Wednesday, June 20, 2018

Nature Communications - 20 June 2018

Nature Communications

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Brain-actuated functional electrical stimulation elicits lasting arm motor recovery after stroke OPEN
A. Biasiucci, R. Leeb, I. Iturrate, S. Perdikis, A. Al-Khodairy, T. Corbet, A. Schnider, T. Schmidlin, H. Zhang, M. Bassolino, D. Viceic, P. Vuadens, A. G. Guggisberg & J. d. R. Millán

Brain-computer interface (BCI) can improve motor skills on stroke patients. This study shows that BCI-controlled neuromuscular electrical stimulation therapy can cause cortical reorganization due to activation of efferent and afferent pathways, and this effect can be long lasting in a brain region specific manner.

20 June 2018 | doi: 10.1038/s41467-018-04673-z
Biomedical engineering  Brain–machine interface 

Intraamniotic Zika virus inoculation of pregnant rhesus macaques produces fetal neurologic disease OPEN
Lark L. Coffey, Rebekah I. Keesler, Patricia A. Pesavento, Kevin Woolard, Anil Singapuri, Jennifer Watanabe, Christina Cruzen, Kari L. Christe, Jodie Usachenko, JoAnn Yee, Victoria A. Heng, Eliza Bliss-Moreau, J. Rachel Reader, Wilhelm von Morgenland, Anne M. Gibbons, Kenneth Jackson, Amir Ardeshir, Holly Heimsath, Sallie Permar, Paranthaman Senthamaraikannan et al.

Zika virus infection of pregnant women can cause congenital brain defects. Here, Coffey et al. establish a pregnant rhesus macaque model, using intravenous and intraamniotic route of infection, that reliably reproduces fetal neurologic defects of congenital Zika syndrome in humans.

20 June 2018 | doi: 10.1038/s41467-018-04777-6
Animal disease models  Neurological disorders  Viral infection  Viral pathogenesis 

miR-143/145 differentially regulate hematopoietic stem and progenitor activity through suppression of canonical TGFβ signaling OPEN
Jeffrey Lam, Marion van den Bosch, Joanna Wegrzyn, Jeremy Parker, Rawa Ibrahim, Kate Slowski, Linda Chang, Sergio Martinez-Høyer, Gianluigi Condorelli, Mark Boldin, Yu Deng, Patricia Umlandt, Megan Fuller & Aly Karsan

Myelodysplastic syndrome (MDS) is characterized by altered hematopoietic stem cell (HSC) and hematopoietic progenitor cell (HPC) regulation and reduction of miR-143 and miR-145 in some subtypes. Here the authors show that miR-143/145 loss leads to HSC depletion, HPC expansion and malignancy through Dab2 -mediated TGFβ pathway activation.

20 June 2018 | doi: 10.1038/s41467-018-04831-3
Gene regulation  Mechanisms of disease  Myelodysplastic syndrome 

Cultural conformity generates extremely stable traditions in bird song OPEN
Robert F. Lachlan, Oliver Ratmann & Stephen Nowicki

‘Conformist bias’, in which individuals learn a common behavioural variant more often than expected by chance, has not been demonstrated convincingly in non-human animals. This study analyses song recordings and models of cultural evolution to show conformist bias in swamp sparrow populations.

20 June 2018 | doi: 10.1038/s41467-018-04728-1
Animal behaviour  Cultural evolution 

Unsupervised clustering and epigenetic classification of single cells OPEN
Mahdi Zamanighomi, Zhixiang Lin, Timothy Daley, Xi Chen, Zhana Duren, Alicia Schep, William J. Greenleaf & Wing Hung Wong

Single cell ATAC-seq (scATAC-seq) data reveals cellular level epigenetic heterogeneity but its application in delineating distinct subpopulations is still challenging. Here, the authors develop scABC, a statistical method for unsupervised clustering of scATAC-seq data and identification of open chromatin regions specific to cell identity.

20 June 2018 | doi: 10.1038/s41467-018-04629-3
Computational biology and bioinformatics  Epigenetics  Functional clustering  Software  Statistical methods 

Assigning the absolute configuration of single aliphatic molecules by visual inspection OPEN
Daniel Ebeling, Marina Šekutor, Marvin Stiefermann, Jalmar Tschakert, Jeremy E. P. Dahl, Robert M. K. Carlson, André Schirmeisen & Peter R. Schreiner

Deciphering absolute configuration of individual molecules directly by visual inspection remains a highly attractive goal. Here, the authors determine the absolute configuration and orientation of a single [123]tetramantane molecule adsorbed on Cu(111) using low temperature atomic force microscopy with a CO-functionalized tip.

20 June 2018 | doi: 10.1038/s41467-018-04843-z
Chemical physics  Computational chemistry  Scanning probe microscopy 

Molecular basis for the production of cyclic peptides by plant asparaginyl endopeptidases OPEN
M. A. Jackson, E. K. Gilding, T. Shafee, K. S. Harris, Q. Kaas, S. Poon, K. Yap, H. Jia, R. Guarino, L. Y. Chan, T. Durek, M. A. Anderson & D. J. Craik

Asparaginyl endopeptidases (AEPs) are plant proteases that can also function as ligases, catalyzing the production of cyclic plant peptides. Here, the authors identify structural features that govern AEP ligase activity, providing insights to aid the discovery and engineering of ligase-type AEPs.

20 June 2018 | doi: 10.1038/s41467-018-04669-9
Enzymes  Molecular engineering in plants  Peptides 

Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract OPEN
Philip Burnham, Darshana Dadhania, Michael Heyang, Fanny Chen, Lars F. Westblade, Manikkam Suthanthiran, John Richard Lee & Iwijn De Vlaminck

Urinary tract infections are one of the most common infections in humans. Here, the authors use urinary cell-free DNA (cfDNA) to comprehensively monitor host and pathogen dynamics in bacterial and viral urinary tract infections, and show that it is a versatile analyte for monitoring urinary tract infections.

20 June 2018 | doi: 10.1038/s41467-018-04745-0
Infectious-disease diagnostics  Infectious diseases  Medical genomics  Urology 

Double thermoelectric power factor of a 2D electron system OPEN
Yuqiao Zhang, Bin Feng, Hiroyuki Hayashi, Cheng-Ping Chang, Yu-Miin Sheu, Isao Tanaka, Yuichi Ikuhara & Hiromichi Ohta

The accelerated growth of thermoelectric technology that efficiently converts waste heat to electricity necessitates the development of high-performance materials. Here, the authors experimentally demonstrate a 2D electron system with enhanced two-dimensionality and thermoelectric power factor.

20 June 2018 | doi: 10.1038/s41467-018-04660-4
Electronic properties and materials  Surfaces, interfaces and thin films  Thermoelectric devices and materials  Thermoelectrics  Two-dimensional materials 

FGF signalling controls the specification of hair placode-derived SOX9 positive progenitors to Merkel cells OPEN
Minh Binh Nguyen, Idan Cohen, Vinod Kumar, Zijian Xu, Carmit Bar, Katherine L. Dauber-Decker, Pai-Chi Tsai, Pauline Marangoni, Ophir D. Klein, Ya-Chieh Hsu, Ting Chen, Marja L. Mikkola & Elena Ezhkova

Merkel cells are mechanoreceptors located in the epidermis whose developmental origin is unclear. Here the authors show that Merkel cells originate from SOX9 positive cells inside hair follicles and that FGFR2-mediated epithelial signalling is required for their specification.

