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Nature Communications

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https://www.readbyqxmd.com/read/29143808/corrigendum-a-simple-and-versatile-design-concept-for-fluorophore-derivatives-with-intramolecular-photostabilization
#1
Jasper H M van der Velde, Jens Oelerich, Jingyi Huang, Jochem H Smit, Atieh Aminian Jazi, Silvia Galiani, Kirill Kolmakov, Giorgos Gouridis, Christian Eggeling, Andreas Herrmann, Gerard Roelfes, Thorben Cordes
This corrects the article DOI: 10.1038/ncomms10144.
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142318/the-natural-product-carolacton-inhibits-folate-dependent-c1-metabolism-by-targeting-fold-mthfd
#2
Chengzhang Fu, Asfandyar Sikandar, Jannik Donner, Nestor Zaburannyi, Jennifer Herrmann, Michael Reck, Irene Wagner-Döbler, Jesko Koehnke, Rolf Müller
The natural product carolacton is a macrolide keto-carboxylic acid produced by the myxobacterium Sorangium cellulosum, and was originally described as an antibacterial compound. Here we show that carolacton targets FolD, a key enzyme from the folate-dependent C1 metabolism. We characterize the interaction between bacterial FolD and carolacton biophysically, structurally and biochemically. Carolacton binds FolD with nanomolar affinity, and the crystal structure of the FolD-carolacton complex reveals the mode of binding...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142300/structure-and-immunogenicity-of-pre-fusion-stabilized-human-metapneumovirus-f-glycoprotein
#3
Michael B Battles, Vicente Más, Eduardo Olmedillas, Olga Cano, Mónica Vázquez, Laura Rodríguez, José A Melero, Jason S McLellan
Human metapneumovirus (hMPV) is a frequent cause of bronchiolitis in young children. Its F glycoprotein mediates virus-cell membrane fusion and is the primary target of neutralizing antibodies. The inability to produce recombinant hMPV F glycoprotein in the metastable pre-fusion conformation has hindered structural and immunological studies. Here, we engineer a pre-fusion-stabilized hMPV F ectodomain and determine its crystal structure to 2.6 Å resolution. This structure reveals molecular determinants of strain-dependent acid-induced fusion, as well as insights into refolding from pre- to post-fusion conformations...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142298/shaping-bacterial-population-behavior-through-computer-interfaced-control-of-individual-cells
#4
Remy Chait, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, Călin C Guet
Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142274/super-achromatic-monolithic-microprobe-for-ultrahigh-resolution-endoscopic-optical-coherence-tomography-at-800%C3%A2-nm
#5
Wu Yuan, Robert Brown, Wayne Mitzner, Lonny Yarmus, Xingde Li
Endoscopic optical coherence tomography (OCT) has emerged as a valuable tool for advancing our understanding of the histomorphology of various internal luminal organs and studying the pathogenesis of relevant diseases. To date, this technology affords limited resolving power for discerning subtle pathological changes associated with early diseases. In addition, it remains challenging to access small luminal organs or pass through narrow luminal sections without potentially causing trauma to tissue with a traditional OCT endoscope of a 1-1...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142260/possible-nematic-to-smectic-phase-transition-in-a-two-dimensional-electron-gas-at-half-filling
#6
Q Qian, J Nakamura, S Fallahi, G C Gardner, M J Manfra
Liquid crystalline phases of matter permeate nature and technology, with examples ranging from cell membranes to liquid-crystal displays. Remarkably, electronic liquid-crystal phases can exist in two-dimensional electron systems (2DES) at half Landau-level filling in the quantum Hall regime. Theory has predicted the existence of a liquid-crystal smectic phase that breaks both rotational and translational symmetries. However, previous experiments in 2DES are most consistent with an anisotropic nematic phase breaking only rotational symmetry...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142259/drip-tectonics-and-the-enigmatic-uplift-of-the-central-anatolian-plateau
#7
