturbations in endoplasmic reticulum and mitochondria of human pluripotent stem cell derivatives OPEN
Uthra Rajamani, Andrew R. Gross, Camille Ocampo, Allen M. Andres, Roberta A. Gottlieb & Dhruv Sareen

Harmful chemicals that disrupt the endocrine system and hormone regulation have been associated with obesity. Here the authors apply a human pluripotent stem cell-based platform to study the effects of such compounds on developing gut endocrine and neuroendocrine systems.

09 August 2017 | doi: 10.1038/s41467-017-00254-8
Induced pluripotent stem cells  Metabolic syndrome  Obesity 

Structural and functional insights into the lipopolysaccharide ABC transporter LptB2FG OPEN
Haohao Dong, Zhengyu Zhang, Xiaodi Tang, Neil G. Paterson & Changjiang Dong

Lipopolysaccharides (LPS) are synthesized at the periplasmic side of the inner membrane of Gram-negative bacteria and are then extracted by the LptB2FG complex during the first step of LPS transport to the outer membrane. Here the authors present the LptB2FG structure, which supports an alternating lateral access mechanism for LPS extraction.

09 August 2017 | doi: 10.1038/s41467-017-00273-5
Bacteriology  Membrane structure and assembly  X-ray crystallography 

Activated NK cells cause placental dysfunction and miscarriages in fetal alloimmune thrombocytopenia OPEN
Issaka Yougbaré, Wei-She Tai, Darko Zdravic, Brigitta Elaine Oswald, Sean Lang, Guangheng Zhu, Howard Leong-Poi, Dawei Qu, Lisa Yu, Caroline Dunk, Jianhong Zhang, John G. Sled, Stephen J. Lye, Jelena Brkić, Chun Peng, Petter Höglund, B. Anne Croy, S. Lee Adamson, Xiao-Yan Wen, Duncan J. Stewart et al.

Fetal/neonatal alloimmune thrombocytopenia (FNAIT) is a gestational disease caused by maternal immune responses against fetal platelets. Using a FNAIT mouse model and human trophoblast cell lines, here the authors show that uterine natural killer cell-mediated trophoblast apoptosis contributes to FNAIT pathogenesis.

09 August 2017 | doi: 10.1038/s41467-017-00269-1
Cell death and immune response  Embryology  Innate immunity  NK cells 

Evolution of new regulatory functions on biophysically realistic fitness landscapes OPEN
Tamar Friedlander, Roshan Prizak, Nicholas H. Barton & Gašper Tkačik

Gene networks evolve by transcription factor (TF) duplication and divergence of their binding site specificities, but little is known about the global constraints at play. Here, the authors study the coevolution of TFs and binding sites using a biophysical-evolutionary approach, and show that the emerging complex fitness landscapes strongly influence regulatory evolution with a role for crosstalk.

09 August 2017 | doi: 10.1038/s41467-017-00238-8
Biological physics  Evolutionary theory  Molecular evolution  Regulatory networks 

The non-coding RNA landscape of human hematopoiesis and leukemia OPEN
Adrian Schwarzer, Stephan Emmrich, Franziska Schmidt, Dominik Beck, Michelle Ng, Christina Reimer, Felix Ferdinand Adams, Sarah Grasedieck, Damian Witte, Sebastian Käbler, Jason W. H. Wong, Anushi Shah, Yizhou Huang, Razan Jammal, Aliaksandra Maroz, Mojca Jongen-Lavrencic, Axel Schambach, Florian Kuchenbauer, John E. Pimanda, Dirk Reinhardt et al.

While micro-RNAs are known regulators of haematopoiesis and leukemogenesis, the role of long non-coding RNAs is less clear. Here the authors provide a non-coding RNA expression landscape of the human hematopoietic system, highlighting their role in the formation and maintenance of the human blood hierarchy.

09 August 2017 | doi: 10.1038/s41467-017-00212-4
Acute myeloid leukaemia  Long non-coding RNAs 

A Plasmodium yoelii HECT-like E3 ubiquitin ligase regulates parasite growth and virulence OPEN
Sethu C. Nair, Ruixue Xu, Sittiporn Pattaradilokrat, Jian Wu, Yanwei Qi, Martine Zilversmit, Sundar Ganesan, Vijayaraj Nagarajan, Richard T. Eastman, Marlene S. Orandle, John C. Tan, Timothy G. Myers, Shengfa Liu, Carole A. Long, Jian Li & Xin-zhuan Su

Many strains of Plasmodium differ in virulence, but factors that control these distinctions are not known. Here the authors comparatively map virulence loci using the offspring from a P. yoelii YM and N67 genetic cross, and identify a putative HECT E3 ubiquitin ligase that may explain the variance.