20 June 2018 | doi: 10.1038/s41467-018-04399-y
Differentiation  Skin stem cells  Stem-cell differentiation 

C-terminal truncation of IFN-γ inhibits proinflammatory macrophage responses and is deficient in autoimmune disease OPEN
Antoine Dufour, Caroline L. Bellac, Ulrich Eckhard, Nestor Solis, Theo Klein, Reinhild Kappelhoff, Nikolaus Fortelny, Parker Jobin, Jacob Rozmus, Jennifer Mark, Paul Pavlidis, Vincent Dive, Sean J. Barbour & Christopher M. Overall

IFN-γ is central in inflammatory pathogenesis, response to infection and autoimmune diseases. Here the authors show that MMP12 expression is reduced in patients with SLE and that MMP12 post-translationally truncates IFN-y, inhibiting its function and affecting pathogenesis of mouse models of peritonitis, SLE and rheumatoid arthritis.

20 June 2018 | doi: 10.1038/s41467-018-04717-4
Proteases  Rheumatoid arthritis  Systemic lupus erythematosus 

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity OPEN
Emelie Berglund, Jonas Maaskola, Niklas Schultz, Stefanie Friedrich, Maja Marklund, Joseph Bergenstråhle, Firas Tarish, Anna Tanoglidi, Sanja Vickovic, Ludvig Larsson, Fredrik Salmén, Christoph Ogris, Karolina Wallenborg, Jens Lagergren, Patrik Ståhl, Erik Sonnhammer, Thomas Helleday & Joakim Lundeberg

Heterogeneity within tumors presents a challenge to cancer treatment. Here, the authors investigate transcriptional heterogeneity in prostate cancer, examining expression profiles of different tissue components and highlighting expression gradients in the tumor microenvironment.

20 June 2018 | doi: 10.1038/s41467-018-04724-5
Computational models  Probabilistic data networks  RNA sequencing  Transcription  Tumour heterogeneity 

Giant intrinsic circular dichroism of prolinol-derived squaraine thin films OPEN
Matthias Schulz, Jennifer Zablocki, Oliya S. Abdullaeva, Stefanie Brück, Frank Balzer, Arne Lützen, Oriol Arteaga & Manuela Schiek

The use of chiral molecules for optoelectronics remains underexplored. Here, the authors perform Mueller matrix spectroscopy on thin films of enantiopure prolinol functionalized squaraines and report an extraordinarily high circular dichroism, thus providing a benchmark material for chiroptical applications.

20 June 2018 | doi: 10.1038/s41467-018-04811-7
Optical materials and structures  Organic molecules in materials science 

A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection OPEN
Akul Singhania, Raman Verma, Christine M. Graham, Jo Lee, Trang Tran, Matthew Richardson, Patrick Lecine, Philippe Leissner, Matthew P. R. Berry, Robert J. Wilkinson, Karine Kaiser, Marc Rodrigue, Gerrit Woltmann, Pranabashis Haldar & Anne O’Garra

Mass screening diagnostics for Mycobacterium tuberculosis exist, but criticisms exist regarding the sensitivity and specificity of these tools. Here the authors use RNA-Seq and a modular bioinformatics approach using data from their own cohorts and meta-analysis of published cohorts to create a reduced signature for detection of tuberculosis that does not detect other diseases.

19 June 2018 | doi: 10.1038/s41467-018-04579-w
Immunology  Infectious diseases 

Nuclear PTEN safeguards pre-mRNA splicing to link Golgi apparatus for its tumor suppressive role OPEN
Shao-Ming Shen, Yan Ji, Cheng Zhang, Shuang-Shu Dong, Shuo Yang, Zhong Xiong, Meng-Kai Ge, Yun Yu, Li Xia, Meng Guo, Jin-Ke Cheng, Jun-Ling Liu, Jian-Xiu Yu & Guo-Qiang Chen

Cytoplasmic PTEN is a tumor suppressor that antagonises PI3K signalling. Here, the authors show that nuclear PTEN can interact with the spliceosomal proteins and drive pre-mRNA splicing in a phosphatase-independent manner, in particular, PTEN depletion promotes Golgi extension and secretion through GOLGA2 exon skipping.

19 June 2018 | doi: 10.1038/s41467-018-04760-1
Alternative splicing  Golgi  Targeted therapies  Tumour-suppressor proteins 

Covalent-supramolecular hybrid polymers as muscle-inspired anisotropic actuators OPEN
Stacey M. Chin, Christopher V. Synatschke, Shuangping Liu, Rikkert J. Nap, Nicholas A. Sather, Qifeng Wang, Zaida Álvarez, Alexandra N. Edelbrock, Timmy Fyrner, Liam C. Palmer, Igal Szleifer, Monica Olvera de la Cruz & Samuel I. Stupp

Skeletal muscles are impressive as they can achieve reversible, macroscopic, anisotropic motion in soft materials. Here the authors show a bottom-up design of macroscopic hydrogel tubes containing supramolecular nanofibers that can undergo anisotropic actuation by thermal stimuli.

19 June 2018 | doi: 10.1038/s41467-018-04800-w
Polymers  Self-assembly 

Late-life targeting of the IGF-1 receptor improves healthspan and lifespan in female mice OPEN
Kai Mao, Gabriela Farias Quipildor, Tahmineh Tabrizian, Ardijana Novaj, Fangxia Guan, Ryan O. Walters, Fabien Delahaye, Gene B. Hubbard, Yuji Ikeno, Keisuke Ejima, Peng Li, David B. Allison, Hossein Salimi-Moosavi, Pedro J. Beltran, Pinchas Cohen, Nir Barzilai & Derek M. Huffman

Reduced IGF-1 signaling increases longevity in many organisms. Here, Mao et al. show that administration of an anti-IGF-1R antibody is well tolerated and delays aging in female mice; importantly, late-life targeting is sufficient to achieve the beneficial effects.

19 June 2018 | doi: 10.1038/s41467-018-04805-5
Ageing  Endocrine system and metabolic diseases 

Caffeine-inducible gene switches controlling experimental diabetes OPEN
Daniel Bojar, Leo Scheller, Ghislaine Charpin-El Hamri, Mingqi Xie & Martin Fussenegger

Control of transgene expression should ideally be easy and with minimal side effects. Here the authors present a synthetic biology-based approach in which the caffeine in coffee regulates a genetic circuit controlling glucagon-like peptide 1 expression in diabetic mice.

19 June 2018 | doi: 10.1038/s41467-018-04744-1
Synthetic biology  Type 2 diabetes 

DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis OPEN
Lara Kular, Yun Liu, Sabrina Ruhrmann, Galina Zheleznyakova, Francesco Marabita, David Gomez-Cabrero, Tojo James, Ewoud Ewing, Magdalena Lindén, Bartosz Górnikiewicz, Shahin Aeinehband, Pernilla Stridh, Jenny Link, Till F. M. Andlauer, Christiane Gasperi, Heinz Wiendl, Frauke Zipp, Ralf Gold, Björn Tackenberg, Frank Weber et al.

The human leukocyte antigen (HLA) haplotype DRB1*15:01 is the major risk factor for multiple sclerosis (MS).  Here the authors find that DNA methylation at HLA-DRB1 gene mediates the effect of DRB1*15:01 and of a protective HLA variant on HLA-DRB1 expression and the risk of MS.