Oğuz H Göğüş, Russell N Pysklywec, A M C Şengör, Erkan Gün
Lithospheric drips have been interpreted for various regions around the globe to account for the recycling of the continental lithosphere and rapid plateau uplift. However, the validity of such hypothesis is not well documented in the context of geological, geophysical and petrological observations that are tested against geodynamical models. Here we propose that the folding of the Central Anatolian (Kırşehir) arc led to thickening of the lithosphere and onset of "dripping" of the arc root. Our geodynamic model explains the seismic data showing missing lithosphere and a remnant structure characteristic of a dripping arc root, as well as enigmatic >1 km uplift over the entire plateau, Cappadocia and Galatia volcanism at the southern and northern plateau margins since ~10 Ma, respectively...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142258/in-situ-detection-of-the-protein-corona-in-complex-environments
#8
Monica Carril, Daniel Padro, Pablo Del Pino, Carolina Carrillo-Carrion, Marta Gallego, Wolfgang J Parak
Colloidal nanoparticles (NPs) are a versatile potential platform for in vivo nanomedicine. Inside blood circulation, NPs may undergo drastic changes, such as by formation of a protein corona. The in vivo corona cannot be completely emulated by the corona formed in blood. Thus, in situ detection in complex media, and ultimately in vivo, is required. Here we present a methodology for determining protein corona formation in complex media. NPs are labeled with (19)F and their diffusion coefficient measured using (19)F diffusion-ordered nuclear magnetic resonance (NMR) spectroscopy...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142254/a-soft-selective-sweep-during-rapid-evolution-of-gentle-behaviour-in-an-africanized-honeybee
#9
Arian Avalos, Hailin Pan, Cai Li, Jenny P Acevedo-Gonzalez, Gloria Rendon, Christopher J Fields, Patrick J Brown, Tugrul Giray, Gene E Robinson, Matthew E Hudson, Guojie Zhang
Highly aggressive Africanized honeybees (AHB) invaded Puerto Rico (PR) in 1994, displacing gentle European honeybees (EHB) in many locations. Gentle AHB (gAHB), unknown anywhere else in the world, subsequently evolved on the island within a few generations. Here we sequence whole genomes from gAHB and EHB populations, as well as a North American AHB population, a likely source of the founder AHB on PR. We show that gAHB retains high levels of genetic diversity after evolution of gentle behaviour, despite selection on standing variation...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142246/a-comprehensive-structural-biochemical-and-biological-profiling-of-the-human-nudix-hydrolase-family
#10
Jordi Carreras-Puigvert, Marinka Zitnik, Ann-Sofie Jemth, Megan Carter, Judith E Unterlass, Björn Hallström, Olga Loseva, Zhir Karem, José Manuel Calderón-Montaño, Cecilia Lindskog, Per-Henrik Edqvist, Damian J Matuszewski, Hammou Ait Blal, Ronnie P A Berntsson, Maria Häggblad, Ulf Martens, Matthew Studham, Bo Lundgren, Carolina Wählby, Erik L L Sonnhammer, Emma Lundberg, Pål Stenmark, Blaz Zupan, Thomas Helleday
The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142225/comparative-genomic-analysis-of-esophageal-squamous-cell-carcinoma-between-asian-and-caucasian-patient-populations
#11
Jiaying Deng, Hu Chen, Daizhan Zhou, Junhua Zhang, Yun Chen, Qi Liu, Dashan Ai, Hanting Zhu, Li Chu, Wenjia Ren, Xiaofei Zhang, Yi Xia, Menghong Sun, Huiwen Zhang, Jun Li, Xinxin Peng, Liang Li, Leng Han, Hui Lin, Xiujun Cai, Jiaqing Xiang, Shufeng Chen, Yihua Sun, Yawei Zhang, Jie Zhang, Haiquan Chen, Shijian Zhang, Yi Zhao, Yun Liu, Han Liang, Kuaile Zhao
Esophageal squamous cell carcinoma is a major histological type of esophageal cancer, with distinct incidence and survival patterns among races. Although previous studies have characterized somatic mutations in this disease, a rigorous comparison between different patient populations has not been conducted. Here we sequence the samples of 316 Chinese patients, combine them with those from The Cancer Genome Atlas, and perform a comparative analysis between Asian and Caucasian patients. We find that mutated CSMD3 is associated with better prognosis in Asian patients...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142216/polymer-mimics-of-biomacromolecular-antifreezes