09 August 2017 | doi: 10.1038/s41467-017-00267-3
Malaria  Parasite genetics 

An early mechanical coupling of planktonic bacteria in dilute suspensions OPEN
Simon Sretenovic, Biljana Stojković, Iztok Dogsa, Rok Kostanjšek, Igor Poberaj & David Stopar

Planktonic bacteria are untethered to surfaces or to each other, and thus are expected to move independently when at low cell densities. Here Sretenovic et al. show, using optical tweezers, that bacteria in dilute suspensions are mechanically coupled and show long-range correlated motion.

09 August 2017 | doi: 10.1038/s41467-017-00295-z
Biofilms  Biophysics  Cellular microbiology  Microbial communities 

Living GenoChemetics by hyphenating synthetic biology and synthetic chemistry in vivo OPEN
Sunil V. Sharma, Xiaoxue Tong, Cristina Pubill-Ulldemolins, Christopher Cartmell, Emma J. A. Bogosyan, Emma J. Rackham, Enrico Marelli, Refaat B. Hamed & Rebecca J. M. Goss

Coupling synthetic biology and chemical reactions in cells is a challenging task. The authors engineer bacteria capable of generating bromo-metabolites, develop a mild Suzuki-Miyaura cross-coupling reaction compatible with cell growth and carry out the cross-coupling chemistry in live cell cultures.

09 August 2017 | doi: 10.1038/s41467-017-00194-3
Biocatalysis  Metabolic engineering  Natural products 

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence OPEN
Yun Kit Yeoh, Paul G. Dennis, Chanyarat Paungfoo-Lonhienne, Lui Weber, Richard Brackin, Mark A. Ragan, Susanne Schmidt & Philip Hugenholtz

Yeoh et al. study root microbiomes of different plant phyla across a tropical soil chronosequence. They confirm that soil type is the primary determinant of root-associated bacterial communities, but also observe a clear correlation with plant phylogeny and define a core root microbiome at this site.

09 August 2017 | doi: 10.1038/s41467-017-00262-8
Microbial ecology  Microbiome  Soil microbiology 

Origin of charge transfer and enhanced electron–phonon coupling in single unit-cell FeSe films on SrTiO3  OPEN
Huimin Zhang, Ding Zhang, Xiaowei Lu, Chong Liu, Guanyu Zhou, Xucun Ma, Lili Wang, Peng Jiang, Qi-Kun Xue & Xinhe Bao

The origin of interface charge transfer and electron-phonon coupling in single unit-cell FeSe on SrTiO3 remains elusive. Here, Zhang et al. report strengthened Ti-O bond and band bending at the FeSe/SrTiO3 interface, which leads to several important processes.

09 August 2017 | doi: 10.1038/s41467-017-00281-5
Electronic properties and materials  Superconducting properties and materials  Surfaces, interfaces and thin films 

Single cardiomyocyte nuclear transcriptomes reveal a lincRNA-regulated de-differentiation and cell cycle stress-response in vivo OPEN
Kelvin See, Wilson L. W. Tan, Eng How Lim, Zenia Tiang, Li Ting Lee, Peter Y. Q. Li, Tuan D. A. Luu, Matthew Ackers-Johnson & Roger S. Foo

Adult mammalian cardiomyocytes are predominantly binucleated and unable to divide. Using single nuclear RNA-sequencing of cardiomyocytes from mouse and human failing and non-failing adult hearts, See et al. show that some cardiomyocytes respond to stress by dedifferentiation and cell cycle re-entry regulated by lncRNAs.

09 August 2017 | doi: 10.1038/s41467-017-00319-8
Cardiac regeneration  Cell-cycle exit  Gene expression 

Focal cortical seizures start as standing waves and propagate respecting homotopic connectivity OPEN
L. Federico Rossi, Robert C. Wykes, Dimitri M. Kullmann & Matteo Carandini

Focal cortical seizures result from local and widespread propagation of excitatory activity. Here the authors employ widefield calcium imaging in mouse visual areas to demonstrate that these seizures start as local synchronous activation and then propagate along the connectivity that underlies normal sensory processing.

09 August 2017 | doi: 10.1038/s41467-017-00159-6
Dynamical systems  Epilepsy  Extrastriate cortex 

Plasmonic silver nanoshells for drug and metabolite detection OPEN
Lin Huang, Jingjing Wan, Xiang Wei, Yu Liu, Jingyi Huang, Xuming Sun, Ru Zhang, Deepanjali D. Gurav, Vadanasundari Vedarethinam, Yan Li, Ruoping Chen & Kun Qian

Preparation of samples for diagnosis can affect the detection of biomarkers and metabolites. Here, the authors use a silver nanoparticle plasmonics approach for the detection of biomarkers in patients as well as investigate the distribution of drugs in serum and cerebral spinal fluid.

