Wednesday, January 31, 2018

Nature Communications - 31 January 2018

Nature Communications

Nature Collection: 2017 Nobel Prize in Chemistry 

Nature Research present this Collection of articles celebrating the 2017 Nobel Prize in Chemistry to Jacques Dubochet, Joachim Frank and Richard Henderson, recognised "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution". 

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31 January 2018 
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Speeding up the sequencing
In the age of genomic big data, the worlds of medicine and IT are rapidly colliding.

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Poster on: The expanding CRISPR toolbox

The CRISPR-Cas9 system can do a lot more than gene editing. This Poster, from Nature Methods, explores the newest possibilities of CRISPR. 

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Springer Nature presents a custom webcast on: Untangling Neurodegenerative Diseases using Cryo-Electron Microscopy
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Engineering yeast for the production of breviscapine by genomic analysis and synthetic biology approaches OPEN
Xiaonan Liu, Jian Cheng, Guanghui Zhang, Wentao Ding, Lijin Duan, Jing Yang, Ling Kui, Xiaozhi Cheng, Jiangxing Ruan, Wei Fan, Junwen Chen, Guangqiang Long, Yan Zhao, Jing Cai, Wen Wang, Yanhe Ma, Yang Dong, Shengchao Yang & Huifeng Jiang

Breviscapine is the flavonoid extract from medical plant Erigeron breviscapus for the treatment of cardio- and cerebrovascular disease. Here, the authors identify the key enzymes of the biosynthetic pathway from the plant genome and engineer yeast to produce breviscapine from glucose.

31 January 2018 | doi: 10.1038/s41467-018-02883-z
Metabolic engineering  Metabolic pathways  Synthetic biology 

Directing lateral growth of lithium dendrites in micro-compartmented anode arrays for safe lithium metal batteries OPEN
Peichao Zou, Yang Wang, Sum-Wai Chiang, Xuanyu Wang, Feiyu Kang & Cheng Yang

The formation of lithium dendrites remains a great challenge to lithium metal batteries. Here the authors show an anode design to laterally direct the dendrite growth inside the compartments, providing a feasible post-mortem solution to batteries with lithium dendrites already present.

31 January 2018 | doi: 10.1038/s41467-018-02888-8
Batteries  Surface patterning 

IL-6 receptor blockade corrects defects of XIAP-deficient regulatory T cells OPEN
Wan-Chen Hsieh, Tzu-Sheng Hsu, Ya-Jen Chang & Ming-Zong Lai

XLP-2 syndrome is caused by XIAP mutation. Here the authors show that mouse and human XIAP-deficient regulatory T cells have defective suppressive function as a result of conversion to proinflammatory cytokine producing cells, an effect that can be prevented by blocking the IL-6 receptor.

31 January 2018 | doi: 10.1038/s41467-018-02862-4
Chronic inflammation  Immunoproliferative disorders  Regulatory T cells 

Integrated circuits based on conjugated polymer monolayer OPEN
Mengmeng Li, Deepthi Kamath Mangalore, Jingbo Zhao, Joshua H. Carpenter, Hongping Yan, Harald Ade, He Yan, Klaus Müllen, Paul W. M. Blom, Wojciech Pisula, Dago M. de Leeuw & Kamal Asadi

Polymer monolayer field-effect transistors hold promise for faster circuits, but their performance is currently limited by the polymer packing disorder. Li et al. pre-aggregate polymers in a solution to achieve high carrier mobility of 3 cm2 V−1s−1 in monolayers and utilize them in integrated circuits.

31 January 2018 | doi: 10.1038/s41467-017-02805-5
Electronic and spintronic devices  Electronic devices 

Liquid crystal elastomer coatings with programmed response of surface profile OPEN
Greta Babakhanova, Taras Turiv, Yubing Guo, Matthew Hendrikx, Qi-Huo Wei, Albert P. H. J. Schenning, Dirk J. Broer & Oleg D. Lavrentovich

Liquid crystal elastomers are anisotropic rubbers which can be actuated by an external trigger. Here the authors develop elastomer coatings with pre-patterned molecular orientation that induces deterministic topography changes in response to changes in temperature.

31 January 2018 | doi: 10.1038/s41467-018-02895-9
Liquid crystals  Polymers 

Improved security bound for the round-robin-differential-phase-shift quantum key distribution OPEN
Zhen-Qiang Yin, Shuang Wang, Wei Chen, Yun-Guang Han, Rong Wang, Guang-Can Guo & Zheng-Fu Han

Round-robin differential phase shift QKD protocol offers unique advantages, but typically requires long trains of pulses to encode information. Here, the authors provide an improved security bound which allows operation in the more practical regime of few-pulse trains.

31 January 2018 | doi: 10.1038/s41467-017-02211-x
Fibre optics and optical communications  Quantum information  Single photons and quantum effects 

A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions OPEN
Li He, Wenwu Wu, Gaurav Zinta, Lan Yang, Dong Wang, Renyi Liu, Huiming Zhang, Zhimin Zheng, Huan Huang, Qingzhu Zhang & Jian-Kang Zhu

Epigenetic variation underlies various aspects of phenotypic diversity of plants. Here, He et al show a naturally occurring epiallele controls Arabidopsis leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE (PPH), and is associated with local climate adaptation.

31 January 2018 | doi: 10.1038/s41467-018-02839-3
DNA methylation  Natural variation in plants 

Cellular stressors contribute to the expansion of hematopoietic clones of varying leukemic potential OPEN
Terrence N. Wong, Christopher A. Miller, Matthew R. M. Jotte, Nusayba Bagegni, Jack D. Baty, Amy P. Schmidt, Amanda F. Cashen, Eric J. Duncavage, Nichole M. Helton, Mark Fiala, Robert S. Fulton, Sharon E. Heath, Megan Janke, Kierstin Luber, Peter Westervelt, Ravi Vij, John F. DiPersio, John S. Welch, Timothy A. Graubert, Matthew J. Walter et al.

Cellular stressors can impact clonal hematopoiesis. Here, the authors explore the impact of cytotoxic therapy and hematopoietic transplantation on clonal expansion, suggesting different stressors can promote expansion of distinct long-lived clones.

31 January 2018 | doi: 10.1038/s41467-018-02858-0
Acute myeloid leukaemia  Cancer genomics  Myelodysplastic syndrome  Next-generation sequencing 

Nucleotide resolution mapping of influenza A virus nucleoprotein-RNA interactions reveals RNA features required for replication OPEN
Graham D. Williams, Dana Townsend, Kristine M. Wylie, Preston J. Kim, Gaya K. Amarasinghe, Sebla B. Kutluay & Adrianus C. M. Boon

Influenza A virus packaging depends on interactions between nucleoprotein (NP) and viral RNA (vRNA), but the pattern of NP binding is unclear. Using PAR-CLIP, Williams et al. here show that NP binds vRNA non-uniformly and that RNA structures in low-NP binding regions are important for packaging.

31 January 2018 | doi: 10.1038/s41467-018-02886-w
Influenza virus  Next-generation sequencing 

Joint coding of shape and blur in area V4 OPEN
Timothy D. Oleskiw, Amy Nowack & Anitha Pasupathy

Blurred edges of objects can aid in depth perception and segmentation, yet how it is combined with shape information in the visual pathway is unknown. Here the authors report that neurons in higher visual area V4 represent both object shape and boundary blur, controlling for stimulus size, intensity and curvature.

31 January 2018 | doi: 10.1038/s41467-017-02438-8
Extrastriate cortex  Object vision 

Adenoviral vector with shield and adapter increases tumor specificity and escapes liver and immune control OPEN
Markus Schmid, Patrick Ernst, Annemarie Honegger, Maarit Suomalainen, Martina Zimmermann, Lukas Braun, Sarah Stauffer, Cristian Thom, Birgit Dreier, Matthias Eibauer, Anja Kipar, Viola Vogel, Urs F. Greber, Ohad Medalia & Andreas Plückthun

Viral gene therapy can be limited by the efficacy of virion sequestration, immune responses and the silencing of genetic payloads. Here the authors engineer an advenovirus protein coat which shields the virion from the immune system while targeting cancer cells.

31 January 2018 | doi: 10.1038/s41467-017-02707-6
Cryoelectron microscopy  Genetic vectors  Targeted therapies  Viral proteins 

A-to-I miR-378a-3p editing can prevent melanoma progression via regulation of PARVA expression OPEN
Guermarie Velazquez-Torres, Einav Shoshan, Cristina Ivan, Li Huang, Enrique Fuentes-Mattei, Harrison Paret, Sun Jin Kim, Cristian Rodriguez-Aguayo, Victoria Xie, Denise Brooks, Steven J. M. Jones, A. Gordon Robertson, George Calin, Gabriel Lopez-Berenstein, Anil Sood & Menashe Bar-Eli

In melanoma, reduced ADAR1 impairs A-to-I microRNA editing. Here, the authors show that miR-378a-3p undergoes this editing in non-metastatic cells and the edited form of miR-378a-3p binds to the PARVA oncogene, inhibiting its expression and preventing melanoma progression and metastasis.