19 June 2018 | doi: 10.1038/s41467-018-04732-5
DNA methylation  Epigenomics  Multiple sclerosis 

ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range OPEN
Andrey Aristov, Benoit Lelandais, Elena Rensen & Christophe Zimmer

3D single-molecule localization is limited in depth and often requires using a wide range of point spread functions (PSFs). Here the authors present an optical solution featuring a deformable mirror to generate different PSFs and easy-to-use software for super-resolution imaging up to 5 µm deep.

19 June 2018 | doi: 10.1038/s41467-018-04709-4
Image processing  Single-molecule biophysics  Super-resolution microscopy 

HEPATOKIN1 is a biochemistry-based model of liver metabolism for applications in medicine and pharmacology OPEN
Nikolaus Berndt, Sascha Bulik, Iwona Wallach, Tilo Wünsch, Matthias König, Martin Stockmann, David Meierhofer & Hermann-Georg Holzhütter

In silico models of cells can provide insight into the causes and effects of disease states and reduce the need for in vivo studies. Here, the authors present a kinetic model of hepatocyte metabolism including energy, carbohydrate, lipid and nitrogen metabolism and hormonal and allosteric regulation of enzymatic activity.

19 June 2018 | doi: 10.1038/s41467-018-04720-9
Biochemical reaction networks  Enzyme mechanisms  Metabolic engineering 

Electron–electron interactions and the paired-to-nematic quantum phase transition in the second Landau level OPEN
K. A. Schreiber, N. Samkharadze, G. C. Gardner, Y. Lyanda-Geller, M. J. Manfra, L. N. Pfeiffer, K. W. West & G. A. Csáthy

Two-dimensional electron systems at half-filled Landau levels can form unusual electronic states such as paired fractional quantum Hall and nematic phases. Here the authors observe the transition between these two phases at filling factors 5/2 and 7/2 and demonstrate the important influence of interactions.

19 June 2018 | doi: 10.1038/s41467-018-04879-1
Electronic properties and materials  Phase transitions and critical phenomena  Quantum Hall  Semiconductors 

Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells OPEN
Jessie A. G. van Buggenum, Jan P. Gerlach, Sabine E. J. Tanis, Mark Hogeweg, Pascal W. T. C. Jansen, Jesse Middelwijk, Ruud van der Steen, Michiel Vermeulen, Hendrik G. Stunnenberg, Cornelis A. Albers & Klaas W. Mulder

Detecting proteins and post-translational modifications is important for drug screens, but the number of proteins measurable simultaneously is limited. Here the authors use antibodies tagged with DNA barcodes and high-throughput sequencing to detect up to 70 (phospho-)proteins in stem cells.

19 June 2018 | doi: 10.1038/s41467-018-04761-0
Cell proliferation  Phenotypic screening  Phosphorylation  Proteomic analysis  Skin stem cells 

Dispositional free riders do not free ride on punishment OPEN
Till O. Weber, Ori Weisel & Simon Gächter

Strong positive and strong negative reciprocators reward cooperation and punish defection, respectively, regardless of future benefits. Here, Weber and colleagues demonstrate that dispositions towards strong positive and strong negative reciprocity are not correlated within individuals.

19 June 2018 | doi: 10.1038/s41467-018-04775-8
Cooperation  Economics  Human behaviour  Social evolution 

Optimization of the structural characteristics of CaO and its effective stabilization yield high-capacity CO2 sorbents OPEN
Muhammad Awais Naeem, Andac Armutlulu, Qasim Imtiaz, Felix Donat, Robin Schäublin, Agnieszka Kierzkowska & Christoph R. Müller

The economic operation of a carbon dioxide capture technique of calcium looping necessitates highly effective CaO-based CO2 sorbents. Here, the authors report a facile one-pot synthesis approach to yield highly effective, MgO-stabilized, CaO-based CO2 sorbents featuring highly porous multishelled morphologies.

19 June 2018 | doi: 10.1038/s41467-018-04794-5
Carbon capture and storage  Chemical engineering  Materials for energy and catalysis 

The synaptic receptor Lrp4 promotes peripheral nerve regeneration OPEN
Katherine D. Gribble, Lauren J. Walker, Louis Saint-Amant, John Y. Kuwada & Michael Granato

Axons of the peripheral nervous system regenerate along Schwann cells following injury. Here, the authors show that regenerating axons follow pioneer axons and this process is mediated by lipoprotein receptor-related protein 4 (Lrp4), a protein otherwise known for its role in synapse formation.

19 June 2018 | doi: 10.1038/s41467-018-04806-4
Peripheral nervous system  Regeneration and repair in the nervous system 

Out-of-equilibrium microcompartments for the bottom-up integration of metabolic functions OPEN
Thomas Beneyton, Dorothee Krafft, Claudia Bednarz, Christin Kleineberg, Christian Woelfer, Ivan Ivanov, Tanja Vidaković-Koch, Kai Sundmacher & Jean-Christophe Baret

Generating artificial cells able to carry out metabolic activities out-of-equilibrium is a current challenge in synthetic biology. Here the authors use a microfluidic platform for integration and analysis of minimal metabolic reactions in artificial microcompartments formed of water-in-oil droplets.

19 June 2018 | doi: 10.1038/s41467-018-04825-1
Fluids  Microfluidics  Synthetic biology 

Scalable training of artificial neural networks with adaptive sparse connectivity inspired by network science OPEN
Decebal Constantin Mocanu, Elena Mocanu, Peter Stone, Phuong H. Nguyen, Madeleine Gibescu & Antonio Liotta

Artificial neural networks are artificial intelligence computing methods which are inspired by biological neural networks. Here the authors propose a method to design neural networks as sparse scale-free networks, which leads to a reduction in computational time required for training and inference.

19 June 2018 | doi: 10.1038/s41467-018-04316-3
Complex networks  Computer science  Machine learning 

Patient derived organoids to model rare prostate cancer phenotypes OPEN
Loredana Puca, Rohan Bareja, Davide Prandi, Reid Shaw, Matteo Benelli, Wouter R. Karthaus, Judy Hess, Michael Sigouros, Adam Donoghue, Myriam Kossai, Dong Gao, Joanna Cyrta, Verena Sailer, Aram Vosoughi, Chantal Pauli, Yelena Churakova, Cynthia Cheung, Lesa Dayal Deonarine, Terra J. McNary, Rachele Rosati et al.

There are few available models to study neuroendocrine prostate cancer. Here they develop and characterize patient derived organoids from metastatic lesions, use these models to show the role of EZH2 in driving neuroendocrine phenotype, and perform high throughput organoid screening to identify therapeutic drug combinations.

19 June 2018 | doi: 10.1038/s41467-018-04495-z
Cancer models  Cancer therapy 

A phosphorylation switch turns a positive regulator of phototropism into an inhibitor of the process OPEN
Paolo Schumacher, Emilie Demarsy, Patrice Waridel, Laure Allenbach Petrolati, Martine Trevisan & Christian Fankhauser

Light conditions modify plant growth and development via photoreceptors such as phototropins. Here the authors show that while phot1 promotes phototropism under low light, it can act to suppress phototropism in high-light environments through phosphorylation of PKS4.

19 June 2018 | doi: 10.1038/s41467-018-04752-1
Kinases  Light responses 

Thermodynamic and structural anomalies of water nanodroplets OPEN
Shahrazad M. A. Malek, Peter H. Poole & Ivan Saika-Voivod

Nanoscale water droplets can remain liquid far below the homogenous nucleation temperature, at which bulk cooled water inevitably crystallizes. Malek et al. show that water in nanodroplets as small as a few hundred molecules reproduce the thermodynamic anomalies of bulk water. 