09 August 2017 | doi: 10.1038/s41467-017-00220-4
Diagnostic markers  Mass spectrometry  Metabolomics  Nanoparticles 

Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling OPEN
Julian Petersen, Shane C. Wright, David Rodríguez, Pierre Matricon, Noa Lahav, Aviv Vromen, Assaf Friedler, Johan Strömqvist, Stefan Wennmalm, Jens Carlsson & Gunnar Schulte

Frizzled 6 (FZD6) is a G protein-coupled receptor (GPCR) involved in several cellular processes. Here, the authors use live cell imaging and spectroscopy to show that FZD6 forms dimers, whose association is regulated by WNT proteins and that dimer dissociation is crucial for FZD6 signaling.

09 August 2017 | doi: 10.1038/s41467-017-00253-9
Cellular imaging  G protein-coupled receptors  Hormone receptors  Membrane structure and assembly 

Single-cell analyses identify bioengineered niches for enhanced maintenance of hematopoietic stem cells OPEN
Aline Roch, Sonja Giger, Mukul Girotra, Vasco Campos, Nicola Vannini, Olaia Naveiras, Samy Gobaa & Matthias P. Lutolf

Haematopoietic stem cell (HSC) self-renewal is not sufficiently understood to recapitulate in vitro. Here, the authors generate gene signature and cell cycle hallmarks of single murine HSCs, and use identified endothelial receptors Esam and JamC as substrates to enhance HSC growth in engineered niches.

09 August 2017 | doi: 10.1038/s41467-017-00291-3
Biomaterials – cells  Haematopoiesis  Stem-cell niche 

Zhamanshin astrobleme provides evidence for carbonaceous chondrite and post-impact exchange between ejecta and Earth’s atmosphere OPEN
Tomáš Magna, Karel Žák, Andreas Pack, Frédéric Moynier, Bérengère Mougel, Stefan Peters, Roman Skála, Šárka Jonášová, Jiří Mizera & Zdeněk Řanda

Identifying the original impactor from craters remains challenging. Here, the authors use chromium and oxygen isotopes to indicate that the Zhamanshin astrobleme impactor was a carbonaceous chrondrite by demonstrating that depleted 17O values are due to exchange with atmospheric oxygen.

09 August 2017 | doi: 10.1038/s41467-017-00192-5
Geochemistry  Meteoritics 

Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer OPEN
Ruli Gao, Charissa Kim, Emi Sei, Theodoros Foukakis, Nicola Crosetto, Leong-Keat Chan, Maithreyan Srinivasan, Hong Zhang, Funda Meric-Bernstam & Nicholas Navin

Single cell RNA sequencing is a powerful tool for understanding cellular diversity but is limited by cost, throughput and sample preparation. Here the authors use nanogrid technology with integrated imaging to sequence thousands of cancer nuclei in parallel from fresh or frozen tissue.

09 August 2017 | doi: 10.1038/s41467-017-00244-w
Cancer genomics  RNA sequencing 

Discovery and ramifications of incidental Magnéli phase generation and release from industrial coal-burning OPEN
Yi Yang, Bo Chen, James Hower, Michael Schindler, Christopher Winkler, Jessica Brandt, Richard Giulio, Jianping Ge, Min Liu, Yuhao Fu, Lijun Zhang, Yuru Chen, Shashank Priya & Michael F. Hochella

Solid-state emissions from coal burning remain an environmental concern. Here, the authors have found that TiO2 minerals present in coal are converted into titanium suboxides during burning, and initial biotoxicity screening suggests that further testing is needed to look into human lung consequences.

08 August 2017 | doi: 10.1038/s41467-017-00276-2
Atmospheric chemistry  Carbon cycle  Environmental impact  Geochemistry 

Gap-state engineering of visible-light-active ferroelectrics for photovoltaic applications OPEN
Hiroki Matsuo, Yuji Noguchi & Masaru Miyayama

Overcoming the optical transparency of wide bandgap of ferroelectric oxides by narrowing its bandgap tends to result in a loss of polarization. By utilizing defect states within the bandgap, Matsuo et al. report visible-light-active ferroelectrics without sacrificing polarization.

08 August 2017 | doi: 10.1038/s41467-017-00245-9
Ferroelectrics and multiferroics  Solar cells 

A pluripotent stem cell-based model for post-implantation human amniotic sac development OPEN
Yue Shao, Kenichiro Taniguchi, Ryan F. Townshend, Toshio Miki, Deborah L. Gumucio & Jianping Fu

Early in human embryonic development, it is unclear how amniotic sac formation is regulated. Here, the authors use a human pluripotent stem cell-based model, termed the post-implantation amniotic sac embryoid, to recapitulate early embryogenic events of human amniotic sac development.