31 January 2018 | doi: 10.1038/s41467-018-02851-7
Cancer epigenetics  Mechanisms of disease  Melanoma  Metastasis 

Platinum-bearing chromite layers are caused by pressure reduction during magma ascent OPEN
Rais Latypov, Gelu Costin, Sofya Chistyakova, Emma J. Hunt, Ria Mukherjee & Tony Naldrett

Some basaltic melts become first superheated upon their ascent towards the Earth’s surface and then saturated in chromite alone after cooling in shallow chambers. Here the authors show that large volumes of these chromite-only-saturated melts are responsible for monomineralic layers of massive chromitites in layered intrusions.

31 January 2018 | doi: 10.1038/s41467-017-02773-w
Geochemistry  Petrology 

DNA-assisted swarm control in a biomolecular motor system OPEN
Jakia Jannat Keya, Ryuhei Suzuki, Arif Md. Rashedul Kabir, Daisuke Inoue, Hiroyuki Asanuma, Kazuki Sada, Henry Hess, Akinori Kuzuya & Akira Kakugo

Self-propelled molecular entities enable studying swarm behavior on a macroscopic scale but programmability of interactions has yet not been achieved. Here the authors show reversible regulation of DNA-functionalized microtubules by DNA signals and switching between solitary and swarm behaviour by employing photoresponsive DNA strands.

31 January 2018 | doi: 10.1038/s41467-017-02778-5
DNA nanostructures  Nanoscale biophysics  Organizing materials with DNA 

Hexokinase-2 depletion inhibits glycolysis and induces oxidative phosphorylation in hepatocellular carcinoma and sensitizes to metformin OPEN
Dannielle DeWaal, Veronique Nogueira, Alexander R. Terry, Krushna C. Patra, Sang-Min Jeon, Grace Guzman, Jennifer Au, Christopher P. Long, Maciek R. Antoniewicz & Nissim Hay

Hexokinase 2 (HK2) is selectively upregulated in hepatocellular carcinoma (HCC). Here the authors show that HK2 ablation decreases glycolysis and triggers oxidative phosphorylation (OXPHO) rendering HCC more susceptible to the OXPHO inhibitor metformin and to the FDA-approved drug sorafenib.

31 January 2018 | doi: 10.1038/s41467-017-02733-4
Cancer metabolism  Hepatocellular carcinoma  Molecular biology 

A peculiar low-luminosity short gamma-ray burst from a double neutron star merger progenitor OPEN
B.-B. Zhang, B. Zhang, H. Sun, W.-H. Lei, H. Gao, Y. Li, L. Shao, Y. Zhao, Y.-D. Hu, H.-J. Lü, X.-F. Wu, X.-L. Fan, G. Wang, A. J. Castro-Tirado, S. Zhang, B.-Y. Yu, Y.-Y. Cao & E.-W. Liang

A short-duration gamma-ray burst was detected along with a double neutron start merger gravitational wave by LIGO-Virgo on August 17th 2017. Here, the authors show that the fluence and spectral peak energy of this event fall into the lower portion of the distribution of known short-duration gamma-ray bursts.

31 January 2018 | doi: 10.1038/s41467-018-02847-3
High-energy astrophysics  Stars 

Overcoming mcr-1 mediated colistin resistance with colistin in combination with other antibiotics OPEN
Craig R. MacNair, Jonathan M. Stokes, Lindsey A. Carfrae, Aline A. Fiebig-Comyn, Brian K. Coombes, Michael R. Mulvey & Eric D. Brown

The plasmid-borne mcr-1 gene confers resistance to the antibiotic colistin. Here, MacNair et al. show that mcr-1 positive bacteria are however susceptible to colistin-mediated disruption of the outer membrane, and can be killed in vitro and in vivo by combining colistin with other antibiotics.

31 January 2018 | doi: 10.1038/s41467-018-02875-z
Antibiotics  Target validation 

Continental shelves as a variable but increasing global sink for atmospheric carbon dioxide OPEN
Goulven G. Laruelle, Wei-Jun Cai, Xinping Hu, Nicolas Gruber, Fred T. Mackenzie & Pierre Regnier

It remains unclear whether surface water partial pressure of CO2 (pCO2) in continental shelves tracks with increasing atmospheric pCO2. Here, the authors show that pCO2 in shelf waters lags behind rising atmospheric CO2 in a number of shelf regions, suggesting shelf uptake of atmospheric CO2.

31 January 2018 | doi: 10.1038/s41467-017-02738-z
Carbon cycle  Marine chemistry 

Practical device-independent quantum cryptography via entropy accumulation OPEN
Rotem Arnon-Friedman, Frédéric Dupuis, Omar Fawzi, Renato Renner & Thomas Vidick

The security of DIQKD is difficult to prove, as one needs to take into account every possible attack strategy. Here, the authors develop a method to determine the entropy of a system as the sum of the entropies of its parts. Applied to DIQKD, this implies that it suffices to consider i.i.d. attacks.

31 January 2018 | doi: 10.1038/s41467-017-02307-4
Computer science  Information theory and computation  Quantum information 

Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase OPEN
Ana S. Ramírez, Jérémy Boilevin, Ahmad Reza Mehdipour, Gerhard Hummer, Tamis Darbre, Jean-Louis Reymond & Kaspar P. Locher

The glycosyltransferase PglH transfers three terminal N-acetylgalactosamine (GalNAc) residues to a carrier, which is a prerequisite for bacterial protein N-glycosylation. Here authors present the crystal structures of PglH in three distinct states and show that a ‘ruler helix’ facilitates membrane attachment and glycan counting.

31 January 2018 | doi: 10.1038/s41467-018-02880-2
Carbohydrates  X-ray crystallography 

Control of cell morphology and differentiation by substrates with independently tunable elasticity and viscous dissipation OPEN
Elisabeth E. Charrier, Katarzyna Pogoda, Rebecca G. Wells & Paul A. Janmey

Purely elastic biomimetic soft materials are used to characterize the mechanical response of cells, but do not resemble real tissues. Here the authors develop a viscoelastic solid hydrogel, based on polyacrylamide, that can be tuned to closely resemble soft tissue, and show the influence of viscous dissipation on cellular mechanical sensing.

31 January 2018 | doi: 10.1038/s41467-018-02906-9
Bioinspired materials  Extracellular matrix  Focal adhesion 

Anderson light localization in biological nanostructures of native silk OPEN
Seung Ho Choi, Seong-Wan Kim, Zahyun Ku, Michelle A. Visbal-Onufrak, Seong-Ryul Kim, Kwang-Ho Choi, Hakseok Ko, Wonshik Choi, Augustine M. Urbas, Tae-Won Goo & Young L. Kim

Light in biological media is known as freely diffusing because interference is negligible. Here, the authors demonstrate Anderson localization of light from quasi-two-dimensional nanostructures in silk fibres.

31 January 2018 | doi: 10.1038/s41467-017-02500-5
Biomaterials  Nanoscience and technology  Photonic devices  Renewable energy 

HTLV-1 Tax plugs and freezes UPF1 helicase leading to nonsense-mediated mRNA decay inhibition OPEN
Francesca Fiorini, Jean-Philippe Robin, Joanne Kanaan, Malgorzata Borowiak, Vincent Croquette, Hervé Le Hir, Pierre Jalinot & Vincent Mocquet

UPF1 is a central protein in nonsense-mediated mRNA decay (NMD), but contribution of its RNA processivity to NMD is unclear. Here, the authors show how the retroviral Tax protein interacts with and inhibits UPF1, and demonstrate that UPF1’s translocase activity contributes to NMD.

30 January 2018 | doi: 10.1038/s41467-017-02793-6
Enzyme mechanisms  Retrovirus  RNA decay 

Single-cell replication profiling to measure stochastic variation in mammalian replication timing OPEN
Vishnu Dileep & David M. Gilbert

While DNA replication is temporally regulated during S-phase, variation in replication timing is not well understood. Here, the authors measure variation in replication timing using DNA copy number in single mouse ESCs and find stochastic variation to be independent of elements that regulate timing.

30 January 2018 | doi: 10.1038/s41467-017-02800-w
Chromatin structure  DNA replication 

Cardiogenic programming of human pluripotent stem cells by dose-controlled activation of EOMES OPEN
Martin J. Pfeiffer, Roberto Quaranta, Ilaria Piccini, Jakob Fell, Jyoti Rao, Albrecht Röpke, Guiscard Seebohm & Boris Greber

The T-box transcription factor eomesodermin (EOMES) acts both in endoderm specification as well as heart development, suggesting context-specific function. Here, the authors show that dose-controlled EOMES induction is sufficient for cardiogenic programming of human pluripotent stem cells.