19 June 2018 | doi: 10.1038/s41467-018-04816-2
Chemical physics  Nanoscale materials 

Single-walled carbon-nanohorns improve biocompatibility over nanotubes by triggering less protein-initiated pyroptosis and apoptosis in macrophages OPEN
Bing He, Yujie Shi, Yanqin Liang, Anpu Yang, Zhipu Fan, Lan Yuan, Xiajuan Zou, Xin Chang, Hua Zhang, Xueqing Wang, Wenbin Dai, Yiguang Wang & Qiang Zhang

Carbon-nanohorns have a unique morphology and structure yet little is known about the biocompatibility. Here, the authors investigate the biocompatibility and bio-interaction of carbon nanohorns, compare them to carbon nanotubes and show the superior biocompatibility and safety of the nanohorns.

19 June 2018 | doi: 10.1038/s41467-018-04700-z
Biomaterials  Cell death  Cell–particle interactions 

Enhanced ocean-atmosphere carbon partitioning via the carbonate counter pump during the last deglacial OPEN
Stéphanie Duchamp-Alphonse, Giuseppe Siani, Elisabeth Michel, Luc Beaufort, Yves Gally & Samuel L. Jaccard

The contribution of the carbonate counter pump (CCP) to the last deglacial atmospheric CO2 rise has yet been largely ignored. Here, the authors show that an increased CCP in the Subantarctic Pacific along with high surface ocean fertility and [CO2aq], contributed in propelling the Earth out of the last ice age.

19 June 2018 | doi: 10.1038/s41467-018-04625-7
Carbon cycle  Palaeoceanography  Palaeoclimate 

Improving formaldehyde consumption drives methanol assimilation in engineered E. coli OPEN
Benjamin M. Woolston, Jason R. King, Michael Reiter, Bob Van Hove & Gregory Stephanopoulos

Engineering E. coli for metabolization of methanol to produce fuels and chemicals has not been fully achieved. Here, the authors combine metabolic engineering and chemical inhibition to improve methanol assimilation and distinguish the role of kinetics and thermodynamics under various culture conditions.

19 June 2018 | doi: 10.1038/s41467-018-04795-4
Chemical genetics  Metabolic engineering  Metabolomics 

Efficient and self-adaptive in-situ learning in multilayer memristor neural networks OPEN
Can Li, Daniel Belkin, Yunning Li, Peng Yan, Miao Hu, Ning Ge, Hao Jiang, Eric Montgomery, Peng Lin, Zhongrui Wang, Wenhao Song, John Paul Strachan, Mark Barnell, Qing Wu, R. Stanley Williams, J. Joshua Yang & Qiangfei Xia

Memristor-based neural networks hold promise for neuromorphic computing, yet large-scale experimental execution remains difficult. Here, Xia et al. create a multi-layer memristor neural network with in-situ machine learning and achieve competitive image classification accuracy on a standard dataset.

19 June 2018 | doi: 10.1038/s41467-018-04484-2
Computer science  Electrical and electronic engineering 

Carbon costs and benefits of Indonesian rainforest conversion to plantations OPEN
Thomas Guillaume, Martyna M. Kotowska, Dietrich Hertel, Alexander Knohl, Valentyna Krashevska, Kukuh Murtilaksono, Stefan Scheu & Yakov Kuzyakov

Rainforest conversion to plantations driven by global demand for agricultural products generates high environmental costs. Here, the authors show that the high oil palm plantation production efficiency is associated with decreased carbon storage and slower organic matter cycling that affect ecosystem services.

19 June 2018 | doi: 10.1038/s41467-018-04755-y
Agroecology  Carbon cycle  Ecosystem services  Environmental impact  Tropical ecology 

Co-regulatory activity of hnRNP K and NS1-BP in influenza and human mRNA splicing OPEN
Matthew G. Thompson, Raquel Muñoz-Moreno, Prasanna Bhat, Renat Roytenberg, John Lindberg, Matthew R. Gazzara, Michael J. Mallory, Ke Zhang, Adolfo García-Sastre, Beatriz M. A. Fontoura & Kristen W. Lynch

Alternative splicing of influenza A virus (IAV) M transcript is regulated by hnRNP K and NS1-BP, but mechanistic details are unknown. Here, Thompson et al. show how hnRNP K and NS1-BP bind M mRNA and that these proteins regulate splicing of host transcripts in both the absence and presence of IAV infection.

19 June 2018 | doi: 10.1038/s41467-018-04779-4
Alternative splicing  Influenza virus  RNA splicing  Virus–host interactions 

Nanoscale electrical conductivity imaging using a nitrogen-vacancy center in diamond OPEN
Amila Ariyaratne, Dolev Bluvstein, Bryan A. Myers & Ania C. Bleszynski Jayich

Nitrogen-vacancy centres in diamond are highly sensitive to their environment, making them well suited to quantum sensing applications. Here, the authors demonstrate the capabilities of a scanning nitrogen-vacancy sensor for nanoscale measurements of electrical conductivity.

19 June 2018 | doi: 10.1038/s41467-018-04798-1
Optical properties of diamond  Electronic properties and materials  Magnetic properties and materials  Surfaces, interfaces and thin films 

Tailoring exciton and excimer emission in an exfoliated ultrathin 2D metal-organic framework OPEN
Wei-Ming Liao, Jian-Hua Zhang, Shao-Yun Yin, He Lin, Xingmin Zhang, Jihong Wang, Hai-Ping Wang, Kai Wu, Zheng Wang, Ya-Nan Fan, Mei Pan & Cheng-Yong Su

Two dimensional (2D) metal-organic frameworks have demonstrated unique photophysical properties compared to their bulk analogs. Here, the authors demonstrate that exfoliation of 2D MOFs can suppress interlayer exciton-related emission, allowing for modulation of the overall emission color and switching of optical memory states.

19 June 2018 | doi: 10.1038/s41467-018-04833-1
Metal–organic frameworks  Optical materials  Optical materials and structures 

Neural mechanisms for selectively tuning in to the target speaker in a naturalistic noisy situation OPEN
Bohan Dai, Chuansheng Chen, Yuhang Long, Lifen Zheng, Hui Zhao, Xialu Bai, Wenda Liu, Yuxuan Zhang, Li Liu, Taomei Guo, Guosheng Ding & Chunming Lu

When many people are speaking, e.g. at a party, we can selectively attend to just one speaker. Here, using ‘hyperscanning’, the authors show that interpersonal neural synchronization is selectively increased between a listener and the attended speaker, compared to between the listener and an unattended speaker.

19 June 2018 | doi: 10.1038/s41467-018-04819-z
Attention  Cortex  Psychology  Sensory processing 

In situ architecture of the algal nuclear pore complex OPEN
Shyamal Mosalaganti, Jan Kosinski, Sahradha Albert, Miroslava Schaffer, Daniela Strenkert, Patrice A. Salomé, Sabeeha S. Merchant, Jürgen M. Plitzko, Wolfgang Baumeister, Benjamin D. Engel & Martin Beck

While the architecture of vertebrate nuclear pore complexes (NPCs) is well understood, the extent of its evolutionary conservation is still unclear. Here, the authors analyze the in situ architecture of an algal NPC, revealing distinct structural features that provide insights into NPC evolution.