08 August 2017 | doi: 10.1038/s41467-017-00236-w
Biological models  Biomaterials  Embryonic induction  Pluripotent stem cells 

Formation and suppression of acoustic memories during human sleep OPEN
Thomas Andrillon, Daniel Pressnitzer, Damien Léger & Sid Kouider

Though memory and sleep are related, it is still unclear whether new memories can be formed during sleep. Here, authors show that people could learn new sounds during REM or light non-REM sleep, but that learning was suppressed when sounds were played during deep NREM sleep.

08 August 2017 | doi: 10.1038/s41467-017-00071-z
Human behaviour  Perception  Sleep 

Fragmentation in spin ice from magnetic charge injection OPEN
E. Lefrançois, V. Cathelin, E. Lhotel, J. Robert, P. Lejay, C. V. Colin, B. Canals, F. Damay, J. Ollivier, B. Fåk, L. C. Chapon, R. Ballou & V. Simonet

Exploring unconventional magnetism facilities both fundamental understanding of materials and their real applications. Here the authors demonstrate that a magnetic monopole crystal is stabilized by a staggered magnetic field in the pyrochlore iridate Ho2Ir2O7, leading to a fragmented magnetization.

08 August 2017 | doi: 10.1038/s41467-017-00277-1
Magnetic properties and materials 

Structural insights into the mechanism and E2 specificity of the RBR E3 ubiquitin ligase HHARI OPEN
Lingmin Yuan, Zongyang Lv, James H. Atkison & Shaun K. Olsen

HHARI is a RING-in-between-RING (RBR) ubiquitin (Ub) E3 ligase. Here the authors present the crystal structure of HHARI with the UbcH7 ~ Ub thioester intermediate mimetic, which reveals that HHARI binds this E2 ~ Ub in an open conformation and explains the specificity of this cognate RBR E3/E2 pair.

08 August 2017 | doi: 10.1038/s41467-017-00272-6
Enzyme mechanisms  Ubiquitin ligases  Ubiquitylation  X-ray crystallography 

Ensa controls S-phase length by modulating Treslin levels OPEN
Sophie Charrasse, Aicha Gharbi-Ayachi, Andrew Burgess, Jorge Vera, Khaled Hached, Peggy Raynaud, Etienne Schwob, Thierry Lorca & Anna Castro

The Greatwall/Ensa/PP2A-B55 pathway controls mitotic substrate phosphorylation and mitotic entry. Here the authors show that cells regulate S phase duration by controlling the ubiquitin-proteasome degradation of Treslin in a Gwl/Ensa-dependent pathway.

08 August 2017 | doi: 10.1038/s41467-017-00339-4
Origin firing  Ubiquitin ligases 

Gradient light interference microscopy for 3D imaging of unlabeled specimens OPEN
Tan H. Nguyen, Mikhail E. Kandel, Marcello Rubessa, Matthew B. Wheeler & Gabriel Popescu

Challenges in biological imaging include labeling, photobleaching and phototoxicity, as well as light scattering. Here, Nguyen et al. develop a quantitative phase method that uses low-coherence interferometry for label-free 3D imaging in scattering tissue.

08 August 2017 | doi: 10.1038/s41467-017-00190-7
Imaging techniques  Interference microscopy  Optical imaging  Phase-contrast microscopy 

Uncoupling conformational states from activity in an allosteric enzyme OPEN
João P. Pisco, Cesira de Chiara, Kamila J. Pacholarz, Acely Garza-Garcia, Roksana W. Ogrodowicz, Philip A. Walker, Perdita E. Barran, Stephen J. Smerdon & Luiz Pedro S. de Carvalho

Active and inactive state ATP-phosphoribosyltransferases (ATP-PRTs) are believed to have different conformations. Here the authors show that in both states, ATP-PRT has a similar structural arrangement, suggesting that dynamic alterations are involved in ATP-PRT regulation by allosteric modulators.

07 August 2017 | doi: 10.1038/s41467-017-00224-0
Enzymes  Screening  Transferases  X-ray crystallography 

In situ atomic-scale observation of oxygen-driven core-shell formation in Pt3Co nanoparticles OPEN
Sheng Dai, Yuan You, Shuyi Zhang, Wei Cai, Mingjie Xu, Lin Xie, Ruqian Wu, George W. Graham & Xiaoqing Pan

Core-shell platinum alloy nanoparticles are promising catalysts for oxygen reduction, however a deeper understanding of core-shell formation is still required. Here the authors report oxygen-driven formation of core-shell Pt3Co nanoparticles, seen at the atomic scale with in situ electron microscopy at ambient pressure.