30 January 2018 | doi: 10.1038/s41467-017-02812-6
Heart development  Reprogramming  Stem-cell differentiation 

Activated CD8+ T cell extracellular vesicles prevent tumour progression by targeting of lesional mesenchymal cells OPEN
Naohiro Seo, Yoshitaka Shirakura, Yoshiro Tahara, Fumiyasu Momose, Naozumi Harada, Hiroaki Ikeda, Kazunari Akiyoshi & Hiroshi Shiku

Immune cells have an important role in tumour progression. Here, the authors show that extracellular vesicles from activated CD8+ T cells attenuate tumour progression by depletion of mesenchymal tumour stromal cells.

30 January 2018 | doi: 10.1038/s41467-018-02865-1
Apoptosis  Immunosurveillance 

Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space OPEN
Philippe Leone, Jennifer Roche, Maxence S. Vincent, Quang Hieu Tran, Aline Desmyter, Eric Cascales, Christine Kellenberger, Christian Cambillau & Alain Roussel

No structural data for the bacterial type IX secretion system (T9SS) are available so far. Here, the authors present the crystal structures of the periplasmic domains from two major T9SS components PorM and GldM, which span most of the periplasmic space, and propose a putative model of the T9SS core membrane complex.

30 January 2018 | doi: 10.1038/s41467-017-02784-7
Bacterial secretion  X-ray crystallography 

A clean and membrane-free chlor-alkali process with decoupled Cl2 and H2/NaOH production OPEN
Mengyan Hou, Long Chen, Zhaowei Guo, Xiaoli Dong, Yonggang Wang & Yongyao Xia

The chlor-alkali process is an important industrial process to make commodity chemicals; however, it usually requires the use of dangerous chemicals as membrane material. Here, the authors demonstrate clean, membrane-free chlor-alkali electrolysis, where chlorine evolution and hydrogen/sodium hydroxide production are completely decoupled.

30 January 2018 | doi: 10.1038/s41467-018-02877-x
Electrochemistry  Physical chemistry 

A carbon nanotube tape for serial-section electron microscopy of brain ultrastructure OPEN
Yoshiyuki Kubota, Jaerin Sohn, Sayuri Hatada, Meike Schurr, Jakob Straehle, Anjali Gour, Ralph Neujahr, Takafumi Miki, Shawn Mikula & Yasuo Kawaguchi

Electron microscopy requires electrically conductive and grounded samples to provide high-resolution, high-contrast images. Here, Kubota et al. describe a suitable carbon nanotube based tape for automated serial section collection and imaging, as in ATUM-based electron microscopy.

30 January 2018 | doi: 10.1038/s41467-017-02768-7
Imaging techniques  Neural circuits  Scanning electron microscopy 

Extension of the growing season increases vegetation exposure to frost OPEN
Qiang Liu, Shilong Piao, Ivan A. Janssens, Yongshuo Fu, Shushi Peng, Xu Lian, Philippe Ciais, Ranga B. Myneni, Josep Peñuelas & Tao Wang

Plant growing season increases under a warming climate, but it is not known whether this will alter plant exposure to frost days. Here Liu et al. investigate trends in the Northern Hemisphere over 30 years and find increased exposure to frost days in regions that have longer growing seasons.

30 January 2018 | doi: 10.1038/s41467-017-02690-y
Climate-change ecology  Phenology 

The genetic prehistory of the Baltic Sea region OPEN
Alissa Mittnik, Chuan-Chao Wang, Saskia Pfrengle, Mantas Daubaras, Gunita Zariņa, Fredrik Hallgren, Raili Allmäe, Valery Khartanovich, Vyacheslav Moiseyev, Mari Tõrv, Anja Furtwängler, Aida Andrades Valtueña, Michal Feldman, Christos Economou, Markku Oinonen, Andrejs Vasks, Elena Balanovska, David Reich, Rimantas Jankauskas, Wolfgang Haak et al.

The population history of Europe is complex and its very north has not yet been comprehensively studied at a genetic level. Here, Mittnik et al. report genome-wide data from 38 ancient individuals from the Eastern Baltic, Russia and Scandinavia to analyse gene flow throughout the Mesolithic and Bronze Age.

30 January 2018 | doi: 10.1038/s41467-018-02825-9
Evolutionary biology  Evolutionary genetics  Genomics  Population genetics 

Tbx5a lineage tracing shows cardiomyocyte plasticity during zebrafish heart regeneration OPEN
Héctor Sánchez-Iranzo, María Galardi-Castilla, Carolina Minguillón, Andrés Sanz-Morejón, Juan Manuel González-Rosa, Anastasia Felker, Alexander Ernst, Gabriela Guzmán-Martínez, Christian Mosimann & Nadia Mercader

It is not clear if it is the embryonic origin or anatomical location of cardiomyocytes that restrict their contribution to zebrafish heart regeneration. Here, the authors show a plasticity of embryonic precursors following tbx5a fate mapping and that trabecular cardiomyocytes help to rebuild the cortical myocardium.

30 January 2018 | doi: 10.1038/s41467-017-02650-6
Cardiac regeneration  Heart development  Regeneration  Zebrafish 

Structure of tick-borne encephalitis virus and its neutralization by a monoclonal antibody OPEN
Tibor Füzik, Petra Formanová, Daniel Růžek, Kentaro Yoshii, Matthias Niedrig & Pavel Plevka

The tick-borne encephalitis virus (TBEV) causes thousands of cases of meningitis and encephalitis annually. Here, the authors describe a cryo-EM structure of the TBEV virion bound by Fab fragments of the neutralizing antibody 19/1786, revealing a mechanism whereby this antibody prevents virus membrane fusion.

30 January 2018 | doi: 10.1038/s41467-018-02882-0
Cryoelectron microscopy  Virus–host interactions  Virus structures 

Probability of phenotypically detectable protein damage by ENU-induced mutations in the Mutagenetix database OPEN
Tao Wang, Chun Hui Bu, Sara Hildebrand, Gaoxiang Jia, Owen M. Siggs, Stephen Lyon, David Pratt, Lindsay Scott, Jamie Russell, Sara Ludwig, Anne R. Murray, Eva Marie Y. Moresco & Bruce Beutler

Programs such as PolyPhen-2 predict the relative severity of damage by missense mutations. Here, Wang et al estimate probabilities that putative null or missense alleles would reduce protein function to cause detectable phenotype by analyzing data from ENU-induced mouse mutations.

30 January 2018 | doi: 10.1038/s41467-017-02806-4
Data processing  Genetic linkage study 

Bismuth antimicrobial drugs serve as broad-spectrum metallo-β-lactamase inhibitors OPEN
Runming Wang, Tsz-Pui Lai, Peng Gao, Hongmin Zhang, Pak-Leung Ho, Patrick Chiu-Yat Woo, Guixing Ma, Richard Yi-Tsun Kao, Hongyan Li & Hongzhe Sun

Metallo-β-lactamases (MBL) are zinc containing enzymes that cause resistance to β-lactam antibiotics. Here the authors show that the anti-Helicobacter pylori drug colloidal bismuth subcitrate inhibits MBLs by displacing the zinc ions with Bi(III), which is of great interest for the development of antibiotics.

30 January 2018 | doi: 10.1038/s41467-018-02828-6
Antimicrobials  Drug screening  Enzyme mechanisms 

Topology-dependent self-structure mediation and efficient energy conversion in heat-flux-driven rotors of cholesteric droplets OPEN
Jun Yoshioka & Fumito Araoka

The Lehmann effect describes the spontaneous rotation of cholesteric liquid crystals in response to heat input. Here, the authors stabilise it by dispersing cholesteric droplets into a poorly miscible solvent and show dependences of rotation speed and conversion efficiency on the topological states.

30 January 2018 | doi: 10.1038/s41467-018-02910-z
Fluid dynamics  Liquid crystals  Materials science 

A peak in the critical current for quantum critical superconductors OPEN
Soon-Gil Jung, Soonbeom Seo, Sangyun Lee, Eric D. Bauer, Han-Oh Lee & Tuson Park

Knowledge of critical current may provide important information to understand unconventional superconductivity and quantum critical behavior. Here, Jung et al. observe a peak in the pressure dependence of the zero-field critical current at a hidden quantum critical point in pure and Sn-doped heavy fermion superconductor CeRhIn5.

30 January 2018 | doi: 10.1038/s41467-018-02899-5
Electronic properties and materials  Superconducting properties and materials 

Targeting Tyro3 ameliorates a model of PGRN-mutant FTLD-TDP via tau-mediated synaptic pathology OPEN
Kyota Fujita, Xigui Chen, Hidenori Homma, Kazuhiko Tagawa, Mutsuki Amano, Ayumu Saito, Seiya Imoto, Hiroyasu Akatsu, Yoshio Hashizume, Kozo Kaibuchi, Satoru Miyano & Hitoshi Okazawa

Progranulin (PGRN) mutations cause frontotemporal lobe dementia with TDP-43 pathology. Here the authors develop a mutant PGRN knock-in mouse model of the disease, and show that Tyro3, a tyrosine kinase membrane receptor that acts upstream of PKC and MAPK, is inhibited by PGRN which contributes to pathology in this model.

