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Nature Communications

Motoko Y Kimura, Akemi Igi, Koji Hayashizaki, Yukiyoshi Mita, Miho Shinzawa, Tejas Kadakia, Yukihiro Endo, Satomi Ogawa, Ryoji Yagi, Shinichiro Motohashi, Alfred Singer, Toshinori Nakayama
While CD69 may regulate thymocyte egress by inhibiting S1P1 expression, CD69 expression is not thought to be required for normal thymocyte development. Here we show that CD69 is in fact specifically required for the differentiation of mature NKT2 cells, which do not themselves express CD69. Mechanistically, CD69 expression is required on CD24+ PLZFhi innate precursors for their retention in the thymus and completion of their differentiation into mature NKT2 cells. By contrast, CD69-deficient CD24+ PLZFhi innate precursors express S1P1 and prematurely exit the thymus, while S1P1 inhibitor treatment of CD69-deficient mice retains CD24+ PLZFhi innate precursors in the thymus and restores NKT2 cell differentiation...
September 14, 2018: Nature Communications
Li Cheng, Qi Xu, Youbin Zheng, Xiaofeng Jia, Yong Qin
Charge density is one of the most important parameters of triboelectric nanogenerators since it directly determines performance; unfortunately, it is largely restricted by the phenomenon of air breakdown. Here, we design a self-improving triboelectric nanogenerator with improved charge density. A maximum effective charge density of 490 μC m-2 is obtained, which is about two times higher than the highest reported charge density of a triboelectric nanogenerator that operates in an air environment. At the beginning of the working process, the charge accumulation speed is increased 5...
September 14, 2018: Nature Communications
Elsa Neubert, Daniel Meyer, Francesco Rocca, Gökhan Günay, Anja Kwaczala-Tessmann, Julia Grandke, Susanne Senger-Sander, Claudia Geisler, Alexander Egner, Michael P Schön, Luise Erpenbeck, Sebastian Kruss
Neutrophilic granulocytes are able to release their own DNA as neutrophil extracellular traps (NETs) to capture and eliminate pathogens. DNA expulsion (NETosis) has also been documented for other cells and organisms, thus highlighting the evolutionary conservation of this process. Moreover, dysregulated NETosis has been implicated in many diseases, including cancer and inflammatory disorders. During NETosis, neutrophils undergo dynamic and dramatic alterations of their cellular as well as sub-cellular morphology whose biophysical basis is poorly understood...
September 14, 2018: Nature Communications
Rudy Lerosey-Aubril, Stephen Pates
The rapid diversification of metazoans and their organisation in modern-style marine ecosystems during the Cambrian profoundly transformed the biosphere. What initially sparked this Cambrian explosion remains passionately debated, but the establishment of a coupling between pelagic and benthic realms, a key characteristic of modern-day oceans, might represent a primary ecological cause. By allowing the transfer of biomass and energy from the euphotic zone-the locus of primary production-to the sea floor, this biological pump would have boosted diversification within the emerging metazoan-dominated benthic communities...
September 14, 2018: Nature Communications
Jedidiah Carlson, Adam E Locke, Matthew Flickinger, Matthew Zawistowski, Shawn Levy, Richard M Myers, Michael Boehnke, Hyun Min Kang, Laura J Scott, Jun Z Li, Sebastian Zöllner
A detailed understanding of the genome-wide variability of single-nucleotide germline mutation rates is essential to studying human genome evolution. Here, we use ~36 million singleton variants from 3560 whole-genome sequences to infer fine-scale patterns of mutation rate heterogeneity. Mutability is jointly affected by adjacent nucleotide context and diverse genomic features of the surrounding region, including histone modifications, replication timing, and recombination rate, sometimes suggesting specific mutagenic mechanisms...
September 14, 2018: Nature Communications
Xufeng Chen, Jingyao Zhao, Chan Gu, Yu Cui, Yuling Dai, Guangrong Song, Haifeng Liu, Hao Shen, Yuanhua Liu, Yuya Wang, Huayue Xing, Xiaoyan Zhu, Pei Hao, Fan Guo, Xiaolong Liu
In response to myeloablative stresses, HSCs are rapidly activated to replenish myeloid progenitors, while maintaining full potential of self-renewal to ensure life-long hematopoiesis. However, the key factors that orchestrate HSC activities during physiological stresses remain largely unknown. Here we report that Med23 controls the myeloid potential of activated HSCs. Ablation of Med23 in hematopoietic system leads to lymphocytopenia. Med23-deficient HSCs undergo myeloid-biased differentiation and lose the self-renewal capacity...
September 14, 2018: Nature Communications
Christiaan A de Leeuw, Sven Stringer, Ilona A Dekkers, Tom Heskes, Danielle Posthuma
Gene-set analysis provides insight into which functional and biological properties of genes are aetiologically relevant for a particular phenotype. But genes have multiple properties, and these properties are often correlated across genes. This can cause confounding in a gene-set analysis, because one property may be statistically associated even if biologically irrelevant to the phenotype, by being correlated with gene properties that are relevant. To address this issue we present a novel conditional and interaction gene-set analysis approach, which attains considerable functional refinement of its conclusions compared to traditional gene-set analysis...