07 August 2017 | doi: 10.1038/s41467-017-00161-y
Characterization and analytical techniques  Fuel cells  Nanoparticles 

Dynamically induced robust phonon transport and chiral cooling in an optomechanical system OPEN
Seunghwi Kim, Xunnong Xu, Jacob M. Taylor & Gaurav Bahl

Chiral transport can provide robustness against disorder, resulting in improved resonant modes for sensing and metrology. Here, Kim et al. demonstrate chiral phonon transport, disorder suppression and anomalous cooling without damping in an asymmetrically-pumped optomechanical system.

07 August 2017 | doi: 10.1038/s41467-017-00247-7
Optical physics  Optomechanics  Photoacoustics 

Therapeutic radiation for childhood cancer drives structural aberrations of NF2 in meningiomas OPEN
Sameer Agnihotri, Suganth Suppiah, Peter D. Tonge, Shahrzad Jalali, Arnavaz Danesh, Jeffery P. Bruce, Yasin Mamatjan, George Klironomos, Lior Gonen, Karolyn Au, Sheila Mansouri, Sharin Karimi, Felix Sahm, Andreas Deimling, Michael D. Taylor, Normand J. Laperriere, Trevor J. Pugh, Kenneth D. Aldape & Gelareh Zadeh

Radiation-induced meningiomas are often more aggressive than sporadic ones. In this study, the authors perform an exome, methylation and RNA-seq analysis of 31 cases of radiation-induced meningioma and show NF2 rearrangement, an observation previously unreported in the sporadic tumors.

04 August 2017 | doi: 10.1038/s41467-017-00174-7
Cancer  Genetics 

Long-range transport of airborne microbes over the global tropical and subtropical ocean OPEN
Eva Mayol, Jesús M. Arrieta, Maria A. Jiménez, Adrián Martínez-Asensio, Neus Garcias-Bonet, Jordi Dachs, Belén González-Gaya, Sarah-J. Royer, Verónica M. Benítez-Barrios, Eugenio Fraile-Nuez & Carlos M. Duarte

The extent to which the ocean acts as a sink and source of airborne particles to the atmosphere is unresolved. Here, the authors report high microbial loads over the tropical Atlantic, Pacific and Indian oceans and propose islands as stepping stones for the transoceanic transport of terrestrial microbes..

04 August 2017 | doi: 10.1038/s41467-017-00110-9
Air microbiology  Biodiversity  Marine biology  Marine microbiology  Microbial ecology 

Ex vivo pretreatment of human vessels with siRNA nanoparticles provides protein silencing in endothelial cells OPEN
Jiajia Cui, Lingfeng Qin, Junwei Zhang, Parwiz Abrahimi, Hong Li, Guangxin Li, Gregory T. Tietjen, George Tellides, Jordan S. Pober & W. Mark Saltzman

The use of gene silencing techniques in the treatment of post-transplantation host rejection is not long lasting and can have systemic effects. Here, the authors utilize a nanocarrier for siRNA for treatment of arteries ex vivo prior to implantation subsequently attenuating immune reaction in vivo.

04 August 2017 | doi: 10.1038/s41467-017-00297-x
Allotransplantation  Nanoparticles 

HIPP neurons in the dentate gyrus mediate the cholinergic modulation of background context memory salience OPEN
Syed Ahsan Raza, Anne Albrecht, Gürsel Çalışkan, Bettina Müller, Yunus Emre Demiray, Susann Ludewig, Susanne Meis, Nicolai Faber, Roland Hartig, Burkhart Schraven, Volkmar Lessmann, Herbert Schwegler & Oliver Stork

Intra-hippocampal circuits are essential for associating a background context with behaviorally salient stimuli and involve cholinergic modulation at SST+ interneurons. Here the authors show that the salience of the background context memory is modulated through muscarinic activation of NPY+ hilar perforant path associated interneurons and NPY signaling in the dentate gyrus.

04 August 2017 | doi: 10.1038/s41467-017-00205-3
Fear conditioning  Hippocampus  Neural circuits  Post-traumatic stress disorder 

Molecular characterization of breast cancer CTCs associated with brain metastasis OPEN
Debasish Boral, Monika Vishnoi, Haowen N. Liu, Wei Yin, Marc L. Sprouse, Antonio Scamardo, David S. Hong, Tuan Z. Tan, Jean P. Thiery, Jenny C. Chang & Dario Marchetti

Characterization of CTCs derived from breast cancer patients with brain metastasis (BCBM) may allow for early diagnosis of brain metastasis and/or help for treatment choice and its efficacy. In this study, the authors identify a unique signature, based on patient-derived CTCs transcriptomes, for BCBM- CTCs that is different from primary tumors.