30 January 2018 | doi: 10.1038/s41467-018-02821-z
Dementia  Neurodegeneration  Spine structure 

Gimap5-dependent inactivation of GSK3β is required for CD4+ T cell homeostasis and prevention of immune pathology OPEN
Andrew R. Patterson, Mehari Endale, Kristin Lampe, Halil I. Aksoylar, Aron Flagg, Jim R. Woodgett, David Hildeman, Michael B. Jordan, Harinder Singh, Zeynep Kucuk, Jack Bleesing & Kasper Hoebe

Loss of function GIMAP5 mutation is associated with lymphopenia, but how it mediates T cell homeostasis is unclear. Here the authors study Gimap5−/− mice and a patient with GIMAP5 deficiency to show how this GTPAse negatively regulates GSK3β activity to prevent DNA damage and cell death.

30 January 2018 | doi: 10.1038/s41467-018-02897-7
Autoimmunity  Lymphocyte activation  Primary immunodeficiency disorders 

Structure-guided design of an Hsp90β N-terminal isoform-selective inhibitor OPEN
Anuj Khandelwal, Caitlin N. Kent, Maurie Balch, Shuxia Peng, Sanket J. Mishra, Junpeng Deng, Victor W. Day, Weiya Liu, Chitra Subramanian, Mark Cohen, Jeffery M. Holzbeierlein, Robert Matts & Brian S. J. Blagg

The molecular chaperone Hsp90 oversees the folding of many proteins associated with cancer progression but existing small-molecule inhibitors of this pathway are not isoform-selective. Here, the authors rationally design an Hsp90 inhibitor that displays high selectivity for the Hsp90β isoform.

30 January 2018 | doi: 10.1038/s41467-017-02013-1
Drug delivery  Molecular medicine  Structure-based drug design 

RASSF1A uncouples Wnt from Hippo signalling and promotes YAP mediated differentiation via p73 OPEN
Angelos Papaspyropoulos, Leanne Bradley, Asmita Thapa, Chuen Yan Leung, Konstantinos Toskas, Delia Koennig, Dafni-Eleftheria Pefani, Cinzia Raso, Claudia Grou, Garth Hamilton, Nikola Vlahov, Anna Grawenda, Syed Haider, Jagat Chauhan, Ludovico Buti, Alexander Kanapin, Xin Lu, Francesca Buffa, Grigory Dianov, Alex von Kriegsheim et al.

In development, the switch from pluripotency to differentiation is important but it is often unclear how it is regulated. Here, the authors show that the tumour suppressor RASSF1A mediates this switch by promoting YAP-p73 transcription, which in turn enables differentiation.

30 January 2018 | doi: 10.1038/s41467-017-02786-5
Cell signalling  Embryonic stem cells  Pluripotency 

Similar neural responses predict friendship OPEN
Carolyn Parkinson, Adam M. Kleinbaum & Thalia Wheatley

Though we are often friends with people similar to ourselves, it is unclear if neural responses to perceptual stimuli are also similar. Here, authors show that the similarity of neural responses evoked by a range of videos was highest for close friends and decreased with increasing social distance.

30 January 2018 | doi: 10.1038/s41467-017-02722-7
Cognitive neuroscience  Human behaviour  Social neuroscience 

Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly OPEN
Peer Aramillo Irizar, Sascha Schäuble, Daniela Esser, Marco Groth, Christiane Frahm, Steffen Priebe, Mario Baumgart, Nils Hartmann, Shiva Marthandan, Uwe Menzel, Julia Müller, Silvio Schmidt, Volker Ast, Amke Caliebe, Rainer König, Michael Krawczak, Michael Ristow, Stefan Schuster, Alessandro Cellerino, Stephan Diekmann et al.

Ageing is associated with a pronounced shift in mortality from cancer to degenerative diseases. Here, the authors show that in concordance with this shift, conserved transcriptional alterations during ageing across four vertebrates align with degenerative diseases but are opposite to those in cancer.

30 January 2018 | doi: 10.1038/s41467-017-02395-2
Ageing  Cancer  Computational biology and bioinformatics  Genetic association study 

Streamlined ex vivo and in vivo genome editing in mouse embryos using recombinant adeno-associated viruses OPEN
Yeonsoo Yoon, Dan Wang, Phillip W. L. Tai, Joy Riley, Guangping Gao & Jaime A. Rivera-Pérez

CRISPR-Cas9 has been widely adopted for genetically manipulating rodents for scientific research. Here the authors transduce mouse embryos with CRISPR-Cas9 components using rAAVs in explant culture or in vivo to produce gene-edited animals.

29 January 2018 | doi: 10.1038/s41467-017-02706-7
CRISPR-Cas9 genome editing  Genetic engineering 

Competition between electron pairing and phase coherence in superconducting interfaces OPEN
G. Singh, A. Jouan, L. Benfatto, F. Couëdo, P. Kumar, A. Dogra, R. C. Budhani, S. Caprara, M. Grilli, E. Lesne, A. Barthélémy, M. Bibes, C. Feuillet-Palma, J. Lesueur & N. Bergeal

The nature of the doping dependent superconducting transition remains elusive for a two dimensional electron gas at the LaAlO3/SrTiO3 interface. Here, Singh et al. report superfluid stiffness and the superconducting gap energy at such interface as a function of carrier density.

29 January 2018 | doi: 10.1038/s41467-018-02907-8
Superconducting properties and materials  Surfaces, interfaces and thin films 

Hotspots of dendritic spine turnover facilitate clustered spine addition and learning and memory OPEN
Adam C. Frank, Shan Huang, Miou Zhou, Amos Gdalyahu, George Kastellakis, Tawnie K. Silva, Elaine Lu, Ximiao Wen, Panayiota Poirazi, Joshua T. Trachtenberg & Alcino J. Silva

Structural remodeling of dendritic spines is thought to be a mechanism of memory storage. Here, the authors look at how spine turnover and clustering predict future learning and memory performance, and see that a genetically modified mouse with enhanced spine turnover has enhanced learning.

29 January 2018 | doi: 10.1038/s41467-017-02751-2
Fear conditioning  Network models  Spatial memory  Spine plasticity  Spine structure 

An artificial nociceptor based on a diffusive memristor OPEN
Jung Ho Yoon, Zhongrui Wang, Kyung Min Kim, Huaqiang Wu, Vignesh Ravichandran, Qiangfei Xia, Cheol Seong Hwang & J. Joshua Yang

The development of humanoid robots with artificial intelligence calls for smart solutions for tactile sensing systems that respond to dynamic changes in the environment. Here, Yoon et al. emulate non-adaption and sensitization function of a nociceptor—a sensory neuron—using diffusive oxide-based memristors.

29 January 2018 | doi: 10.1038/s41467-017-02572-3
Electrical and electronic engineering  Electronic devices  Materials for devices 

Membrane bending occurs at all stages of clathrin-coat assembly and defines endocytic dynamics OPEN
Brandon L. Scott, Kem A. Sochacki, Shalini T. Low-Nam, Elizabeth M. Bailey, QuocAhn Luu, Amy Hor, Andrea M. Dickey, Steve Smith, Jason G. Kerkvliet, Justin W. Taraska & Adam D. Hoppe

Two distinct and opposing models for clathrin-mediated endocytosis have been inferred from EM and structural biology data. Here the authors develop an optical method to directly visualize membrane-bending dynamics and show that coat assembly accommodates membrane bending during or after the assembly of the clathrin lattice, which is not predicted by either model.

29 January 2018 | doi: 10.1038/s41467-018-02818-8
Endocytosis  Membrane biophysics 

Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1 OPEN
Baixing Wu, Shichen Su, Deepak P. Patil, Hehua Liu, Jianhua Gan, Samie R. Jaffrey & Jinbiao Ma

RNA-binding protein hnRNP A2/B1 is suggested to promote miRNA processing as a m6A 'reader'. Here, the authors determine crystal structures of RRM domains of hnRNP A2/B1 in complex with various RNA substrates and determine that hnRNP A2/B1 may function as an auxiliary factor in 'm6A switch' instead.

