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| | 21 February 2018 | | | | Advertisement | nature.com webcasts Springer Nature presents a custom webcast on: Sequencing Structural Variants for Disease Gene Discovery and Population Genetics Date: Thursday, March 8, 2018 | | | | | | Advertisement | | | | | Advertisement | | Online-only and open access, npj Primary Care Respiratory Medicine is the only fully-indexed scientific journal devoted to the management of respiratory diseases in primary care. | | | | | | Advertisement | | npj Regenerative Medicine is an online-only, open access journal dedicated to publishing the highest quality research on ways to help the human body repair, replace and regenerate damaged tissues and organs. | | | | | | | | 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 | | | Searching for an exotic spin-dependent interaction with a single electron-spin quantum sensor OPEN | | Xing Rong, Mengqi Wang, Jianpei Geng, Xi Qin, Maosen Guo, Man Jiao, Yijin Xie, Pengfei Wang, Pu Huang, Fazhan Shi, Yi-Fu Cai, Chongwen Zou & Jiangfeng Du | | | Investigation of exotic electron–nucleon interactions with few-micrometers range requires micrometer-scale, highly-sensitive and well-isolated sensors. Here, the authors use an NV center to set limits on the monopole–dipole interaction between its electron spin and the nucleons of a half-ball lens. | | 21 February 2018 | doi: 10.1038/s41467-018-03152-9 | | Experimental particle physics Quantum physics | High-efficiency RNA-based reprogramming of human primary fibroblasts OPEN | | Igor Kogut, Sandra M. McCarthy, Maryna Pavlova, David P. Astling, Xiaomi Chen, Ana Jakimenko, Kenneth L. Jones, Andrew Getahun, John C. Cambier, Anna M. G. Pasmooij, Marcel F. Jonkman, Dennis R. Roop & Ganna Bilousova | | | Induced pluripotent stem cells (iPSCs) have potential for regenerative medicine applications, but are generated with very low efficiency. Here, the authors show highly efficient reprogramming of human primary fibroblasts to iPSCs via the synergistic activity of synthetic modified mRNAs, mature miRNA mimics, and optimized culture methods. | | 21 February 2018 | doi: 10.1038/s41467-018-03190-3 | | Cell culture Induced pluripotent stem cells Reprogramming Stem-cell biotechnology | A neuronal mechanism underlying decision-making deficits during hyperdopaminergic states OPEN | | Jeroen P. H. Verharen, Johannes W. de Jong, Theresia J. M. Roelofs, Christiaan F. M. Huffels, Ruud van Zessen, Mieneke C. M. Luijendijk, Ralph Hamelink, Ingo Willuhn, Hanneke E. M. den Ouden, Geoffrey van der Plasse, Roger A. H. Adan & Louk J. M. J. Vanderschuren | | | Aberrant increased dopaminergic function results in impaired value-based decision making. Here the authors report pathway-specific effects of VTA activation on distinct aspects of flexible value-based decisions in rats. | | 21 February 2018 | doi: 10.1038/s41467-018-03087-1 | | Cognitive neuroscience Reward | Effector CD4+ T cells recognize intravascular antigen presented by patrolling monocytes OPEN | | Clare L. V. Westhorpe, M. Ursula Norman, Pam Hall, Sarah L. Snelgrove, Michaela Finsterbusch, Anqi Li, Camden Lo, Zhe Hao Tan, Songhui Li, Susan K. Nilsson, A. Richard Kitching & Michael J. Hickey | | | Monocytes constitutively adhere and crawl along the glomerular endothelium and are thought to contribute to glomerulonephritis. Here the authors use multiphoton microscopy to show local antigen presentation by MHCII+ monocytes to T cells in glomerular capillaries of mice. | | 21 February 2018 | doi: 10.1038/s41467-018-03181-4 | | Antigen processing and presentation Imaging the immune system | Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus OPEN | | Yan Zhang, Lin An, Jie Xu, Bo Zhang, W. Jim Zheng, Ming Hu, Jijun Tang & Feng Yue | | | Despite its popularity for measuring the spatial organization of mammalian genomes, the resolution of most Hi-C datasets is coarse due