04 August 2017 | doi: 10.1038/s41467-017-00196-1
Breast cancer  Metastasis 

Modulation of the tick gut milieu by a secreted tick protein favors Borrelia burgdorferi colonization OPEN
Sukanya Narasimhan, Tim J. Schuijt, Nabil M. Abraham, Nallakkandi Rajeevan, Jeroen Coumou, Morven Graham, Andrew Robson, Ming-Jie Wu, Sirlei Daffre, Joppe W. Hovius & Erol Fikrig

Borrelia burgdorferi, the causative agent of Lyme disease, is transmitted by the tick Ixodes scapularis. Here, the authors show that a tick secreted protein (PIXR) modulates the tick gut microbiota and facilitates B. burgdorferi colonization.

04 August 2017 | doi: 10.1038/s41467-017-00208-0
Antimicrobial responses  Microbiome  Pathogens  Zoology 

Oscillatory vapour shielding of liquid metal walls in nuclear fusion devices OPEN
G. G. Eden, V. Kvon, M. C. M. Sanden & T. W. Morgan

Vapour shielding is one of the interesting mechanisms for reducing the heat load to plasma facing components in fusion reactors. Here the authors report on the observation of a dynamic equilibrium between the plasma and the divertor liquid Sn surface leading to an overall stable surface temperature.

04 August 2017 | doi: 10.1038/s41467-017-00288-y
Magnetically confined plasmas  Metals and alloys  Nuclear fusion and fission 

53-attosecond X-ray pulses reach the carbon K-edge OPEN
Jie Li, Xiaoming Ren, Yanchun Yin, Kun Zhao, Andrew Chew, Yan Cheng, Eric Cunningham, Yang Wang, Shuyuan Hu, Yi Wu, Michael Chini & Zenghu Chang

Isolated attosecond pulses are produced using high harmonic generation and sources of these pulses often suffer from low photon flux in soft X-ray regime. Here the authors demonstrate efficient generation and characterization of 53 as pulses with photon energy near the water window.

04 August 2017 | doi: 10.1038/s41467-017-00321-0
High-harmonic generation  X-rays 

Structural basis of Notch O-glucosylation and O–xylosylation by mammalian protein–O-glucosyltransferase 1 (POGLUT1) OPEN
Zhijie Li, Michael Fischer, Malathy Satkunarajah, Dongxia Zhou, Stephen G. Withers & James M. Rini

POGLUT1 is a protein-O-glucosyltransferase that transfers glucose and xylose to the EGF-like domains of Notch and other signaling receptors. Here the authors report the structure of human POGLUT1 in complexes with 3 different EGF-like domains and donor substrates and shed light on the enzyme’s substrate specificity and catalytic mechanism

04 August 2017 | doi: 10.1038/s41467-017-00255-7
Enzyme mechanisms  Glycobiology  X-ray crystallography 

CLICs-dependent chloride efflux is an essential and proximal upstream event for NLRP3 inflammasome activation OPEN
Tiantian Tang, Xueting Lang, Congfei Xu, Xiaqiong Wang, Tao Gong, Yanqing Yang, Jun Cui, Li Bai, Jun Wang, Wei Jiang & Rongbin Zhou

The NLRP3 inflammasome is key to the regulation of innate immunity against pathogens or stress, but the underlying signaling regulation is still unclear. Here the authors show that chloride intracellular channels (CLIC) interface between mitochondria stress and inflammasome activation to modulate inflammatory responses.

04 August 2017 | doi: 10.1038/s41467-017-00227-x
Inflammasome  Monocytes and macrophages  NOD-like receptors  Signal transduction 

Retrograde BDNF to TrkB signaling promotes synapse elimination in the developing cerebellum OPEN
Myeongjeong Choo, Taisuke Miyazaki, Maya Yamazaki, Meiko Kawamura, Takanobu Nakazawa, Jianling Zhang, Asami Tanimura, Naofumi Uesaka, Masahiko Watanabe, Kenji Sakimura & Masanobu Kano

During development, synapses are selectively strengthened or eliminated by activity-dependent competition. Here, the authors show that BDNF-TrkB retrograde signaling is a “punishment” signal that leads to elimination of climbing fiber-onto-Purkinje cell synapses in the developing cerebellum.

04 August 2017 | doi: 10.1038/s41467-017-00260-w
Neural circuits  Neurotrophic factors  Synaptic development 

Broadband achromatic optical metasurface devices OPEN
Shuming Wang, Pin Chieh Wu, Vin-Cent Su, Yi-Chieh Lai, Cheng Hung Chu, Jia-Wern Chen, Shen-Hung Lu, Ji Chen, Beibei Xu, Chieh-Hsiung Kuan, Tao Li, Shining Zhu & Din Ping Tsai

Metasurfaces suffer from large chromatic aberration due to the high phase dispersion of their building blocks, limiting their applications. Here, Wang et al. design achromatic metasurface devices which eliminate the chromatic aberration over a continuous region from 1200 to 1680 nm in a reflection schleme.