29 January 2018 | doi: 10.1038/s41467-017-02770-z
RNA-binding proteins  RNA modification  X-ray crystallography 

Dual catalysis for enantioselective convergent synthesis of enantiopure vicinal amino alcohols OPEN
Chen-Xi Ye, Yared Yohannes Melcamu, Heng-Hui Li, Jiang-Tao Cheng, Tian-Tian Zhang, Yuan-Ping Ruan, Xiao Zheng, Xin Lu & Pei-Qiang Huang

Chiral vicinal amino alcohols are found in many bioactive compounds and may serve as chiral ligands. Here, the authors report a photocatalytic enantioselective cross-coupling of nitrones with aromatic aldehydes with a chiral ligand-coordinated rare earth ion synergistically producing enantiopure vicinal amino alcohols.

29 January 2018 | doi: 10.1038/s41467-017-02698-4
Asymmetric catalysis  Asymmetric synthesis  Homogeneous catalysis 

Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen OPEN
Rémi Peyraud, Ludovic Cottret, Lucas Marmiesse & Stéphane Genin

How pathogens maintain phenotypic robustness during infection is poorly understood. Here the authors couple the virulence regulatory network (VRN) of the pathogen R. solanacearum to a model of its metabolic network, and find that the VRN activates functionally redundant primary metabolism genes to promote phenotypic robustness during infection.

29 January 2018 | doi: 10.1038/s41467-017-02660-4
Pathogens  Regulatory networks  Robustness 

An evolutionary NS1 mutation enhances Zika virus evasion of host interferon induction OPEN
Hongjie Xia, Huanle Luo, Chao Shan, Antonio E. Muruato, Bruno T. D. Nunes, Daniele B. A. Medeiros, Jing Zou, Xuping Xie, Maria Isabel Giraldo, Pedro F. C. Vasconcelos, Scott C. Weaver, Tian Wang, Ricardo Rajsbaum & Pei-Yong Shi

The Asian lineage of Zika virus (ZIKV) has acquired a mutation in NS1 that enhances mosquito infection. Here, Xia et al. show that the same mutation interferes with interferon production through interaction with TBK1 and affects ZIKV replication in mice.

29 January 2018 | doi: 10.1038/s41467-017-02816-2
Viral evolution  Viral immune evasion 

Active sites of copper-complex catalytic materials for electrochemical carbon dioxide reduction OPEN
Zhe Weng, Yueshen Wu, Maoyu Wang, Jianbing Jiang, Ke Yang, Shengjuan Huo, Xiao-Feng Wang, Qing Ma, Gary W. Brudvig, Victor S. Batista, Yongye Liang, Zhenxing Feng & Hailiang Wang

The catalytic conversion of carbon dioxide into value-added products requires an understanding of the active species present under working conditions. Here, the authors discover copper-containing complexes to reversibly transform during electrocatalysis into methane-producing copper nanoclusters.

29 January 2018 | doi: 10.1038/s41467-018-02819-7
Electrocatalysis  Materials chemistry 

Large magneto-thermopower in MnGe with topological spin texture OPEN
Y. Fujishiro, N. Kanazawa, T. Shimojima, A. Nakamura, K. Ishizaka, T. Koretsune, R. Arita, A. Miyake, H. Mitamura, K. Akiba, M. Tokunaga, J. Shiogai, S. Kimura, S. Awaji, A. Tsukazaki, A. Kikkawa, Y. Taguchi & Y. Tokura

Topological spin textures produce versatile electronic functionalities, but are scarcely exploited for achieving heat to electricity conversion. Here, Fujishiro et al. attribute an enhanced magneto-thermopower in MnGe with topological spin hedgehogs, to electron scattering via the dynamics of an emergent magnetic field.

29 January 2018 | doi: 10.1038/s41467-018-02857-1
Magnetic properties and materials  Thermoelectrics 

Isolated proton bunch acceleration by a petawatt laser pulse OPEN

Monoenergetic proton beams can be useful in many applications but their generation from laser irradiation of targets is challenging. Here the authors demonstrate a laser-accelerated proton bunch with improved density and energy resolution by using a refined target.

29 January 2018 | doi: 10.1038/s41467-017-02663-1
Laser-produced plasmas  Plasma-based accelerators 

In-situ liquid cell transmission electron microscopy investigation on oriented attachment of gold nanoparticles OPEN
Chao Zhu, Suxia Liang, Erhong Song, Yuanjun Zhou, Wen Wang, Feng Shan, Yantao Shi, Ce Hao, Kuibo Yin, Tong Zhang, Jianjun Liu, Haimei Zheng & Litao Sun

The non-classical oriented attachment crystallization pathway explains the growth of many nanocrystals. Here, the authors study citrate-stabilized gold nanoparticles by in-situ liquid transmission electron microscopy to reveal that surface ligands are a critical driving force in the oriented attachment process.

29 January 2018 | doi: 10.1038/s41467-018-02925-6
Nanoparticles  Surface chemistry  Transmission electron microscopy 

The SAM domain of mouse SAMHD1 is critical for its activation and regulation OPEN
Olga Buzovetsky, Chenxiang Tang, Kirsten M. Knecht, Jenna M. Antonucci, Li Wu, Xiaoyun Ji & Yong Xiong

The sterile alpha-motif and histidine-aspartate domain-containing protein 1 (SAMHD1) is a dNTP phosphohydrolase that blocks HIV-1 infection by depleting cellular dNTPs. Here the authors present the structures of full-length mouse SAMHD1 in different nucleotide bound states and give insights into SAMHD1 activity regulation.

29 January 2018 | doi: 10.1038/s41467-017-02783-8
Nucleotide-binding proteins  X-ray crystallography 

Fused electron deficient semiconducting polymers for air stable electron transport OPEN
Ada Onwubiko, Wan Yue, Cameron Jellett, Mingfei Xiao, Hung-Yang Chen, Mahesh Kumar Ravva, David A. Hanifi, Astrid-Caroline Knall, Balaji Purushothaman, Mark Nikolka, Jean-Charles Flores, Alberto Salleo, Jean-Luc Bredas, Henning Sirringhaus, Pascal Hayoz & Iain McCulloch

Semiconducting polymers are usually prepared by transition metal mediated coupling reactions that cause problems for sustainability and biological applications. Here the authors synthesise fused electron deficient polymers that are air stable and have high electron affinities, via metal free aldol polymerisation reactions.

29 January 2018 | doi: 10.1038/s41467-018-02852-6
Electronic materials  Polymer synthesis 

Differential coding of reward and movement information in the dorsomedial striatal direct and indirect pathways OPEN
Jung Hwan Shin, Dohoung Kim & Min Whan Jung

Classically the direct and indirect pathways of basal ganglia are understood to have opposing roles in movement and reward learning, but recent work suggests a more complicated view. Here the authors further study indirect and direct pathway neurons, in the context of a probabilistic reward task.

26 January 2018 | doi: 10.1038/s41467-017-02817-1
Basal ganglia  Reward 

Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation OPEN
Seongjoon Joo, In Jin Cho, Hogyun Seo, Hyeoncheol Francis Son, Hye-Young Sagong, Tae Joo Shin, So Young Choi, Sang Yup Lee & Kyung-Jin Kim

Poly(ethylene terephthalate) (PET) is a widely used plastic and its accumulation in the environment has become global problem. Here the authors report the crystal structure of a Ideonella sakaiensis PET-degrading enzyme and propose a molecular mechanism for PET degradation.

26 January 2018 | doi: 10.1038/s41467-018-02881-1
Environmental biotechnology  Enzyme mechanisms  Enzymes  Structural biology 

GWAS of epigenetic aging rates in blood reveals a critical role for TERT OPEN
Ake T. Lu, Luting Xue, Elias L. Salfati, Brian H. Chen, Luigi Ferrucci, Daniel Levy, Roby Joehanes, Joanne M. Murabito, Douglas P. Kiel, Pei-Chien Tsai, Idil Yet, Jordana T. Bell, Massimo Mangino, Toshiko Tanaka, Allan F. McRae, Riccardo E. Marioni, Peter M. Visscher, Naomi R. Wray, Ian J. Deary, Morgan E. Levine et al.

Epigenetic clocks based on DNA methylation levels are estimators of chronological age. Here, the authors perform a GWAS of epigenetic aging rates in blood and find SNP variants in the TERT locus associated with increased intrinsic epigenetic age are also associated with longer telomeres.

26 January 2018 | doi: 10.1038/s41467-017-02697-5
Diseases  Genome-wide association studies 

Pronounced centennial-scale Atlantic Ocean climate variability correlated with Western Hemisphere hydroclimate OPEN
Kaustubh Thirumalai, Terrence M. Quinn, Yuko Okumura, Julie N. Richey, Judson W. Partin, Richard Z. Poore & Eduardo Moreno-Chamarro

Knowledge of surface-ocean circulation in the Atlantic over the late Holocene is incomplete. Here, the authors show that Atlantic Ocean surface-circulation varied in concert with Western Hemisphere rainfall anomalies on centennial timescales and that this link played an essential role during the Little Ice Age.

