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Journal Nature Communications

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22,973 articles
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Jinsong Zhang, Ankun Yang, Xi Wu, Jorik Van De Groep, Peizhe Tang, Shaorui Li, Bofei Liu, Feifei Shi, Jiayu Wan, Qitong Li, et al.
Published: 11 December 2018
Nature Communications, Volume 9; doi:10.1038/s41467-018-07710-z

Abstract:Electrochemical intercalation of ions into the van der Waals gap of two-dimensional (2D) layered materials is a promising low-temperature synthesis strategy to tune their physical and chemical properties. It is widely believed that ions prefer intercalation into the van der Waals gap through the edges of the 2D flake, which generally causes wrinkling and distortion. Here we demonstrate that the ions can also intercalate through the top surface of few-layer MoS2 and this type of intercalation is more reversible and stable compared to the intercalation through the edges. Density functional theory calculations show that this intercalation is enabled by the existence of natural defects in exfoliated MoS2 flakes. Furthermore, we reveal that sealed-edge MoS2 allows intercalation of small alkali metal ions (e.g., Li+ and Na+) and rejects large ions (e.g., K+). These findings imply potential applications in developing functional 2D-material-based devices with high tunability and ion selectivity.
Fiona M. Rudkin, Ingrida Raziunaite, Hillary Workman, Sosthene Essono, Rodrigo Belmonte, Donna M. Maccallum, Elizabeth M. Johnson, Lisete M. Silva, Angelina S. Palma, Ten Feizi, et al.
Published: 11 December 2018
Nature Communications, Volume 9; doi:10.1038/s41467-018-07738-1

Nobutoshi Yamaguchi, Jiangbo Huang, Yoshitaka Tatsumi, Masato Abe, Shigeo S. Sugano, Mikiko Kojima, Yumiko Takebayashi, Takatoshi Kiba, Ryusuke Yokoyama, Kazuhiko Nishitani, et al.
Published: 11 December 2018
Nature Communications, Volume 9; doi:10.1038/s41467-018-07763-0

Abstract:In flowering plants, the switch from floral stem cell maintenance to gynoecium (female structure) formation is a critical developmental transition for reproductive success. In Arabidopsis thaliana, AGAMOUS (AG) terminates floral stem cell activities to trigger this transition. Although CRABS CLAW (CRC) is a direct target of AG, previous research has not identified any common targets. Here, we identify an auxin synthesis gene, YUCCA4 (YUC4) as a common direct target. Ectopic YUC4 expression partially rescues the indeterminate phenotype and cell wall defects that are caused by the crc mutation. The feed-forward YUC4 activation by AG and CRC directs a precise change in chromatin state for the shift from floral stem cell maintenance to gynoecium formation. We also showed that two auxin-related direct CRC targets, YUC4 and TORNADO2, cooperatively contribute to the termination of floral stem cell maintenance. This finding provides new insight into the CRC-mediated auxin homeostasis regulation for proper gynoecium formation.
Ravit Netzer, Dina Listov, Rosalie Lipsh, Orly Dym, Shira Albeck, Orli Knop, Colin Kleanthous, Sarel J. Fleishman
Published: 11 December 2018
Nature Communications, Volume 9; doi:10.1038/s41467-018-07722-9

Abstract:Protein networks in all organisms comprise homologous interacting pairs. In these networks, some proteins are specific, interacting with one or a few binding partners, whereas others are multispecific and bind a range of targets. We describe an algorithm that starts from an interacting pair and designs dozens of new pairs with diverse backbone conformations at the binding site as well as new binding orientations and sequences. Applied to a high-affinity bacterial pair, the algorithm results in 18 new ones, with cognate affinities from pico- to micromolar. Three pairs exhibit 3-5 orders of magnitude switch in specificity relative to the wild type, whereas others are multispecific, collectively forming a protein-interaction network. Crystallographic analysis confirms design accuracy, including in new backbones and polar interactions. Preorganized polar interaction networks are responsible for high specificity, thus defining design principles that can be applied to program synthetic cellular interaction networks of desired affinity and specificity.
M. E. P. Didier, O. B. Tarun, P. Jourdain, P. Magistretti, S. Roke
Published: 11 December 2018
Nature Communications, Volume 9; doi:10.1038/s41467-018-07713-w

Abstract:Neurons communicate through electrochemical signaling within a complex network. These signals are composed of changes in membrane potentials and are traditionally measured with the aid of (toxic) fluorescent labels or invasive electrical probes. Here, we demonstrate an improvement in label-free second harmonic neuroimaging sensitivity by ~3 orders of magnitude using a wide-field medium repetition rate illumination. We perform a side-by-side patch-clamp and second harmonic imaging comparison to demonstrate the theoretically predicted linear correlation between whole neuron membrane potential changes and the square root of the second harmonic intensity. We assign the ion induced changes to the second harmonic intensity to changes in the orientation of membrane interfacial water, which is used to image spatiotemporal changes in the membrane potential and K+ ion flux. We observe a non-uniform spatial distribution and temporal activity of ion channels in mouse brain neurons.
Hai-Qing Tu, Xuan-He Qin, Zhi-Bin Liu, Zeng-Qing Song, Huai-Bin Hu, Yu-Cheng Zhang, Yan Chang, Min Wu, Yan Huang, Yun-Feng Bai, et al.
Published: 11 December 2018
Nature Communications, Volume 9; doi:10.1038/s41467-018-07664-2