04 August 2017 | doi: 10.1038/s41467-017-00166-7
Metamaterials  Nanophotonics and plasmonics  Sub-wavelength optics 

Rationalizing the light-induced phase separation of mixed halide organic–inorganic perovskites OPEN
Sergiu Draguta, Onise Sharia, Seog Joon Yoon, Michael C. Brennan, Yurii V. Morozov, Joseph M. Manser, Prashant V. Kamat, William F. Schneider & Masaru Kuno

Mixed halide hybrid perovskites possess tunable band gaps, however, under illumination they undergo phase separation. Using spectroscopic measurements and theoretical modelling, Draguta and Sharia et al. quantitatively rationalize the microscopic processes that occur during phase separation.

04 August 2017 | doi: 10.1038/s41467-017-00284-2
Energy  Solar cells 

Pan-urologic cancer genomic subtypes that transcend tissue of origin OPEN
Fengju Chen, Yiqun Zhang, Dominick Bossé, Aly-Khan A. Lalani, A. Ari Hakimi, James J. Hsieh, Toni K. Choueiri, Don L. Gibbons, Michael Ittmann & Chad J. Creighton

Urological cancers have disparate tissues and cells of origin but share many molecular features. Here, the authors use multidimensional and comprehensive molecular characterization to classify urological cancers into nine major genomic subtypes, highlighting potential therapeutic targets.

04 August 2017 | doi: 10.1038/s41467-017-00289-x
Cancer genomics  Urological cancer 

Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures OPEN
Faiz M. Khan, Stephan Marquardt, Shailendra K. Gupta, Susanne Knoll, Ulf Schmitz, Alf Spitschak, David Engelmann, Julio Vera, Olaf Wolkenhauer & Brigitte M. Pützer

Deregulation of E2F family transcription factors is associated with cancer progression and metastasis. Here, the authors construct a map of the regulatory network around the E2F family, and using gene expression profiles, identify tumour type-specific regulatory cores and receptor expression signatures associated with epithelial-mesenchymal transition in bladder and breast cancer.

04 August 2017 | doi: 10.1038/s41467-017-00268-2
Cellular signalling networks  Computational models  Tumour biomarkers 

Mechanistic and structural basis for activation of cardiac myosin force production by omecamtiv mecarbil OPEN
Vicente J. Planelles-Herrero, James J. Hartman, Julien Robert-Paganin, Fady I. Malik & Anne Houdusse

Omecamtiv mecarbil (OM) is a cardiac myosin activator that is currently in clinical trials for heart failure treatment. Here, the authors give insights into its mode of action and present the crystal structure of OM bound to bovine cardiac myosin, which shows that OM stabilizes the pre-powerstroke state of myosin.

04 August 2017 | doi: 10.1038/s41467-017-00176-5
Drug discovery  X-ray crystallography 

Onion-like multilayered polymer capsules synthesized by a bioinspired inside-out technique OPEN
Brady C. Zarket & Srinivasa R. Raghavan

Multiple concentric layers are present in a variety of structures present in nature, including the onion. Here, the authors show an inside-out strategy to synthesize multilayered polymer capsules, with different layers having specific composition and thereby specific responses to stimuli such as pH and temperature.

04 August 2017 | doi: 10.1038/s41467-017-00077-7
Gels and hydrogels  Polymers 

Electromagnetic reprogrammable coding-metasurface holograms OPEN
Lianlin Li, Tie Jun Cui, Wei Ji, Shuo Liu, Jun Ding, Xiang Wan, Yun Bo Li, Menghua Jiang, Cheng-Wei Qiu & Shuang Zhang

Realizing metasurfaces with reconfigurability, high efficiency, and control over phase and amplitude is a challenge. Here, Li et al. introduce a reprogrammable hologram based on a 1-bit coding metasurface, where the state of each unit cell of the coding metasurface can be switched electrically.

04 August 2017 | doi: 10.1038/s41467-017-00164-9
Electrical and electronic engineering  Metamaterials  Microwave photonics 

Solution nuclear magnetic resonance spectroscopy on a nanostructured diamond chip OPEN
P. Kehayias, A. Jarmola, N. Mosavian, I. Fescenko, F. M. Benito, A. Laraoui, J. Smits, L. Bougas, D. Budker, A. Neumann, S. R. J. Brueck & V. M. Acosta

Nitrogen vacancy (NV) centres in diamond can be used for NMR spectroscopy, but increased sensitivity is needed to avoid long measurement times. Kehayias et al. present a nanostructured diamond grating with a high density of NV centres, enabling NMR spectroscopy of picoliter-volume solutions.

