Nature Communications - 20 June 2018

Advertisement nature.com webcasts Nature Research Custom presents a webcast on: Structural Tools In Your MS Tool Box Date: Wednesday, June 27, 2018 Dr. David Schriemer will provide some insights on how data from electron microscopy, H/D exchange and crosslinking mass spectrometry can be used together to solve complex structure-function problems. This webcast has been produced on behalf of the sponsor who retains sole responsibility for content  Register for FREE >>  Sponsored by: Thermo Fisher Scientific      Weekly Content Alert Nature Communications is fully open access. Read more. 20 June 2018  Latest content: Articles Author Corrections Journal homepage Recommend to library Web feed   Advertisement Innovators in Science Award Nominations will be accepted until June 25th from around the world for this prestigious award, administered by the New York Academy of Sciences and sponsored by Takeda Pharmaceuticals. An Early-Career Scientist and a Senior Scientist in Regenerative Medicine will each be recognized for their research and receive US$200,000.  Nominate today    Advertisement Nature Ecology & Evolution publishes the best research from across the fields of ecology and evolutionary biology. Need access to content at your work place or institution?  Recommend institutional license access to your librarian.   Advertisement nature.com webcasts Nature Research Custom Media presents a webcast on: Rspondin3 from stromal myofibroblasts orchestrates gastric epithelial stem cells2 Date: Wednesday, July 11, 2018 Join our webcast to learn how the RNAscope® Dual ISH technology was utilized to thoroughly characterize the gastric antral gland stem cell niche. This webcast has been produced on behalf of the sponsor who retains sole responsibility for content  Register for FREE  Sponsored by: ACD        Nature Communications - fully open access All new submissions, if accepted, will be published open access and an article processing charge (APC) will apply. For more information visit the website. Visit our open access funding page or contact openaccess@nature.com to learn more about APC funding.       Latest Articles View all Articles     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    Nature Communications JOBS of the week Postdoctoral Research Scholar Washington University School of Medicine Postdoctoral Fellowship in Microbiology / Proteomics University of Calgary Post-Doctoral Fellow Position #00017839 University of North Dakota, School of Medicine Health Sciences Postdoctoral Researcher in Tumor Immunology University of Lausanne - Faculty of Biology and Medicine Postdoctoral Position in Cancer Research (ref. PD / 18 / 02) Institute for Research in Biomedicine (IRB Barcelona) Research position – Image Guided Surgery Netherlands Cancer Institute Faculty Positions for Chairs, Readers and Early Career Researchers Queen Mary University of London Postdoc (f / m) Time-resolved Serial Crystalography DESY Deutsches Elektronen Synchrotron Postdoctoral Training Fellow – Synthetic Systems Biochemistry The Francis Crick Institute IQST Postdoctoral Fellowship Center for Integrated Quantum Science and Technology (IQST) More Science jobs from Nature Communications EVENT 6th Annual International Conference on Chemistry 23.07.18 Athens, Greece More science events from     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      Advertisement 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   Advertisement   Nature Sustainability publishes significant original research from a broad range of natural, social and engineering fields about sustainability, its policy dimensions and possible solutions. Need access to content at your work place or institution? 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