September 14, 2018: Nature Communications
Hila Winer, Milana Fraiberg, Adi Abada, Tali Dadosh, Bat-Chen Tamim-Yecheskel, Zvulun Elazar
Autophagy, a conserved membrane trafficking process, sequesters cytoplasmic components into autophagosomes and targets them for lysosomal degradation. The TNF receptor Fn14 participates in multiple intracellular signaling pathways and is strongly induced upon tissue injury and solid tumorigenesis. While Fn14 is a short-lived protein, the regulation of its levels is largely obscure. Here we uncover a role for autophagy in Fn14 turnover, wherein specific core autophagy Atg8 proteins play distinct roles: Fn14 accumulates in the ERGIC in absence of GABARAP but within endosomes in the vicinity of autophagic membranes in absence of GATE-16...
September 14, 2018: Nature Communications
Chih-Chan Lee, Jiunn-Chang Lin, Wei-Lun Hwang, Ying-Ju Kuo, Hung-Kai Chen, Shyh-Kuan Tai, Chun-Chi Lin, Muh-Hwa Yang
A favorable interplay between cancer cells and the tumor microenvironment (TME) facilitates the outgrowth of metastatic tumors. Because of the distinct initiating processes between primary and metastatic tumors, we investigate the differences in tumor-associated macrophages (TAMs) from primary and metastatic cancers. Here we show that dual expression of M1 and M2 markers is noted in TAMs from primary tumors, whereas predominant expression of M2 markers is shown in metastatic TAMs. At metastatic sites, TAMs secrete interleukin-35 (IL-35) to facilitate metastatic colonization through activation of JAK2-STAT6-GATA3 signaling to reverse epithelial-mesenchymal transition (EMT) in cancer cells...
September 14, 2018: Nature Communications
Yoshinori Tokura, Naoto Nagaosa
Directional transport and propagation of quantum particle and current, such as electron, photon, spin, and phonon, are known to occur in the materials system with broken inversion symmetry, as exemplified by the diode in semiconductor p-n junction and the natural optical activity in chiral materials. Such a nonreciprocal response in the quantum materials of noncentrosymmetry occurs ubiquitously when the time-reversal symmetry is further broken by applying a magnetic field or with spontaneous magnetization, such as the magnetochiral effect and the nonreciprocal magnon transport or spin current in chiral magnets...
September 14, 2018: Nature Communications
Haocheng Zhou, Qiaosheng Zhang, Erik Martinez, Jahrane Dale, Sile Hu, Eric Zhang, Kevin Liu, Dong Huang, Guang Yang, Zhe Chen, Jing Wang
Chronic pain is known to induce an amplified aversive reaction to peripheral nociceptive inputs. This enhanced affective response constitutes a key pathologic feature of chronic pain syndromes such as fibromyalgia. However, the neural mechanisms that underlie this important aspect of pain processing remain poorly understood, hindering the development of treatments. Here, we show that a single dose of ketamine can produce a persistent reduction in the aversive response to noxious stimuli in rodent chronic pain models, long after the termination of its anti-nociceptive effects...
September 14, 2018: Nature Communications
Nicolas Loyer, Jens Januschke
Controlling the orientation of cell division is important in the context of cell fate choices and tissue morphogenesis. However, the mechanisms providing the required positional information remain incompletely understood. Here we use stem cells of the Drosophila larval brain that stably maintain their axis of polarity and division between cell cycles to identify cues that orient cell division. Using live cell imaging of cultured brains, laser ablation and genetics, we reveal that division axis maintenance relies on their last-born daughter cell...
September 14, 2018: Nature Communications
Alida Kindt, Gerhard Liebisch, Thomas Clavel, Dirk Haller, Gabriele Hörmannsperger, Hongsup Yoon, Daniela Kolmeder, Alexander Sigruener, Sabrina Krautbauer, Claudine Seeliger, Alexandra Ganzha, Sabine Schweizer, Rosalie Morisset, Till Strowig, Hannelore Daniel, Dominic Helm, Bernhard Küster, Jan Krumsiek, Josef Ecker
Interactions between the gut microbial ecosystem and host lipid homeostasis are highly relevant to host physiology and metabolic diseases. We present a comprehensive multi-omics view of the effect of intestinal microbial colonization on hepatic lipid metabolism, integrating transcriptomic, proteomic, phosphoproteomic, and lipidomic analyses of liver and plasma samples from germfree and specific pathogen-free mice. Microbes induce monounsaturated fatty acid generation by stearoyl-CoA desaturase 1 and polyunsaturated fatty acid elongation by fatty acid elongase 5, leading to significant alterations in glycerophospholipid acyl-chain profiles...