to sequencing cost. Here, Zhang et al. develop HiCPlus, a computational approach based on deep convolutional neural network, to infer high-resolution Hi-C interaction matrices from low-resolution Hi-C data. | | 21 February 2018 | doi: 10.1038/s41467-018-03113-2 | | Computational biology and bioinformatics Computational models | Identification of the fungal ligand triggering cytotoxic PRR-mediated NK cell killing of Cryptococcus and Candida OPEN | | Shu Shun Li, Henry Ogbomo, Michael K. Mansour, Richard F. Xiang, Lian Szabo, Fay Munro, Priyanka Mukherjee, Roy A. Mariuzza, Matthias Amrein, Jatin M. Vyas, Stephen M. Robbins & Christopher H. Mody | | | Natural killer (NK) cells has been show to mediate fungi killing via the activating receptor NKp30, but the fungal target for NKp30 is still unclear. Here the authors show, using atomic force microscopy and live cell imaging, that β-1,3-glucan is expressed by Cryptococcus neoformans and Candida albicans and responsible for NKp30-mediated NK killing. | | 21 February 2018 | doi: 10.1038/s41467-018-03014-4 | | Antimicrobial responses Fungal infection Innate immunity NK cells | Analysis of cardiomyocyte clonal expansion during mouse heart development and injury OPEN | | Konstantina-Ioanna Sereti, Ngoc B. Nguyen, Paniz Kamran, Peng Zhao, Sara Ranjbarvaziri, Shuin Park, Shan Sabri, James L. Engel, Kevin Sung, Rajan P. Kulkarni, Yichen Ding, Tzung K. Hsiai, Kathrin Plath, Jason Ernst, Debashis Sahoo, Hanna K.A. Mikkola, M. Luisa Iruela-Arispe & Reza Ardehali | | | During cardiac tissue formation it is unclear whether newly generated myocytes originate from cardiac progenitor cells or from pre-existing cardiomyocytes. Here, the authors use a stochastic four-colour reporter system (Rainbow) to identify the source of new cardiomyocytes during mouse development. | | 21 February 2018 | doi: 10.1038/s41467-018-02891-z | | Cardiac regeneration Gene ontology Heart development | High-performance graphdiyne-based electrochemical actuators OPEN | | Chao Lu, Ying Yang, Jian Wang, Ruoping Fu, Xinxin Zhao, Lei Zhao, Yue Ming, Ying Hu, Hongzhen Lin, Xiaoming Tao, Yuliang Li & Wei Chen | | | Transduction efficiency in electrochemical actuators hardly exceeds 1% because the current electrode materials do not allow to efficiently exploit microstructural changes to achieve large actuation effects. Here the authors demonstrate transduction efficiencies up to 6% in actuators by using graphdiyne as electrode material. | | 21 February 2018 | doi: 10.1038/s41467-018-03095-1 | | Actuators Electronic properties and materials Two-dimensional materials | Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy OPEN | | Rajani Ravi, Kimberly A. Noonan, Vui Pham, Rishi Bedi, Alex Zhavoronkov, Ivan V. Ozerov, Eugene Makarev, Artem V. Artemov, Piotr T. Wysocki, Ranee Mehra, Sridhar Nimmagadda, Luigi Marchionni, David Sidransky, Ivan M. Borrello, Evgeny Izumchenko & Atul Bedi | | | Antitumor T cells can be inhibited by a TGFβ rich tumor microenvironment. The authors develop bifunctional proteins comprising CTLA-4 or PD-L1 immune checkpoint-targeted antibodies fused to a “TGFβ trap” and show that they counteract tumor immune tolerance and enhance the efficacy of these antibodies. | | 21 February 2018 | doi: 10.1038/s41467-017-02696-6 | | Cancer immunotherapy Tumour immunology | Genetic variations in ARE1 mediate grain yield by modulating nitrogen utilization in rice OPEN | | Qing Wang, Jinqiang Nian, Xianzhi Xie, Hong Yu, Jian Zhang, Jiaoteng Bai, Guojun Dong, Jiang Hu, Bo Bai, Lichao Chen, Qingjun Xie, Jian Feng, Xiaolu Yang, Juli Peng, Fan Chen, Qian Qian, Jiayang Li & Jianru Zuo | | | Understanding the regulatory mechanisms of nitrogen assimilation is crucial for developing crop cultivars with improved nitrogen utilization efficiency (NUE). Here the authors identify a new negative regulator of NUE and mutation of this gene increases 10–20% rice grain yield under