18 June 2018 | doi: 10.1038/s41467-018-04739-y
Cryoelectron tomography  Nuclear pore complex 

High-resolution crossover mapping reveals similarities and differences of male and female recombination in maize OPEN
Penny M. A. Kianian, Minghui Wang, Kristin Simons, Farhad Ghavami, Yan He, Stefanie Dukowic-Schulze, Anitha Sundararajan, Qi Sun, Jaroslaw Pillardy, Joann Mudge, Changbin Chen, Shahryar F. Kianian & Wojciech P. Pawlowski

Sex-specific meiotic crossover (CO) landscapes have been identified in multiple species. Here, the authors show that male and female meioses in maize have similar CO landscapes, and differences between COs in the two sexes only exists in their location relative to transcription start sites and some chromatin marks.

18 June 2018 | doi: 10.1038/s41467-018-04562-5
Genetic variation  Plant genetics 

The 3.3 Å structure of a plant geminivirus using cryo-EM OPEN
Emma L. Hesketh, Keith Saunders, Chloe Fisher, Joran Potze, John Stanley, George P. Lomonossoff & Neil A. Ranson

Geminiviruses are an important plant pathogen that causes large food crop losses globally. Here the authors describe a high resolution cryo-EM structure of the Ageratum yellow vein virus and reveal the molecular details of how a single capsid protein sequence can adopt the different conformations needed to build that geminate capsid.

18 June 2018 | doi: 10.1038/s41467-018-04793-6
Cryoelectron microscopy  Plant molecular biology  Virus structures 

A CD4-mimetic compound enhances vaccine efficacy against stringent immunodeficiency virus challenge OPEN
Navid Madani, Amy M. Princiotto, Linh Mach, Shilei Ding, Jérémie Prevost, Jonathan Richard, Bhavna Hora, Laura Sutherland, Connie A. Zhao, Brandon P. Conn, Todd Bradley, M. Anthony Moody, Bruno Melillo, Andrés Finzi, Barton F. Haynes, Amos B. Smith III, Sampa Santra & Joseph Sodroski

The HIV Env trimer exhibits a closed confirmation and restricts access to known antibody binding sites. Here the authors show that a small-molecule CD4-mimetic compound binds the HIV Env trimer and enhances antibody-mediated protection in a non-human primate model of infection.

18 June 2018 | doi: 10.1038/s41467-018-04758-9
Antibodies  Vaccines  Viral infection  Virology 

Global probabilistic projections of extreme sea levels show intensification of coastal flood hazard OPEN
Michalis I. Vousdoukas, Lorenzo Mentaschi, Evangelos Voukouvalas, Martin Verlaan, Svetlana Jevrejeva, Luke P. Jackson & Luc Feyen

Extreme sea levels are a flood risk along the world’s coastlines. Here the authors carry out probabilistic projections of extreme sea levels and show that for the present century coastal flood hazards will increase significantly along most of the global coastlines.

18 June 2018 | doi: 10.1038/s41467-018-04692-w
Climate and Earth system modelling  Natural hazards  Physical oceanography 

PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze OPEN
Katarzyna Niespodziana, Katarina Stenberg-Hammar, Spyridon Megremis, Clarissa R. Cabauatan, Kamila Napora-Wijata, Phyllis C. Vacal, Daniela Gallerano, Christian Lupinek, Daniel Ebner, Thomas Schlederer, Christian Harwanegg, Cilla Söderhäll, Marianne van Hage, Gunilla Hedlin, Nikolaos G. Papadopoulos & Rudolf Valenta

Rhinovirus (RV) infections can trigger acute exacerbations of respiratory diseases. Here, Niespodziana et al. develop a PreDicta chip that identifies the culprit RV strain from small blood samples and show that RV-A and RV-C strains are associated with most severe symptoms.

18 June 2018 | doi: 10.1038/s41467-018-04591-0
Antibodies  Diagnostic markers  Lab-on-a-chip  Viral infection 

The Wave2 scaffold Hem-1 is required for transition of fetal liver hematopoiesis to bone marrow OPEN
Lijian Shao, Jianhui Chang, Wei Feng, Xiaoyan Wang, Elizabeth A. Williamson, Ying Li, Amir Schajnovitz, David Scadden, Luke J. Mortensen, Charles P. Lin, Linheng Li, Ariel Paulson, James Downing, Daohong Zhou & Robert A. Hromas

Hematopoietic stem cells (HSCs) migrate from the fetal liver to the bone marrow (BM) during embryogenesis. Here the authors show that the WAVE2 complex scaffold Hem1 is required for engraftment of HSCs in BM, not through its canonical role regulating actin polymerization, but through c-Abl survival signaling.

18 June 2018 | doi: 10.1038/s41467-018-04716-5
Chemotaxis  Haematopoietic stem cells  Myelopoiesis 

Yu–Shiba–Rusinov screening of spins in double quantum dots OPEN
K. Grove-Rasmussen, G. Steffensen, A. Jellinggaard, M. H. Madsen, R. Žitko, J. Paaske & J. Nygård

Coupling superconductors to mesoscopic systems leads to unusual effects that could be exploited in new devices including topological quantum computers. Here the authors present a double quantum dot with a Yu–Shiba–Rusinov ground state arising from the interplay of Coulomb interactions and superconductivity.

18 June 2018 | doi: 10.1038/s41467-018-04683-x
Electronic devices  Electronic properties and materials  Superconducting devices  Superconducting properties and materials 

Biosynthesis of thiocarboxylic acid-containing natural products OPEN
Liao-Bin Dong, Jeffrey D. Rudolf, Dingding Kang, Nan Wang, Cyndi Qixin He, Youchao Deng, Yong Huang, K. N. Houk, Yanwen Duan & Ben Shen

Thioplatensimycin (thioPTM) and thioplatencin (thioPTN) are recently discovered thiocarboxylic acid congeners of the antibacterial compounds PTM and PTN. Here, the authors identify a thioacid cassette encoding PtmA3 and PtmU4 that are responsible for carboxylate activation and sulfur transfer, respectively.

18 June 2018 | doi: 10.1038/s41467-018-04747-y
Enzyme mechanisms  Metabolomics  Natural product synthesis 

Recurrent intragenic rearrangements of EGFR and BRAF in soft tissue tumors of infants OPEN
Jenny Wegert, Christian Vokuhl, Grace Collord, Martin Del Castillo Velasco-Herrera, Sarah J. Farndon, Charlotte Guzzo, Mette Jorgensen, John Anderson, Olga Slater, Catriona Duncan, Sabrina Bausenwein, Heike Streitenberger, Barbara Ziegler, Rhoikos Furtwängler, Norbert Graf, Michael R. Stratton, Peter J. Campbell, David TW Jones, Christian Koelsche, Stefan M. Pfister et al.

Soft tissue tumors in infants encompass an overlapping spectrum of diseases posing unique diagnostic and clinical challenges. Here, the authors investigate the genetic basis of cryptogenic congenital mesoblastic nephroma and infantile fibrosarcoma lacking the canonical NTRK3-ETV6 fusion gene, and identify therapeutically tractable intragenic rearrangements in EGFR and BRAF.

18 June 2018 | doi: 10.1038/s41467-018-04650-6
Cancer  Genetics 

A recurrent point mutation in PRKCA is a hallmark of chordoid gliomas OPEN
Shai Rosenberg, Iva Simeonova, Franck Bielle, Maite Verreault, Bertille Bance, Isabelle Le Roux, Mailys Daniau, Arun Nadaradjane, Vincent Gleize, Sophie Paris, Yannick Marie, Marine Giry, Marc Polivka, Dominique Figarella-Branger, Marie-Hélène Aubriot-Lorton, Chiara Villa, Alexandre Vasiljevic, Emmanuèle Lechapt-Zalcman, Michel Kalamarides, Ariane Sharif et al.