September 14, 2018: Nature Communications
René Luijk, Haoyu Wu, Cavin K Ward-Caviness, Eilis Hannon, Elena Carnero-Montoro, Josine L Min, Pooja Mandaviya, Martina Müller-Nurasyid, Hailiang Mei, Silvere M van der Maarel, Caroline Relton, Jonathan Mill, Melanie Waldenberger, Jordana T Bell, Rick Jansen, Alexandra Zhernakova, Lude Franke, Peter A C 't Hoen, Dorret I Boomsma, Cornelia M van Duijn, Marleen M J van Greevenbroek, Jan H Veldink, Cisca Wijmenga, Joyce van Meurs, Lucia Daxinger, P Eline Slagboom, Erik W van Zwet, Bastiaan T Heijmans
X-chromosome inactivation (XCI), i.e., the inactivation of one of the female X chromosomes, restores equal expression of X-chromosomal genes between females and males. However, ~10% of genes show variable degrees of escape from XCI between females, although little is known about the causes of variable XCI. Using a discovery data-set of 1867 females and 1398 males and a replication sample of 3351 females, we show that genetic variation at three autosomal loci is associated with female-specific changes in X-chromosome methylation...
September 14, 2018: Nature Communications
Joanne Kanaan, Saurabh Raj, Laurence Decourty, Cosmin Saveanu, Vincent Croquette, Hervé Le Hir
Helicases are molecular engines which translocate along nucleic acids (NA) to unwind double-strands or remodel NA-protein complexes. While they have an essential role in genome structure and expression, the rules dictating their processivity remain elusive. Here, we developed single-molecule methods to investigate helicase binding lifetime on DNA. We found that UPF1, a highly processive helicase central to nonsense-mediated mRNA decay (NMD), tightly holds onto NA, allowing long lasting action. Conversely, the structurally similar IGHMBP2 helicase has a short residence time...
September 14, 2018: Nature Communications
Yara Seif, Erol Kavvas, Jean-Christophe Lachance, James T Yurkovich, Sean-Paul Nuccio, Xin Fang, Edward Catoiu, Manuela Raffatellu, Bernhard O Palsson, Jonathan M Monk
Salmonella strains are traditionally classified into serovars based on their surface antigens. While increasing availability of whole-genome sequences has allowed for more detailed subtyping of strains, links between genotype, serovar, and host remain elusive. Here we reconstruct genome-scale metabolic models for 410 Salmonella strains spanning 64 serovars. Model-predicted growth capabilities in over 530 different environments demonstrate that: (1) the Salmonella accessory metabolic network includes alternative carbon metabolism, and cell wall biosynthesis; (2) metabolic capabilities correspond to each strain's serovar and isolation host; (3) growth predictions agree with 83...
September 14, 2018: Nature Communications
Joshua Fern, Rebecca Schulman
Soft materials that swell or change shape in response to external stimuli show extensive promise in regenerative medicine, targeted therapeutics, and soft robotics. Generally, a stimulus for shape change must interact directly with the material, limiting the types of stimuli that may be used and necessitating high stimulus concentrations. Here, we show how DNA strand-displacement controllers within hydrogels can mediate size change by interpreting, amplifying, and integrating stimuli and releasing signals that direct the response...
September 14, 2018: Nature Communications
Helen R Sharpe, Ana M Geer, Laurence J Taylor, Benjamin M Gridley, Toby J Blundell, Alexander J Blake, E Stephen Davies, William Lewis, Jonathan McMaster, David Robinson, Deborah L Kays
Carbon monoxide is a key C1 feedstock for the industrial production of hydrocarbons, where it is used to make millions of tonnes of chemicals, fuels, and solvents per annum. Many transition metal complexes can coordinate CO, but the formation of new C-C bonds in well-defined compounds from the scission and subsequent coupling of two or more CO moieties at a transition metal centre remains a challenge. Herein, we report the use of low-coordinate iron(II) complexes for the selective scission and homologation of CO affording unusual squaraines and iron carboxylates at ambient temperature and pressure...
September 14, 2018: Nature Communications
Chandan Sarangi, Vijay P Kanawade, Sachchida N Tripathi, Abin Thomas, Dilip Ganguly
Measurements and models show that enhanced aerosol concentrations can modify macro- and micro-physical properties of clouds. Here, we examine the effect of aerosols on continental mesoscale convective cloud systems during the Indian summer monsoon and find that these aerosol-cloud interactions have a net cooling effect at the surface and the top-of-atmosphere. Long-term (2002-2016) satellite data provide evidence of aerosol-induced cloud invigoration effect (AIvE) during the Indian summer monsoon. The AIvE leads to enhanced formation of thicker stratiform anvil clouds at higher altitudes...
September 14, 2018: Nature Communications
Niannian Fan, Zhongxin Chu, Luguang Jiang, Marwan A Hassan, Michael P Lamb, Xingnian Liu
River capture is a dramatic natural process of internal competition through which mountainous landscapes evolve and respond to perturbations in tectonics and climate. River capture may occur when one river network grows at the expense of another, resulting in a victor that steals the neighboring headwaters. While river capture occurs regularly in numerical models, field observations are rare. Here we document a late Pleistocene river capture in the Yimeng Mountains, China that abruptly shifted 25 km2 of drainage area from one catchment to another...
September 14, 2018: Nature Communications
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