04 August 2017 | doi: 10.1038/s41467-017-00266-4
Optical properties of diamond  Solution-state NMR 

A Solar cycle correlation of coronal element abundances in Sun-as-a-star observations OPEN
David H. Brooks, Deborah Baker, Lidia van Driel-Gesztelyi & Harry P. Warren

The Sun’s elemental composition is a vital part of understanding the processes that transport energy from the interior to the outer atmosphere. Here, the authors show that if the Sun is observed as a star, then the variation of coronal composition is highly correlated with the F10.7cm radio flux.

03 August 2017 | doi: 10.1038/s41467-017-00328-7
Solar physics  Stars 

Identification and characterization of a novel botulinum neurotoxin OPEN
Sicai Zhang, Geoffrey Masuyer, Jie Zhang, Yi Shen, Daniel Lundin, Linda Henriksson, Shin-Ichiro Miyashita, Markel Martínez-Carranza, Min Dong & Pål Stenmark

There are seven well-established types of Botulinum neurotoxins (BoNTs). Here the authors report the identification and characterization of a new type of BoNT—BoNT/X—which cleaves a different site on canonical BoNTs substrates and targets SNARE family members not cleaved by known BoNTs.

03 August 2017 | doi: 10.1038/ncomms14130
Cellular microbiology  Pathogens  SNARE 

A promising high-energy-density material OPEN
Wenquan Zhang, Jiaheng Zhang, Mucong Deng, Xiujuan Qi, Fude Nie & Qinghua Zhang

High energy density materials are of interest, but density is the limiting factor for many organic compounds. Here the authors show the formation of a high density energetic compound from a two-step reaction between commercially available compounds that exhibit good heat thermal stability and detonation properties.

03 August 2017 | doi: 10.1038/s41467-017-00286-0
Materials chemistry  Organic chemistry 

Increased mitochondrial fusion allows the survival of older animals in diverse C. elegans longevity pathways OPEN
Snehal N. Chaudhari & Edward T. Kipreos

Mitochondria can undergo shape changes as a result of fusion and fission events. Here the authors describe how insulin signalling regulates mitochondrial fusion in C. elegans, and show that mitochondrial fusion is necessary, but not sufficient, for longevity of worms with mutations that increase lifespan.

03 August 2017 | doi: 10.1038/s41467-017-00274-4
Ageing  Caenorhabditis elegans  Mitochondria 
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Corrigendum: Allelic variation contributes to bacterial host specificity OPEN
Min Yue, Xiangan Han, Leon De Masi, Chunhong Zhu, Xun Ma, Junjie Zhang, Renwei Wu, Robert Schmieder, Radhey S. Kaushik, George P. Fraser, Shaohua Zhao, Patrick F. McDermott, François-Xavier Weill, Jacques G. Mainil, Cesar Arze, W. Florian Fricke, Robert A. Edwards, Dustin Brisson, Nancy R. Zhang, Shelley C. Rankin et al.
08 August 2017 | doi: 10.1038/ncomms15229
Bacterial genetics  Bacterial physiology  Genetic variation 
Corrigendum: Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability OPEN
Susan E. Tsutakawa, Mark J. Thompson, Andrew S. Arvai, Alexander J. Neil, Steven J. Shaw, Sana I. Algasaier, Jane C. Kim, L. David Finger, Emma Jardine, Victoria J. B. Gotham, Altaf H. Sarker, Mai Z. Her, Fahad Rashid, Samir M. Hamdan, Sergei M. Mirkin, Jane A. Grasby & John A. Tainer
07 August 2017 | doi: 10.1038/ncomms16145
DNA  Enzyme mechanisms  Genomic instability  X-ray crystallography 
Corrigendum: A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization OPEN
Jasper H. M. van der Velde, Jens Oelerich, Jingyi Huang, Jochem H. Smit, Atieh Aminian Jazi, Silvia Galiani, Kirill Kolmakov, Giorgos Gouridis, Christian Eggeling, Andreas Herrmann, Gerard Roelfes & Thorben Cordes
04 August 2017 | doi: 10.1038/ncomms16144
Biophysical chemistry  Organic chemistry 
  Latest ERRATA  
Erratum: YAP determines the cell fate of injured mouse hepatocytes in vivo OPEN
Norio Miyamura, Shoji Hata, Tohru Itoh, Minoru Tanaka, Miki Nishio, Michiko Itoh, Yoshihiro Ogawa, Shuji Terai, Isao Sakaida, Akira Suzuki, Atsushi Miyajima & Hiroshi Nishina
07 August 2017 | doi: 10.1038/ncomms16146
Stress signalling 

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