Chordoid glioma is a slow growing diencephalic tumor whose mutational landscape is poorly characterized. Here, the authors perform whole-exome and RNA-sequencing and find that 15 of 16 chordoid glioma cases studied harbor the same PRKCA mutation which results in enhanced proliferation.

18 June 2018 | doi: 10.1038/s41467-018-04622-w
Cancer genetics  Oncogenes  Protein function predictions 

Guided morphogenesis through optogenetic activation of Rho signalling during early Drosophila embryogenesis OPEN
Emiliano Izquierdo, Theresa Quinkler & Stefano De Renzis

Optogenetics is opening the possibility to not only perturb morphogenesis, but also to guide it. Here, the authors use this technique to reconstruct epithelial folding in Drosophila embryos and study the relationship between strength of Rho activation, apical constrictions, and tissue invagination.

18 June 2018 | doi: 10.1038/s41467-018-04754-z
Actin  Gastrulation 

Twinning in metastable high-entropy alloys OPEN
Shuo Huang, He Huang, Wei Li, Dongyoo Kim, Song Lu, Xiaoqing Li, Erik Holmström, Se Kyun Kwon & Levente Vitos

Twinning has been experimentally seen in high-entropy alloys, but understanding how it operates remains a challenge. Here, the authors show that twinning can be a primary deformation mechanism in three well-known medium- and high-entropy alloys that have unstable face-centered cubic lattices.

18 June 2018 | doi: 10.1038/s41467-018-04780-x
Atomistic models  Mechanical properties  Metals and alloys 

Formation of self-assembled gold nanoparticle supercrystals with facet-dependent surface plasmonic coupling OPEN
Kaifu Bian, Hattie Schunk, Dongmei Ye, Austin Hwang, Ting Shan Luk, Ruipeng Li, Zhongwu Wang & Hongyou Fan

Macroscopically large supercrystals are very difficult to assemble from metallic nanoparticles. Here, the authors use a binary solvent diffusion method to form sub-millimeter gold nanoparticle supercrystals with rare hcp symmetry, and discover that they exhibit facet-dependent optical properties.

18 June 2018 | doi: 10.1038/s41467-018-04801-9
Nanoparticles  Nanoscale materials  Self-assembly 

Evolution of thiolate-stabilized Ag nanoclusters from Ag-thiolate cluster intermediates OPEN
Yitao Cao, Jiahao Guo, Run Shi, Geoffrey I. N. Waterhouse, Jinheng Pan, Zhenxia Du, Qiaofeng Yao, Li-Zhu Wu, Chen-Ho Tung, Jianping Xie & Tierui Zhang

Gold nanoclusters are known to grow stepwise from gold-thiolate monomers and oligomers. Here, the authors find that the evolution of silver nanoclusters differs completely from that of gold: rather than following a bottom-up pathway, the clusters evolve from similarly-sized Ag-thiolate cluster intermediates.

18 June 2018 | doi: 10.1038/s41467-018-04837-x
Nanoparticle synthesis  Nanoparticles  Synthesis and processing 

Recipes for improper ferroelectricity in molecular perovskites OPEN
Hanna L. B. Boström, Mark S. Senn & Andrew L. Goodwin

In layered inorganic materials lattice distortions can couple to break inversion symmetry and drive improper ferroelectricity, but in perovskites, symmetry prohibits such an effect. Here, the authors use group-theoretical analysis to provide crystal engineering design principles for improper ferroelectricity in molecular perovskites.

18 June 2018 | doi: 10.1038/s41467-018-04764-x
Electronic devices  Ferroelectrics and multiferroics  Materials chemistry 

Anion insertion enhanced electrodeposition of robust metal hydroxide/oxide electrodes for oxygen evolution OPEN
Zhenhua Yan, Hongming Sun, Xiang Chen, Huanhuan Liu, Yaran Zhao, Haixia Li, Wei Xie, Fangyi Cheng & Jun Chen

Electrodeposition provides a facile fabrication means for electrochemical devices but weak substrate-deposit interactions cause poor performance. Here, authors utilize anion insertion within graphitic layers to improve the material interfaces and construct highly active O2-evolving electrocatalysts.

18 June 2018 | doi: 10.1038/s41467-018-04788-3
Electrocatalysis  Synthesis and processing 

Specific stereochemistry of OP-1074 disrupts estrogen receptor alpha helix 12 and confers pure antiestrogenic activity OPEN
S. W. Fanning, L. Hodges-Gallagher, D. C. Myles, R. Sun, C. E. Fowler, I. N. Plant, B. D. Green, C. L. Harmon, G. L. Greene & P. J. Kushner

Estrogen receptor alpha (ERα) plays critical roles in the etiology and treatment of breast cancer. Here the authors synthesize benzopyrans with variable side chains to identify antiestrogenic compounds and characterize OP-1074, a compound that exhibits pure antiestrogenic activity by inducing the degradation of ERα and possesses greater potency than tamoxifen or fulvestrant in a xenograft model.

18 June 2018 | doi: 10.1038/s41467-018-04413-3
Breast cancer  Drug development 

Structure determination from single molecule X-ray scattering with three photons per image OPEN
Benjamin von Ardenne, Martin Mechelke & Helmut Grubmüller

Existing methods to extract structural information from single-molecule scattering measurements require large number of photons per image. Here the authors discuss a method to reconstruct the structure of a molecule from X-ray scattering data by using only three photons per image.

18 June 2018 | doi: 10.1038/s41467-018-04830-4
Biological physics  Characterization and analytical techniques  Design, synthesis and processing  Single-molecule biophysics 

Conformational switching in the coiled-coil domains of a proteasomal ATPase regulates substrate processing OPEN
Aaron Snoberger, Evan J. Brettrager & David M. Smith

Proteasomal ATPases contain functionally important coiled-coil (CC) domains, the mechanistic role of which is not fully understood. Here, the authors provide evidence for three distinct CC conformations, showing that CC conformational changes enable ATPases to switch between active and resting states.

18 June 2018 | doi: 10.1038/s41467-018-04731-6
Enzyme mechanisms  Proteasome  Structural biology 

Association between post-diagnostic use of cholera vaccine and risk of death in prostate cancer patients OPEN
Jianguang Ji, Jan Sundquist & Kristina Sundquist

Post-diagnostic use of cholera vaccine can improve the prognosis in patients with colorectal cancer suggesting cholera toxin might have an antineoplastic effect. Here the authors perform a nationwide population-based study and report an association between cholera vaccine administration and reduction in prostate cancer mortality.

18 June 2018 | doi: 10.1038/s41467-018-04814-4
Cancer epidemiology  Cancer therapy 

Carbon nitride supported Fe2 cluster catalysts with superior performance for alkene epoxidation OPEN
Shubo Tian, Qiang Fu, Wenxing Chen, Quanchen Feng, Zheng Chen, Jian Zhang, Weng-Chon Cheong, Rong Yu, Lin Gu, Juncai Dong, Jun Luo, Chen Chen, Qing Peng, Claudia Draxl, Dingsheng Wang & Yadong Li

Sub-nano clusters with atomic precision provide a compelling platform for bridging heterogeneous and homogeneous catalysis, but their synthesis remains a great challenge. Here, the authors report a precursor-preselected wet-chemistry strategy to synthesize highly dispersed Fe2 clusters supported on mesoporous carbon nitride.