26 January 2018 | doi: 10.1038/s41467-018-02846-4
Climate and Earth system modelling  Palaeoceanography  Palaeoclimate 

A dual role for the N-terminal domain of the IL-3 receptor in cell signalling OPEN
Sophie E. Broughton, Timothy R. Hercus, Tracy L. Nero, Winnie L. Kan, Emma F. Barry, Mara Dottore, Karen S. Cheung Tung Shing, Craig J. Morton, Urmi Dhagat, Matthew P. Hardy, Nicholas J. Wilson, Matthew T. Downton, Christine Schieber, Timothy P. Hughes, Angel F. Lopez & Michael W. Parker

The N-terminal domain (NTD) of interleukin-3 receptor α-subunit (IL3Rα) is involved in IL-3 recognition but the underlying mechanism is unknown. Here, the authors present crystal structures of the IL3Rα complex and provide biochemical evidence that the NTD regulates IL-3 binding and signalling complex assembly.

26 January 2018 | doi: 10.1038/s41467-017-02633-7
Interleukins  Signal transduction  X-ray crystallography 

Caging tin oxide in three-dimensional graphene networks for superior volumetric lithium storage OPEN
Junwei Han, Debin Kong, Wei Lv, Dai-Ming Tang, Daliang Han, Chao Zhang, Donghai Liu, Zhichang Xiao, Xinghao Zhang, Jing Xiao, Xinzi He, Feng-Chun Hsia, Chen Zhang, Ying Tao, Dmitri Golberg, Feiyu Kang, Linjie Zhi & Quan-Hong Yang

The excessive porous space in carbon anodes for lithium-ion batteries has to be utilized for high volumetric performance. Here the authors show an adaptable sulfur template strategy to yield graphene-caged noncarbon materials with a precisely controlled amount of void, enabling ultrahigh volumetric lithium storage.

26 January 2018 | doi: 10.1038/s41467-017-02808-2

Global observations of reflectors in the mid-mantle with implications for mantle structure and dynamics OPEN
Lauren Waszek, Nicholas C. Schmerr & Maxim D. Ballmer

The Earth’s mantle undergoes changes as temperature and pressure increase with depth. Here, the authors present a global interrogation of reflectors in the Earth’s mid-mantle revealing a significant variation in their properties, with widespread compositional heterogeneity and seismic velocity in the mid-mantle, which signify contrasting styles of mantle flow.

26 January 2018 | doi: 10.1038/s41467-017-02709-4
Geodynamics  Geophysics  Seismology 

Kruppel-like factor 4-dependent Staufen1-mediated mRNA decay regulates cortical neurogenesis OPEN
Byoung-San Moon, Jinlun Bai, Mingyang Cai, Chunming Liu, Jiandang Shi & Wange Lu

While being known as a transcription factor, Kruppel-like factor 4 (Klf4) may have other molecular functions. This study shows that Klf4 in neural progenitor cells regulate neurogenesis and self-renewal by interacting with RNA-binding protein Staufen1 and RNA helicase Ddx5/17 to control mRNA decay.

26 January 2018 | doi: 10.1038/s41467-017-02720-9
Molecular neuroscience  Neural stem cells  RNA decay 

Gamma and beta bursts during working memory readout suggest roles in its volitional control OPEN
Mikael Lundqvist, Pawel Herman, Melissa R. Warden, Scott L. Brincat & Earl K. Miller

Previously, the authors have shown that working memory can be maintained by brief gamma oscillation bursts. Here, the authors use a new task to further demonstrate the dynamics of gamma and beta oscillations in working memory readout, independent of behavioral response.

26 January 2018 | doi: 10.1038/s41467-017-02791-8
Cognitive control  Network models  Working memory 

Subcortical evidence for a contribution of arousal to fMRI studies of brain activity OPEN
Xiao Liu, Jacco A. de Zwart, Marieke L. Schölvinck, Catie Chang, Frank Q. Ye, David A. Leopold & Jeff H. Duyn

Resting cortical activity fluctuates, but it is unclear what underlies these variations in activity. Here, the authors show that large-scale fluctuations in fMRI cortical activity are associated with momentary decreases in cortical arousal and opposite activity changes in the basal forebrain and thalamus.

26 January 2018 | doi: 10.1038/s41467-017-02815-3
Circadian regulation  Data mining  Neural circuits  Neurophysiology 

Identification of a Golgi GPI-N-acetylgalactosamine transferase with tandem transmembrane regions in the catalytic domain OPEN
Tetsuya Hirata, Sushil K. Mishra, Shota Nakamura, Kazunobu Saito, Daisuke Motooka, Yoko Takada, Noriyuki Kanzawa, Yoshiko Murakami, Yusuke Maeda, Morihisa Fujita, Yoshiki Yamaguchi & Taroh Kinoshita

Mammalian GPI membrane anchors are modified by GalNAc to confer structural diversity but the biosynthetic pathway is poorly understood. Here, the authors identify and characterize the Golgi-resident GPI-GalNAc transferase PGAP4, providing insights into the initial step of GPI-GalNAc biosynthesis.

26 January 2018 | doi: 10.1038/s41467-017-02799-0
Glycobiology  Glycolipids  Transferases 

Mitochondrial levels determine variability in cell death by modulating apoptotic gene expression OPEN
Silvia Márquez-Jurado, Juan Díaz-Colunga, Ricardo Pires das Neves, Antonio Martinez-Lorente, Fernando Almazán, Raúl Guantes & Francisco J. Iborra

It is unclear what causes variation in cell death in response to chemotherapy. Here, the authors show that cellular mitochondrial content modulates apoptotic protein levels, which in turn regulates response to agents such as TRAIL.

26 January 2018 | doi: 10.1038/s41467-017-02787-4
Apoptosis  Cellular noise  Mitochondria 

Beyond a phenomenological description of magnetostriction OPEN
A. H. Reid, X. Shen, P. Maldonado, T. Chase, E. Jal, P. W. Granitzka, K. Carva, R. K. Li, J. Li, L. Wu, T. Vecchione, T. Liu, Z. Chen, D. J. Higley, N. Hartmann, R. Coffee, J. Wu, G. L. Dakovski, W. F. Schlotter, H. Ohldag et al.

Although magnetostriction is universal in magnetic materials, understanding its microscopic origin remains challenging. Here the authors use X-ray and ultrafast electron diffraction to separate the material’s sub-picosecond spin and lattice responses and reveal the magnetoelastic stress generated by demagnetization.

26 January 2018 | doi: 10.1038/s41467-017-02730-7
Magnetic properties and materials  Nanoparticles  Structure of solids and liquids 

Dendritic core-shell nickel-iron-copper metal/metal oxide electrode for efficient electrocatalytic water oxidation OPEN
Peili Zhang, Lin Li, Dennis Nordlund, Hong Chen, Lizhou Fan, Biaobiao Zhang, Xia Sheng, Quentin Daniel & Licheng Sun

Splitting water into high-energy fuel represents a renewable way to generate energy, yet the sluggish oxidation kinetics drives up technological costs. Here, the authors prepare tri-metallic core-shell electrodes using nickel, iron, and copper metals to accelerate electricity-driven water splitting.

26 January 2018 | doi: 10.1038/s41467-017-02429-9
Electrocatalysis  Electronic devices  Energy  Heterogeneous catalysis 

Configurable topological textures in strain graded ferroelectric nanoplates OPEN
Kwang-Eun Kim, Seuri Jeong, Kanghyun Chu, Jin Hong Lee, Gi-Yeop Kim, Fei Xue, Tae Yeong Koo, Long-Qing Chen, Si-Young Choi, Ramamoorthy Ramesh & Chan-Ho Yang

Exploring topological textures in ferroelectrics facilitates the understanding and application of topological features in matter. Here the authors demonstrate the strain field induced evolution of topological vortices in nanoplatelets of rhombohedral phase BiFeO3 using the angle-resolved piezoresponse force microscopy.

26 January 2018 | doi: 10.1038/s41467-017-02813-5
Ferroelectrics and multiferroics  Surfaces, interfaces and thin films 

Female sexual behavior in mice is controlled by kisspeptin neurons OPEN
Vincent Hellier, Olivier Brock, Michael Candlish, Elodie Desroziers, Mari Aoki, Christian Mayer, Richard Piet, Allan Herbison, William Henry Colledge, Vincent Prévot, Ulrich Boehm & Julie Bakker

Mate preference and copulatory behavior in female rodents are coordinated with the ovulation cycles of the animal. This study shows that hypothalamic kisspeptin neurons control both mate choice and copulation, and therefore, that sexual behavior and ovulation may be synchronized by the same neuropeptide.

26 January 2018 | doi: 10.1038/s41467-017-02797-2
Pheromone  Sexual dimorphism 

High-resolution patterning of solution-processable materials via externally engineered pinning of capillary bridges OPEN
Shunpu Li, Young Tea Chun, Shuo Zhao, Hyungju Ahn, Docheon Ahn, Jung Inn Sohn, Yongbing Xu, Pawan Shrestha, Mike Pivnenko & Daping Chu

Solution-processed electronics is desirable for large-scale electronics, but it is challenging to fabricate nanometre patterns via liquid processes. Li et al. address this problem using soft molds with groove and ridge structures, which control thin-film morphology upon dying via the pinning effect.