nitrogen-limiting field conditions. | | 21 February 2018 | doi: 10.1038/s41467-017-02781-w | | Agricultural genetics Field trials Natural variation in plants | Prostaglandin D2 amplifies lupus disease through basophil accumulation in lymphoid organs OPEN | | Christophe Pellefigues, Barbara Dema, Yasmine Lamri, Fanny Saidoune, Nathalie Chavarot, Charlotte Lohéac, Emeline Pacreau, Michael Dussiot, Caroline Bidault, Florian Marquet, Mathieu Jablonski, Jonathan M. Chemouny, Fanny Jouan, Antoine Dossier, Marie-Paule Chauveheid, Delphine Gobert, Thomas Papo, Hajime Karasuyama, Karim Sacré, Eric Daugas et al. | | | In a lupus environment, basophils accumulate in secondary lymphoid organs where they affect pathogenesis by stimulating autoantibody production. Here the authors show this accumulation is driven by PGD2-induced CXCR4 surface expression and trafficking of basophils. | | 20 February 2018 | doi: 10.1038/s41467-018-03129-8 | | Innate immune cells Lupus nephritis Translational immunology | Clonal dynamics towards the development of venetoclax resistance in chronic lymphocytic leukemia OPEN | | Carmen D. Herling, Nima Abedpour, Jonathan Weiss, Anna Schmitt, Ron Daniel Jachimowicz, Olaf Merkel, Maria Cartolano, Sebastian Oberbeck, Petra Mayer, Valeska Berg, Daniel Thomalla, Nadine Kutsch, Marius Stiefelhagen, Paula Cramer, Clemens-Martin Wendtner, Thorsten Persigehl, Andreas Saleh, Janine Altmüller, Peter Nürnberg, Christian Pallasch et al. | | | BCL2-inhibitor venetoclax is used to treat relapsed/refractory chronic lymphocytic leukemia (CLL). Here, the authors show the clonal dynamics towards venetoclax resistance by performing whole-exome sequencing of 8 CLL patients undergoing venetoclax treatment. | | 20 February 2018 | doi: 10.1038/s41467-018-03170-7 | | Chronic lymphocytic leukaemia Computational biology and bioinformatics | Ultrafast quantum control of ionization dynamics in krypton OPEN | | Konrad Hütten, Michael Mittermair, Sebastian O. Stock, Randolf Beerwerth, Vahe Shirvanyan, Johann Riemensberger, Andreas Duensing, Rupert Heider, Martin S. Wagner, Alexander Guggenmos, Stephan Fritzsche, Nikolay M. Kabachnik, Reinhard Kienberger & Birgitta Bernhardt | | | Photoionization of atoms and molecules is a complex process and requires sensitive probes to explore the ultrafast dynamics. Here the authors combine transient absorption and photo-ion spectroscopy methods to explore and control the attosecond pulse initiated excitation, ionization and Auger decay in Kr atoms. | | 19 February 2018 | doi: 10.1038/s41467-018-03122-1 | | Attosecond science High-harmonic generation Nonlinear optics Optical spectroscopy | Generalized leaky integrate-and-fire models classify multiple neuron types OPEN | | Corinne Teeter, Ramakrishnan Iyer, Vilas Menon, Nathan Gouwens, David Feng, Jim Berg, Aaron Szafer, Nicholas Cain, Hongkui Zeng, Michael Hawrylycz, Christof Koch & Stefan Mihalas | | | Simplified neuron models, such as generalized leaky integrate-and-fire (GLIF) models, are extensively used in network modeling. Here the authors systematically generate and compare GLIF models of varying complexity for their ability to classify cell types in the Allen Cell Types Database and faithfully reproduce spike trains. | | 19 February 2018 | doi: 10.1038/s41467-017-02717-4 | | Computational neuroscience Computational science | Selection of GalNAc-conjugated siRNAs with limited off-target-driven rat hepatotoxicity OPEN | | Maja M. Janas, Mark K. Schlegel, Carole E. Harbison, Vedat O. Yilmaz, Yongfeng Jiang, Rubina Parmar, Ivan Zlatev, Adam Castoreno, Huilei Xu, Svetlana Shulga-Morskaya, Kallanthottathil G. Rajeev, Muthiah Manoharan, Natalie D. Keirstead, Martin A. Maier & Vasant Jadhav | | | A subset of chemically-modified siRNAs conjugated to trivalent GalNAc may fail during nonclinical development due to rat hepatotoxicity. Here, the authors show that hepatotoxicity may be accounted for by