15 June 2018 | doi: 10.1038/s41467-018-04845-x
Catalyst synthesis  Heterogeneous catalysis  Structural properties 

Liquid phase blending of metal-organic frameworks OPEN
Louis Longley, Sean M. Collins, Chao Zhou, Glen J. Smales, Sarah E. Norman, Nick J. Brownbill, Christopher W. Ashling, Philip A. Chater, Robert Tovey, Carola-Bibiane Schönlieb, Thomas F. Headen, Nicholas J. Terrill, Yuanzheng Yue, Andrew J. Smith, Frédéric Blanc, David A. Keen, Paul A. Midgley & Thomas D. Bennett

The recently introduced glass and liquid states of metal–organic frameworks (MOFs) provide opportunities to design and explore new properties for this class of material. Here, the authors show that a MOF liquid can be blended with another MOF component to produce domain-structured MOF glasses with single, tailorable glass transitions.

15 June 2018 | doi: 10.1038/s41467-018-04553-6
Glasses  Metal–organic frameworks  Soft materials 

Efficient RNA drug delivery using red blood cell extracellular vesicles OPEN
Waqas Muhammad Usman, Tin Chanh Pham, Yuk Yan Kwok, Luyen Tien Vu, Victor Ma, Boya Peng, Yuen San Chan, Likun Wei, Siew Mei Chin, Ajijur Azad, Alex Bai-Liang He, Anskar Y. H. Leung, Mengsu Yang, Ng Shyh-Chang, William C. Cho, Jiahai Shi & Minh T. N. Le

RNA delivery for disease treatment often has low uptake efficiencies and cytotoxicity. Here the authors produce extracellular vesicles from red blood cells for in vivo cargo delivery.

15 June 2018 | doi: 10.1038/s41467-018-04791-8
Gene therapy  Targeted therapies 

Strong lowering of ionization energy of metallic clusters by organic ligands without changing shell filling OPEN
Vikas Chauhan, Arthur C. Reber & Shiv N. Khanna

Metallic clusters with an excess electron beyond a closed shell have very low ionization energies, in analogy to alkali atoms. Here, the authors use select ligands to lower the ionization energy of metallic clusters without changing the number of valence electrons, introducing a route to alkali-like superatoms that is independent of the final shell occupancy.

15 June 2018 | doi: 10.1038/s41467-018-04799-0
Electronic structure of atoms and molecules  Inorganic chemistry  Macromolecules and clusters  Nanoscience and technology 

When optimization for governing human-environment tipping elements is neither sustainable nor safe OPEN
Wolfram Barfuss, Jonathan F. Donges, Steven J. Lade & Jürgen Kurths

Economic optimization in environmental governance was criticized for delivering short-term gains at the expense of long-term environmental degradation. Here, the authors use a stylized model of human-environment tipping elements to show no paradigm guarantees fulfilling another paradigm.

15 June 2018 | doi: 10.1038/s41467-018-04738-z
Applied mathematics  Sustainability 

Dual-functional peptide with defective interfering genes effectively protects mice against avian and seasonal influenza OPEN
Hanjun Zhao, Kelvin K. W. To, Hin Chu, Qiulu Ding, Xiaoyu Zhao, Cun Li, Huiping Shuai, Shuofeng Yuan, Jie Zhou, Kin-Hang Kok, Shibo Jiang & Kwok-Yung Yuen

A limited number of therapeutics is available to treat influenza A virus (IAV) infections. Here, the authors show that defective interfering genes, delivered with a dual-functional peptide that enables intracellular accumulation and prevents endosomal acidification, inhibit IAV replication in vitro and in vivo.

15 June 2018 | doi: 10.1038/s41467-018-04792-7
Antivirals  Drug discovery  Influenza virus 

Nanoscale metal-organic frameworks enhance radiotherapy to potentiate checkpoint blockade immunotherapy OPEN
Kaiyuan Ni, Guangxu Lan, Christina Chan, Bryan Quigley, Kuangda Lu, Theint Aung, Nining Guo, Patrick La Riviere, Ralph R. Weichselbaum & Wenbin Lin

Radiotherapy is known to have local immunomodulatory effects, while an effective systemic immune response is an issue. Here, the authors report on nMOF radiosensitizers for enhanced radiotherapy which in combination with anti-PD-L1 antibodies result in a systemic immune response to distant tumors.

15 June 2018 | doi: 10.1038/s41467-018-04703-w
Cancer  Chemistry  Immunology  Nanoscience and technology 

Single-breath-hold photoacoustic computed tomography of the breast OPEN
Li Lin, Peng Hu, Junhui Shi, Catherine M. Appleton, Konstantin Maslov, Lei Li, Ruiying Zhang & Lihong V. Wang

The current standard for breast cancer diagnostic is a mammogram; however, the sensitivity of mammography can be low in radiographically dense breasts. Here the authors develop a single-breath-hold photoacoustic computed tomography (SBH-PACT) system to reveal detailed angiographic structures in human breasts allowing the detection of higher blood vessel densities associated with tumors.

15 June 2018 | doi: 10.1038/s41467-018-04576-z
Biomedical engineering  Breast cancer  Cancer imaging  Imaging and sensing 

Transmission-clearance trade-offs indicate that dengue virulence evolution depends on epidemiological context OPEN
Rotem Ben-Shachar & Katia Koelle

Theory predicts that pathogens will evolve towards intermediate virulence, yet the necessary trade-offs invoked by this theory have rarely been demonstrated empirically. Here, the authors show that dengue virus dynamics exhibit a trade-off between transmission and clearance rates.

15 June 2018 | doi: 10.1038/s41467-018-04595-w
Evolutionary ecology  Viral infection 

Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia OPEN
Ningbo Chen, Yudong Cai, Qiuming Chen, Ran Li, Kun Wang, Yongzhen Huang, Songmei Hu, Shisheng Huang, Hucai Zhang, Zhuqing Zheng, Weining Song, Zhijie Ma, Yun Ma, Ruihua Dang, Zijing Zhang, Lei Xu, Yutang Jia, Shanzhai Liu, Xiangpeng Yue, Weidong Deng et al.

There are various indigenous cattle breeds in East Asia which have a complex history. Here, the authors analyse the genomes of 49 modern breeds and eight ancient samples and identify three distinct ancestries and multiple adaptive introgressions from other bovine species.

14 June 2018 | doi: 10.1038/s41467-018-04737-0
Agricultural genetics  Animal breeding  Genetic variation  Genome 

Manipulation of emergent vortices in swarms of magnetic rollers OPEN
Gašper Kokot & Alexey Snezhko

Active systems utilize energy input to realize structural complexity and functional diversity. This work shows that magnetic colloidal rollers spontaneously self-organize into unconfined macroscopic vortices under a magnetic field, which can be used to transport inert particles across a flat surface.

14 June 2018 | doi: 10.1038/s41467-018-04765-w
Colloids  Self-assembly 

Deciphering the late steps of rifamycin biosynthesis OPEN
Feifei Qi, Chao Lei, Fengwei Li, Xingwang Zhang, Jin Wang, Wei Zhang, Zhen Fan, Weichao Li, Gong-Li Tang, Youli Xiao, Guoping Zhao & Shengying Li

The enzymes Rif15 and Rif16 are involved in the late steps of the biosynthesis of rifamycins, a group of antibiotics. Here, the authors characterized these two proteins and found that they catalyse unusual biochemical reactions.