26 January 2018 | doi: 10.1038/s41467-018-02835-7
Electronic devices  Synthesis and processing 

Strong indirect coupling between graphene-based mechanical resonators via a phonon cavity OPEN
Gang Luo, Zhuo-Zhi Zhang, Guang-Wei Deng, Hai-Ou Li, Gang Cao, Ming Xiao, Guang-Can Guo, Lin Tian & Guo-Ping Guo

Non-neighbouring mechanical resonators can interact via indirect coupling. Here, the authors leverage a resonant phonon cavity in a graphene-based electromechanical system to demonstrate strong indirect coupling between separated mechanical resonators.

26 January 2018 | doi: 10.1038/s41467-018-02854-4
Mechanical and structural properties and devices  NEMS 

Lipopolysaccharide O-antigen delays plant innate immune recognition of Xylella fastidiosa OPEN
Jeannette N. Rapicavoli, Barbara Blanco-Ulate, Artur Muszyński, Rosa Figueroa-Balderas, Abraham Morales-Cruz, Parastoo Azadi, Justyna M. Dobruchowska, Claudia Castro, Dario Cantu & M. Caroline Roper

Many pathogenic bacteria have evolved to subvert host immune responses triggered by lipopolysaccharides (LPS). Here the authors show that a long terminal polysaccharide chain, known as the O-antigen, present in LPS from the plant pathogen Xylella fastidiosa can delay recognition by grapevine hosts.

26 January 2018 | doi: 10.1038/s41467-018-02861-5
Microbe  Pathogens 

Molecular snapshots of APE1 proofreading mismatches and removing DNA damage OPEN
Amy M. Whitaker, Tony S. Flynn & Bret D. Freudenthal

The essential DNA repair enzyme apurinic/apyrimidinic endonuclease 1 (APE1) has both endonuclease and exonuclease activities. Here, the authors present DNA bound human APE1 crystal structures which give insights into its exonuclease mechanism.

26 January 2018 | doi: 10.1038/s41467-017-02175-y
Enzyme mechanisms  X-ray crystallography 

Room temperature magneto-optic effect in silicon light-emitting diodes OPEN
F. Chiodi, S. L. Bayliss, L. Barast, D. Débarre, H. Bouchiat, R. H. Friend & A. D. Chepelianskii

Silicon is an important material in spintronics but its inefficiency in light emission limits the optical probes for spin transport. Here Chiodi et al. develop ultra-doped silicon light-emitting devices and show that electroluminescence can be used to probe spin phenomena in silicon even at room temperature.

26 January 2018 | doi: 10.1038/s41467-017-02804-6
Electronic and spintronic devices  Photonic devices 

Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra OPEN
Thomas Evangelidis, Santrupti Nerli, Jiří Nováček, Andrew E. Brereton, P. Andrew Karplus, Rochelle R. Dotas, Vincenzo Venditti, Nikolaos G. Sgourakis & Konstantinos Tripsianes

Further automation of NMR structure determination is needed to increase the throughput and accessibility of this method. Here the authors present 4D-CHAINS/autoNOE-Rosetta, a complete pipeline that allows rapid and fully automated structure determination from two highly complementary NMR datasets.

26 January 2018 | doi: 10.1038/s41467-017-02592-z
Protein structure predictions  Solution-state NMR 

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo OPEN
Ralf Gilsbach, Martin Schwaderer, Sebastian Preissl, Björn A. Grüning, David Kranzhöfer, Pedro Schneider, Thomas G. Nührenberg, Sonia Mulero-Navarro, Dieter Weichenhan, Christian Braun, Martina Dreßen, Adam R. Jacobs, Harald Lahm, Torsten Doenst, Rolf Backofen, Markus Krane, Bruce D. Gelb & Lutz Hein

How the cardiac myocyte epigenome is rearranged during development, postnatal maturation and disease is not well understood. Here, the authors investigate the human cardiac myocyte epigenome during development and chronic heart failure and identify distinct epigenetic programs regulating these processes.

26 January 2018 | doi: 10.1038/s41467-017-02762-z
DNA methylation  Epigenetics  Epigenomics  Heart development 

Measurements of growing surface tension of amorphous–amorphous interfaces on approaching the colloidal glass transition OPEN
Divya Ganapathi, K. Hima Nagamanasa, A. K. Sood & Rajesh Ganapathy

The existence of interfaces, separating distinct relaxing regions, has been predicted in glass  theory, but a direct proof remains challenging due to the amorphous nature of glasses. Ganapathi et al. identify and measure the surface tension of these interfaces in bulk supercooled colloidal liquids.

26 January 2018 | doi: 10.1038/s41467-018-02836-6
Phase transitions and critical phenomena  Statistical physics  Structure of solids and liquids  Thermodynamics 

Generalized Fano lineshapes reveal exceptional points in photonic molecules OPEN
Niccolò Caselli, Francesca Intonti, Federico La China, Francesco Biccari, Francesco Riboli, Annamaria Gerardino, Lianhe Li, Edmund H. Linfield, Francesco Pagliano, Andrea Fiore & Massimo Gurioli

Fano lineshapes are found in many photonic systems where discrete and extended spectra interfere. Here, the authors extend this description and introduce generalized Fano lineshapes to describe the results from hyperspectral mapping around an exceptional point in a coupled-cavity system.

26 January 2018 | doi: 10.1038/s41467-018-02855-3
Nanophotonics and plasmonics  Near-infrared spectroscopy 

Reemergence of high-Tc superconductivity in the (Li1-xFe x )OHFe1-ySe under high pressure OPEN

The understanding of the reemergence of pressure induced superconductivity in alkali-metal intercalated FeSe is hampered by sample complexities. Here, Sun et al. report the electronic properties of (Li1–xFe x )OHFe1–ySe single crystal not only in the reemerged superconducting state but also in the normal state.

25 January 2018 | doi: 10.1038/s41467-018-02843-7
Electronic properties and materials  Superconducting properties and materials 

SWELL1 is a glucose sensor regulating β-cell excitability and systemic glycaemia OPEN
Chen Kang, Litao Xie, Susheel K. Gunasekar, Anil Mishra, Yanhui Zhang, Saachi Pai, Yiwen Gao, Ashutosh Kumar, Andrew W. Norris, Samuel B. Stephens & Rajan Sah

Insulin secretion by β-cells is stimulated by glucose and is dependent on the induction of β-cell membrane depolarization, mainly driven by the closure of KATP channels, which in turn promotes voltage-gated Ca2+ channel opening. Here Kang et al. show that the volume-regulated anion channel, SWELL1, is involved in glucose-stimulated calcium increase and insulin secretion.

25 January 2018 | doi: 10.1038/s41467-017-02664-0
Calcium signalling  Insulin signalling  Ion channel signalling 

Endothelial deletion of Ino80 disrupts coronary angiogenesis and causes congenital heart disease OPEN
Siyeon Rhee, Jae I. Chung, Devin A. King, Gaetano D’amato, David T. Paik, Anna Duan, Andrew Chang, Danielle Nagelberg, Bikram Sharma, Youngtae Jeong, Maximilian Diehn, Joseph C. Wu, Ashby J. Morrison & Kristy Red-Horse

Heart development requires compaction of the ventricular wall into a dense myocardium at mid-gestation. Here, Rhee and colleagues show that the chromatin remodeller Ino80 is critical for the formation of the coronary vasculature, and show that coronary vessels are needed for successful cardiac compaction during embryonic development.

25 January 2018 | doi: 10.1038/s41467-017-02796-3
Angiogenesis  Congenital heart defects 

Multiple signaling kinases target Mrc1 to prevent genomic instability triggered by transcription-replication conflicts OPEN
Alba Duch, Berta Canal, Sonia I. Barroso, María García-Rubio, Gerhard Seisenbacher, Andrés Aguilera, Eulàlia de Nadal & Francesc Posas

During S phase of the cell cycle, transcription and replication need to be coordinated in order to avoid conflicts leading to potential genomic instability. Here, the authors find that Mrc1 integrates signals from different kinases to regulate replication during unscheduled transcription events.

25 January 2018 | doi: 10.1038/s41467-017-02756-x
Checkpoints  Stress signalling 

Biosensing with the singular phase of an ultrathin metal-dielectric nanophotonic cavity OPEN
Kandammathe Valiyaveedu Sreekanth, Sivaramapanicker Sreejith, Song Han, Amita Mishra, Xiaoxuan Chen, Handong Sun, Chwee Teck Lim & Ranjan Singh

Optical sensors generally rely on abrupt phase changes to detect the presence of an analyte, but oftentimes they require complex nanostructures. Here, Sreekanth et al. use a simple asymmetric thin-film multilayer stack to demonstrate a point of darkness and phase singularity to develop a sensitive biosensor.