microRNA-like off-target effects of siRNA and can be mitigated by a thermally destabilizing modification in the siRNA seed region. | | 19 February 2018 | doi: 10.1038/s41467-018-02989-4 | | Drug safety Hepatotoxicity RNAi therapy | Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration OPEN | | Wei Huang, Yuliang Feng, Jialiang Liang, Hao Yu, Cheng Wang, Boyu Wang, Mingyang Wang, Lin Jiang, Wei Meng, Wenfeng Cai, Mario Medvedovic, Jenny Chen, Christian Paul, W. Sean Davidson, Sakthivel Sadayappan, Peter J. Stambrook, Xi-Yong Yu & Yigang Wang | | | During early postnatal development in mammals, cardiomyocytes exit the cell cycle, losing their regenerative capacity. Here the authors show that, following myocardial infarction, loss of microRNA-128 promotes cardiomyocyte proliferation and cardiac regeneration in adult mice partly via enhancing the expression of the chromatin modifier SUZ12. | | 16 February 2018 | doi: 10.1038/s41467-018-03019-z | | Cardiac regeneration Cell proliferation Heart development miRNAs | Chemisorption of polysulfides through redox reactions with organic molecules for lithium–sulfur batteries OPEN | | Ge Li, Xiaolei Wang, Min Ho Seo, Matthew Li, Lu Ma, Yifei Yuan, Tianpin Wu, Aiping Yu, Shun Wang, Jun Lu & Zhongwei Chen | | | Novel cathode design holds the key to enabling high performance lithium-sulfur batteries. Here the authors utilize anthraquinone to chemically stabilize polysulfides, revealing that the keto groups of anthraquinone play a critical role in forming strong Lewis acid-based chemical bonding. | | 16 February 2018 | doi: 10.1038/s41467-018-03116-z | | Batteries | Host defense against oral microbiota by bone-damaging T cells OPEN | | Masayuki Tsukasaki, Noriko Komatsu, Kazuki Nagashima, Takeshi Nitta, Warunee Pluemsakunthai, Chisa Shukunami, Yoichiro Iwakura, Tomoki Nakashima, Kazuo Okamoto & Hiroshi Takayanagi | | | IL-17-producing T cells are protective against infection, but the authors of this article previously showed that these cells also contribute to inflammatory bone destruction. Here they show in the context of periodontitis that microbiota-driven Th17-mediated bone destruction may actually be a physiological rather than a pathological process, as associated tooth loss prevents dissemination of oral bacteria. | | 16 February 2018 | doi: 10.1038/s41467-018-03147-6 | | Bacterial infection Bone Mucosal immunology Osteoimmunology | Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation OPEN | | Juliana Durack, Nikole E. Kimes, Din L. Lin, Marcus Rauch, Michelle McKean, Kathryn McCauley, Ariane R. Panzer, Jordan S. Mar, Michael D. Cabana & Susan V. Lynch | | | Gut microbial dysbiosis in infancy is associated with childhood atopy and the development of asthma. Here, the authors show that gut microbiota perturbation is evident in the very earliest stages of postnatal life, continues throughout infancy, and can be partially rescued by Lactobacillus supplementation in high-risk for asthma infants. | | 16 February 2018 | doi: 10.1038/s41467-018-03157-4 | | Asthma Microbiome Microbiota Paediatric research | Systematic analysis of protein turnover in primary cells OPEN | | Toby Mathieson, Holger Franken, Jan Kosinski, Nils Kurzawa, Nico Zinn, Gavain Sweetman, Daniel Poeckel, Vikram S. Ratnu, Maike Schramm, Isabelle Becher, Michael Steidel, Kyung-Min Noh, Giovanna Bergamini, Martin Beck, Marcus Bantscheff & Mikhail M. Savitski | | | The proteome-wide characterization of proteostasis depends on robust approaches to determine protein half-lives. Here, the authors improve the accuracy and precision of mass spectrometry-based quantification, enabling reliable protein half-life determination in several non-dividing cell types. | | 15 February 2018 | doi: 10.1038/s41467-018-03106-1 | | Cell biology Nuclear pore complex Proteasome Proteomics | A community approach to mortality prediction in sepsis via gene expression analysis OPEN | | Timothy