14 June 2018 | doi: 10.1038/s41467-018-04772-x
Biocatalysis  Biosynthesis  Enzyme mechanisms 

Inducing Kondo screening of vacancy magnetic moments in graphene with gating and local curvature OPEN
Yuhang Jiang, Po-Wei Lo, Daniel May, Guohong Li, Guang-Yu Guo, Frithjof B. Anders, Takashi Taniguchi, Kenji Watanabe, Jinhai Mao & Eva Y. Andrei

Observing and tuning the Kondo effect in graphene is experimentally challenging. Here, the authors identify the spectroscopic signature of Kondo screening in graphene, along with a quantum phase transition between screened and unscreened phases of vacancy magnetic moments.

14 June 2018 | doi: 10.1038/s41467-018-04812-6
Graphene  Nanoscale materials  Nanoscience and technology 

Cell entry of a host-targeting protein of oomycetes requires gp96 OPEN
Franziska Trusch, Lars Loebach, Stephan Wawra, Elaine Durward, Andreas Wuensch, Nurul Aqilah Iberahim, Irene de Bruijn, Kevin MacKenzie, Ariane Willems, Aleksandra Toloczko, Javier Diéguez-Uribeondo, Tim Rasmussen, Thomas Schrader, Peter Bayer, Chris J. Secombes & Pieter van West

The pathogenic oomycete Saprolegnia parasitica secretes effector proteins that translocate into host cells through unclear mechanisms. Here, Trusch et al. show that the uptake of effector protein SpHtp3, resulting in RNA degradation, depends on a gp96-like host receptor and a second effector protein.

14 June 2018 | doi: 10.1038/s41467-018-04796-3
Hydrolases  Pathogens 

Efficient generation of mouse models of human diseases via ABE- and BE-mediated base editing OPEN
Zhen Liu, Zongyang Lu, Guang Yang, Shisheng Huang, Guanglei Li, Songjie Feng, Yajing Liu, Jianan Li, Wenxia Yu, Yu Zhang, Jia Chen, Qiang Sun & Xingxu Huang

CRISPR-based base editors allow for single nucleotide genome editing in a range of organisms. Here the authors demonstrate the in vivo generation of mouse models carrying clinically relevant mutations using C→T and A→G editors.

14 June 2018 | doi: 10.1038/s41467-018-04768-7
CRISPR-Cas systems  Genetic engineering 

Amino acid-dependent cMyc expression is essential for NK cell metabolic and functional responses in mice OPEN
Róisín M. Loftus, Nadine Assmann, Nidhi Kedia-Mehta, Katie L. O’Brien, Arianne Garcia, Conor Gillespie, Jens L. Hukelmann, Peter J. Oefner, Angus I. Lamond, Clair M. Gardiner, Katja Dettmer, Doreen A. Cantrell, Linda V. Sinclair & David K. Finlay

Glutamine can feed into the TCA cycle as a fuel for oxidative phosphorylation and thereby can affect metabolic pathways in lymphocytes. Yet here the authors show that glutamine serves predominantly as a signalling molecule that sustains cMyc expression to control NK cell metabolism and effector function.

14 June 2018 | doi: 10.1038/s41467-018-04719-2
Gene regulation in immune cells  Interleukins  NK cells  Signal transduction 

Copolymer dielectrics with balanced chain-packing density and surface polarity for high-performance flexible organic electronics OPEN
Deyang Ji, Tao Li, Ye Zou, Ming Chu, Ke Zhou, Jinyu Liu, Guofeng Tian, Zhaoyang Zhang, Xu Zhang, Liqiang Li, Dezhen Wu, Huanli Dong, Qian Miao, Harald Fuchs & Wenping Hu

Developing large-scale flexible display technologies calls for new gate dielectric materials balancing the insulating property and molecular packing of organic semiconductors. Ji et al. synthesize a dielectric copolymer contributing with charge mobility of 5 cm2 V−1 s−1 and low operating voltage of 3 V.

14 June 2018 | doi: 10.1038/s41467-018-04665-z
Electronic devices  Polymer characterization 

Quantification and modeling of mechanical degradation in lithium-ion batteries based on nanoscale imaging OPEN
Simon Müller, Patrick Pietsch, Ben-Elias Brandt, Paul Baade, Vincent De Andrade, Francesco De Carlo & Vanessa Wood

Silicon is a promising electrode material for lithium-ion batteries; however, morphological changes shorten battery lifetimes. Here the authors use imaging techniques based on electrons and X-rays to quantify such processes at micro- and nanoscales and suggest routes to mitigate battery degradation.

14 June 2018 | doi: 10.1038/s41467-018-04477-1
Batteries  Imaging techniques 

Quantitative in vivo whole genome motility screen reveals novel therapeutic targets to block cancer metastasis OPEN
Konstantin Stoletov, Lian Willetts, Robert J. Paproski, David J. Bond, Srijan Raha, Juan Jovel, Benjamin Adam, Amy E. Robertson, Francis Wong, Emma Woolner, Deborah L. Sosnowski, Tarek A. Bismar, Gane Ka-Shu Wong, Andries Zijlstra & John D. Lewis

Tumour metastasis is dependent on tumour cell motility. Here, the authors investigate genes required for tumour cell motility by establishing a quantitative in vivo screening platform based on intravital imaging of human cancer metastasis in ex ovo avian embryos.

14 June 2018 | doi: 10.1038/s41467-018-04743-2
Cancer therapy  Metastasis  Target identification 

Anti-phage islands force their target phage to directly mediate island excision and spread OPEN
Amelia C. McKitterick & Kimberley D. Seed

Mobile genetic elements called PLEs protect Vibrio cholerae from infection with phage ICP1 by unclear mechanisms. Here, McKitterick and Seed show that a PLE-encoded large serine recombinase exploits an ICP1 protein as a recombination directionality factor to excise this PLE in response to phage infection.

14 June 2018 | doi: 10.1038/s41467-018-04786-5
Microbial genetics  Phage biology 
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  Latest Author Corrections    
Author Correction: Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome OPEN
Yi Hu, Jon G. Sanders, Piotr Łukasik, Catherine L. D’Amelio, John S. Millar, David R. Vann, Yemin Lan, Justin A. Newton, Mark Schotanus, Daniel J. C. Kronauer, Naomi E. Pierce, Corrie S. Moreau, John T. Wertz, Philipp Engel & Jacob A. Russell
19 June 2018 | doi: 10.1038/s41467-018-04935-w
Evolutionary ecology  Microbial ecology  Microbiome  Symbiosis 

Author Correction: Ultra-thin high-efficiency mid-infraredtransmissive Huygens meta-optics OPEN
Li Zhang, Jun Ding, Hanyu Zheng, Sensong An, Hongtao Lin, Bowen Zheng, Qingyang Du, Gufan Yin, Jerome Michon, Yifei Zhang, Zhuoran Fang, Mikhail Y. Shalaginov, Longjiang Deng, Tian Gu, Hualiang Zhang & Juejun Hu
14 June 2018 | doi: 10.1038/s41467-018-04890-6
Metamaterials  Mid-infrared photonics  Nanophotonics and plasmonics 

Author Correction: Meridional heat transport variability induced by mesoscale processes in the subpolar North Atlantic OPEN
Jian Zhao, Amy Bower, Jiayan Yang & Xiaopei Lin
14 June 2018 | doi: 10.1038/s41467-018-04809-1
Physical oceanography 

Calls for nominations: 2018
John Maddox Prize for Standing up for Science

Recognising the work of individuals who promote science in the face of hostility


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