25 January 2018 | doi: 10.1038/s41467-018-02860-6
Biosensors  Nanocavities  Nanophotonics and plasmonics 

Astrocytes modulate brainstem respiratory rhythm-generating circuits and determine exercise capacity OPEN
Shahriar Sheikhbahaei, Egor A. Turovsky, Patrick S. Hosford, Anna Hadjihambi, Shefeeq M. Theparambil, Beihui Liu, Nephtali Marina, Anja G. Teschemacher, Sergey Kasparov, Jeffrey C. Smith & Alexander V. Gourine

Circuits of the preBötzinger complex generate rhythms needed for breathing. Here, the authors provide evidence, using a combination of chemogenetic approaches and approaches to inhibit vesicular release, that astrocytes play a role in regulating respiratory rate.

25 January 2018 | doi: 10.1038/s41467-017-02723-6
Neural circuits  Respiration 

Highly-efficient quantum memory for polarization qubits in a spatially-multiplexed cold atomic ensemble OPEN
Pierre Vernaz-Gris, Kun Huang, Mingtao Cao, Alexandra S. Sheremet & Julien Laurat

Future quantum networks will require quantum memories with effective storage-and-retrieval capabilities. Here, the authors use electromagnetically-induced transparency in a high optical-depth, spatially-multiplexed cold atom ensemble to store and retrieve polarization qubits with high efficiency.

25 January 2018 | doi: 10.1038/s41467-017-02775-8
Atomic and molecular interactions with photons  Quantum information  Quantum optics  Ultracold gases 

High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening OPEN
Yoshihito Shinozaki, Philippe Nicolas, Noe Fernandez-Pozo, Qiyue Ma, Daniel J. Evanich, Yanna Shi, Yimin Xu, Yi Zheng, Stephen I. Snyder, Laetitia B. B. Martin, Eliel Ruiz-May, Theodore W. Thannhauser, Kunsong Chen, David S. Domozych, Carmen Catalá, Zhangjun Fei, Lukas A. Mueller, James J. Giovannoni & Jocelyn K. C. Rose

Cell-type transcriptome profiling greatly elucidate organismal development. Here, the authors report a spatiotemporally resolved comprehensive transcriptome analysis of tomato fruit ontogeny and suggest a new model of fruit maturation which initiates in internal tissues then radiates outwards.

25 January 2018 | doi: 10.1038/s41467-017-02782-9
Cell proliferation  Plant molecular biology  Transcriptomics 

A global ocean atlas of eukaryotic genes OPEN
Quentin Carradec, Eric Pelletier, Corinne Da Silva, Adriana Alberti, Yoann Seeleuthner, Romain Blanc-Mathieu, Gipsi Lima-Mendez, Fabio Rocha, Leila Tirichine, Karine Labadie, Amos Kirilovsky, Alexis Bertrand, Stefan Engelen, Mohammed-Amin Madoui, Raphaël Méheust, Julie Poulain, Sarah Romac, Daniel J. Richter, Genki Yoshikawa, Céline Dimier et al.

Marine microbial eukaryotes and zooplankton display enormous diversity and largely unexplored physiologies. Here, the authors use metatranscriptomics to analyze four organismal size fractions from open-ocean stations, providing the largest reference collection of eukaryotic transcripts from any single biome.

25 January 2018 | doi: 10.1038/s41467-017-02342-1
Genomics  Marine biology  Microbial ecology  Water microbiology 

The creation of electric wind due to the electrohydrodynamic force OPEN
Sanghoo Park, Uros Cvelbar, Wonho Choe & Se Youn Moon

The electric wind mechanism remains unclear. Here, the authors report evidence that electric wind is caused by an electrohydrodynamic force generated by charged particle drag as a result of momentum transfer to neutral particles.

25 January 2018 | doi: 10.1038/s41467-017-02766-9
Astrophysical plasmas  Atomic and molecular collision processes  Fluid dynamics  Plasma physics 

Streamlined asymmetric α-difunctionalization of ynones OPEN
Siyu Peng, Zhaofeng Wang, Linxing Zhang, Xinhao Zhang & Yong Huang

Chiral ynones with an α-quaternary carbon are attractive synthetic building blocks for natural and pharmaceutical products. Here, the authors report an asymmetric α-difunctionalization of simple ynones, involving a gold-catalyzed step and yielding enantioenriched fluorinated quaternary stereocentres.

25 January 2018 | doi: 10.1038/s41467-017-02801-9
Homogeneous catalysis  Synthetic chemistry methodology  Stereochemistry 

A quiescent cell population replenishes mesenchymal stem cells to drive accelerated growth in mouse incisors OPEN
Zhengwen An, Maja Sabalic, Ryan F. Bloomquist, Teresa E. Fowler, Todd Streelman & Paul T Sharpe

Mouse incisors constantly renew from a slow cycling population of mesenchymal stem cells. Here, the authors show that upon cutting of adult incisors, a sub-population of dental mesenchymal stem cells reactivates, allowing an increased growth rate and rapid regeneration.

25 January 2018 | doi: 10.1038/s41467-017-02785-6
Developmental biology  Mesenchymal stem cells 

Lsd1 regulates skeletal muscle regeneration and directs the fate of satellite cells OPEN
Milica Tosic, Anita Allen, Dominica Willmann, Christoph Lepper, Johnny Kim, Delphine Duteil & Roland Schüle

Satellite cells can differentiate both into myocytes and brown adipocytes. Here, the authors show that the histone demethylase Lsd1 prevents adipogenic differentiation of satellite cells by repressing expression of Glis1, and that its ablation changes satellite cell fate towards brown adipocytes and delays muscle regeneration in mice.

25 January 2018 | doi: 10.1038/s41467-017-02740-5
Adipocytes  DNA methylation  Muscle stem cells  Skeletal muscle 

The ecological origins of snakes as revealed by skull evolution OPEN
Filipe O. Da Silva, Anne-Claire Fabre, Yoland Savriama, Joni Ollonen, Kristin Mahlow, Anthony Herrel, Johannes Müller & Nicolas Di-Poï

Three alternatives have been proposed for the ecological state of the ancestral snake: fossorial (burrowing), aquatic, or terrestrial. Here, the authors use an integrative geometric morphometric approach that suggests evolution from terrestrial to fossorial in the most recent common ancestor of extant snakes.

25 January 2018 | doi: 10.1038/s41467-017-02788-3
Evolutionary developmental biology  Evolutionary ecology  Herpetology  Palaeontology 

AMPK activation counteracts cardiac hypertrophy by reducing O-GlcNAcylation OPEN
Roselle Gélinas, Florence Mailleux, Justine Dontaine, Laurent Bultot, Bénédicte Demeulder, Audrey Ginion, Evangelos P. Daskalopoulos, Hrag Esfahani, Emilie Dubois-Deruy, Benjamin Lauzier, Chantal Gauthier, Aaron K. Olson, Bertrand Bouchard, Christine Des Rosiers, Benoit Viollet, Kei Sakamoto, Jean-Luc Balligand, Jean-Louis Vanoverschelde, Christophe Beauloye, Sandrine Horman et al.

AMPK activation inhibits cardiac hypertrophy. Here the authors show that this occurs independently of previously proposed mechanisms and that AMPK controls the phosphorylation of the aminotransferase GFAT, thereby preventing cardiac hypertrophy through the reduction of protein O-GlcNAcylation.

25 January 2018 | doi: 10.1038/s41467-017-02795-4
Cardiac hypertrophy  Glycosylation  Kinases 

Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli OPEN
Thomas E. Bohl, Ke Shi, John K. Lee & Hideki Aihara

LpxB is a membrane-associated glycosyltransferase required for bacterial lipopolysaccharide biosynthesis. Here, Bohl et al. solve the crystal structure of a soluble LpxB variant, showing an intertwined C-terminally swapped dimer, and residues likely mediating association with lipidic substrates or the membrane.

25 January 2018 | doi: 10.1038/s41467-017-02712-9
Bacterial structural biology  Enzymes  X-ray crystallography 

Laser-accelerated particle beams for stress testing of materials OPEN
M. Barberio, M. Scisciò, S. Vallières, F. Cardelli, S. N. Chen, G. Famulari, T. Gangolf, G. Revet, A. Schiavi, M. Senzacqua & P. Antici

Recently, there has been significant progress on the application of laser-generated proton beams in material science. Here the authors demonstrate the benefit of employing such beams in stress testing different materials by examining their mechanical, optical, electrical, and morphological properties.

25 January 2018 | doi: 10.1038/s41467-017-02675-x
Characterization and analytical techniques  Mechanical properties  Plasma-based accelerators 
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