E. Sweeney, Thanneer M. Perumal, Ricardo Henao, Marshall Nichols, Judith A. Howrylak, Augustine M. Choi, Jesús F. Bermejo-Martin, Raquel Almansa, Eduardo Tamayo, Emma E. Davenport, Katie L. Burnham, Charles J. Hinds, Julian C. Knight, Christopher W. Woods, Stephen F. Kingsmore, Geoffrey S. Ginsburg, Hector R. Wong, Grant P. Parnell, Benjamin Tang, Lyle L. Moldawer et al. | | | Sepsis is characterized by deregulated host response to infection. Efficient therapies are still needed but a limitation for sepsis treatment is the heterogeneity in patients. Here Sweeney et al. generate prognostic models based on gene expression to improve risk stratification classification and prediction for 30-day mortality of patients. | | 15 February 2018 | doi: 10.1038/s41467-018-03078-2 | | Computational biology and bioinformatics Infection Molecular medicine Prognosis Prognostic markers | Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T-PLL OPEN | | A. Schrader, G. Crispatzu, S. Oberbeck, P. Mayer, S. Pützer, J. von Jan, E. Vasyutina, K. Warner, N. Weit, N. Pflug, T. Braun, E. I. Andersson, B. Yadav, A. Riabinska, B. Maurer, M. S. Ventura Ferreira, F. Beier, J. Altmüller, M. Lanasa, C. D. Herling et al. | | | T-cell prolymphocytic leukemia (T-PLL) is a rare malignancy with a poor prognosis. Here, the authors investigate the genomic landscape, gene expression profiles and functional mechanisms in 111 patients, highlighting TCL1 overexpression and ATM aberrations as core lesions which co-operate to impair DNA damage processing. | | 15 February 2018 | doi: 10.1038/s41467-017-02688-6 | | Cancer genomics Leukaemia | Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure OPEN | | Kieran A. Bates, Frances C. Clare, Simon O’Hanlon, Jaime Bosch, Lola Brookes, Kevin Hopkins, Emilia J. McLaughlin, Olivia Daniel, Trenton W. J. Garner, Matthew C. Fisher & Xavier A. Harrison | | | Amphibian skin microbe communities have been putatively associated with the severity of chytrid fungal disease. Here, the authors show that different types of disease dynamics (enzootic versus epizootic) are associated with different microbiota in the host populations. | | 15 February 2018 | doi: 10.1038/s41467-018-02967-w | | Ecological epidemiology Herpetology Microbial ecology | Mutations in CFAP43 and CFAP44 cause male infertility and flagellum defects in Trypanosoma and human OPEN | | Charles Coutton, Alexandra S. Vargas, Amir Amiri-Yekta, Zine-Eddine Kherraf, Selima Fourati Ben Mustapha, Pauline Le Tanno, Clémentine Wambergue-Legrand, Thomas Karaouzène, Guillaume Martinez, Serge Crouzy, Abbas Daneshipour, Seyedeh Hanieh Hosseini, Valérie Mitchell, Lazhar Halouani, Ouafi Marrakchi, Mounir Makni, Habib Latrous, Mahmoud Kharouf, Jean-François Deleuze, Anne Boland et al. | | | Asthenozoospermia is a major cause of male infertility, and multiple morphological abnormalities of the flagella (MMAF) is a particularly severe form. Here, using whole-exome sequencing of 78 MMAF patients, the authors identify mutations in two WDR proteins, CFAP43 and CFAP44, and confirm that these proteins are required for flagellogenesis in mouse and Trypanosoma brucei. | | 15 February 2018 | doi: 10.1038/s41467-017-02792-7 | | Cilia Genetics Infertility Male factor infertility | | | | | | | | Latest Author Corrections | | | | Author Correction: Uplift of the central transantarctic mountains OPEN | | Phil Wannamaker, Graham Hill, John Stodt, Virginie Maris, Yasuo Ogawa, Kate Selway, Goran Boren, Edward Bertrand, Daniel Uhlmann, Bridget Ayling, A. Marie Green & Daniel Feucht | | 16 February 2018 | doi: 10.1038/s41467-018-03349-y | | Geodynamics Tectonics | | | | | Latest Publisher Corrections | | | | | | | | Advertisement | | Do you have a career question? The Naturejobs podcast features one-on-one Q&As, panel discussions and other exclusive content to help scientists with their careers. 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