Abstract:Defective ciliogenesis causes human developmental diseases termed ciliopathies. Microtubule (MT) asters originating from centrosomes in mitosis ensure the fidelity of cell division by positioning the spindle apparatus. However, the function of microtubule asters in interphase remains largely unknown. Here, we reveal an essential role of MT asters in transition zone (TZ) assembly during ciliogenesis. We demonstrate that the centrosome protein FSD1, whose biological function is largely unknown, anchors MT asters to interphase centrosomes by binding to microtubules. FSD1 knockdown causes defective ciliogenesis and affects embryonic development in vertebrates. We further show that disruption of MT aster anchorage by depleting FSD1 or other known anchoring proteins delocalizes the TZ assembly factor Cep290 from centriolar satellites, and causes TZ assembly defects. Thus, our study establishes FSD1 as a MT aster anchorage protein and reveals an important function of MT asters anchored by FSD1 in TZ assembly during ciliogenesis.
V. A. Ingham, S. Wagstaff, H. Ranson
Published: 11 December 2018
Nature Communications, Volume 9; doi:10.1038/s41467-018-07615-x

Abstract:Increasing insecticide resistance in malaria-transmitting vectors represents a public health threat, but underlying mechanisms are poorly understood. Here, a data integration approach is used to analyse transcriptomic data from comparisons of insecticide resistant and susceptible Anopheles populations from disparate geographical regions across the African continent. An unbiased, integrated analysis of this data confirms previously described resistance candidates but also identifies multiple novel genes involving alternative resistance mechanisms, including sequestration, and transcription factors regulating multiple downstream effector genes, which are validated by gene silencing. The integrated datasets can be interrogated with a bespoke Shiny R script, deployed as an interactive web-based application, that maps the expression of resistance candidates and identifies co-regulated transcripts that may give clues to the function of novel resistance-associated genes.
Gulce Itir Percin, Jiri Eitler, Andrea Kranz, Jun Fu, Jeffrey W. Pollard, Ronald Naumann, Claudia Waskow
Published: 11 December 2018
Nature Communications, Volume 9; doi:10.1038/s41467-018-07685-x

Leonardo Puppulin, Shigekuni Hosogi, Hongxin Sun, Kazuhiko Matsuo, Toshio Inui, Yasuaki Kumamoto, Toshinobu Suzaki, Hideo Tanaka, Yoshinori Marunaka
Published: 11 December 2018
Nature Communications, Volume 9; doi:10.1038/s41467-018-07726-5

Abstract:Regulation of intracellular pH is critically important for many cellular functions. The quantification of proton extrusion in different types of cells and physiological conditions is pivotal to fully elucidate the mechanisms of pH homeostasis. Here we show the use of gold nanoparticles (AuNP) to create a high spatial resolution sensor for measuring extracellular pH in proximity of the cell membrane. We test the sensor on HepG2 liver cancer cells and MKN28 gastric cancer cells before and after inhibition of Na+/H+ exchanger. The gold surface conjugation strategy is conceived with a twofold purpose: i) to anchor the AuNP to the membrane proteins and ii) to quantify the local pH from AuNP using surface enhanced Raman spectroscopy (SERS). The nanometer size of the cell membrane anchored sensor and the use of SERS enable us to visualize highly localized variation of pH induced by H+ extrusion, which is particularly upregulated in cancer cells.
Shahzya Chaudhury, Caitríona O’Connor, Ana Cañete, Joana Bittencourt-Silvestre, Evgenia Sarrou, Áine Prendergast, Jarny Choi, Pamela Johnston, Christine A. Wells, Brenda Gibson, et al.
Published: 11 December 2018
Nature Communications, Volume 9; doi:10.1038/s41467-018-07584-1

Abstract:Acute myeloid leukaemia (AML) affects children and adults of all ages. AML remains one of the major causes of death in children with cancer and for children with AML relapse is the most common cause of death. Here, by modelling AML in vivo we demonstrate that AML is discriminated by the age of the cell of origin. Young cells give rise to myeloid, lymphoid or mixed phenotype acute leukaemia, whereas adult cells give rise exclusively to AML, with a shorter latency. Unlike adult, young AML cells do not remodel the bone marrow stroma. Transcriptional analysis distinguishes young AML by the upregulation of immune pathways. Analysis of human paediatric AML samples recapitulates a paediatric immune cell interaction gene signature, highlighting two genes, RGS10 and FAM26F as prognostically significant. This work advances our understanding of paediatric AML biology, and provides murine models that offer the potential for developing paediatric specific therapeutic strategies.
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