#12
REVIEW
Caroline I Biggs, Trisha L Bailey, Ben Graham, Christopher Stubbs, Alice Fayter, Matthew I Gibson
Antifreeze proteins from polar fish species are remarkable biomacromolecules which prevent the growth of ice crystals. Ice crystal growth is a major problem in cell/tissue cryopreservation for transplantation, transfusion and basic biomedical research, as well as technological applications such as icing of aircraft wings. This review will introduce the rapidly emerging field of synthetic macromolecular (polymer) mimics of antifreeze proteins. Particular focus is placed on designing polymers which have no structural similarities to antifreeze proteins but reproduce the same macroscopic properties, potentially by different molecular-level mechanisms...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142209/fbxo4-mediated-degradation-of-fxr1-suppresses-tumorigenesis-in-head-and-neck-squamous-cell-carcinoma
#13
Shuo Qie, Mrinmoyee Majumder, Katarzyna Mackiewicz, Breege V Howley, Yuri K Peterson, Philip H Howe, Viswanathan Palanisamy, J Alan Diehl
The Fbxo4 tumour suppressor is a component of an Skp1-Cul1-F-box E3 ligase for which two substrates are known. Here we show purification of SCF(Fbxo4) complexes results in the identification of fragile X protein family (FMRP, Fxr1 and Fxr2) as binding partners. Biochemical and functional analyses reveal that Fxr1 is a direct substrate of SCF(Fbxo4). Consistent with a substrate relationship, Fxr1 is overexpressed in Fbxo4 knockout cells, tissues and in human cancer cells, harbouring inactivating Fbxo4 mutations...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142315/hiv-1-counteracts-an-innate-restriction-by-amyloid-precursor-protein-resulting-in-neurodegeneration
#14
Qingqing Chai, Vladimir Jovasevic, Viacheslav Malikov, Yosef Sabo, Scott Morham, Derek Walsh, Mojgan H Naghavi
While beta-amyloid (Aβ), a classic hallmark of Alzheimer's disease (AD) and dementia, has long been known to be elevated in the human immunodeficiency virus type 1 (HIV-1)-infected brain, why and how Aβ is produced, along with its contribution to HIV-associated neurocognitive disorder (HAND) remains ill-defined. Here, we reveal that the membrane-associated amyloid precursor protein (APP) is highly expressed in macrophages and microglia, and acts as an innate restriction against HIV-1. APP binds the HIV-1 Gag polyprotein, retains it in lipid rafts and blocks HIV-1 virion production and spread...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142305/assay-interference-and-off-target-liabilities-of-reported-histone-acetyltransferase-inhibitors
#15
Jayme L Dahlin, Kathryn M Nelson, Jessica M Strasser, Dalia Barsyte-Lovejoy, Magdalena M Szewczyk, Shawna Organ, Matthew Cuellar, Gurpreet Singh, Jonathan H Shrimp, Nghi Nguyen, Jordan L Meier, Cheryl H Arrowsmith, Peter J Brown, Jonathan B Baell, Michael A Walters
Many compounds with potentially reactive chemical motifs and poor physicochemical properties are published as selective modulators of biomolecules without sufficient validation and then propagated in the scientific literature as useful chemical probes. Several histone acetyltransferase (HAT) inhibitors with these liabilities are now routinely used to probe epigenetic pathways. We profile the most commonly used HAT inhibitors and confirm that the majority of them are nonselective interference compounds. Most (15 out of 23, 65%) of the inhibitors are flagged by ALARM NMR, an industry-developed counter-screen for promiscuous compounds...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142265/publisher-correction-tropical-explosive-volcanic-eruptions-can-trigger-el-ni%C3%A3-o-by-cooling-tropical-africa
#16
Myriam Khodri, Takeshi Izumo, Jérôme Vialard, Serge Janicot, Christophe Cassou, Matthieu Lengaigne, Juliette Mignot, Guillaume Gastineau, Eric Guilyardi, Nicolas Lebas, Alan Robock, Michael J McPhaden
A correction to this article has been published and is linked from the HTML version of this article.
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142262/observation-of-replica-symmetry-breaking-in-disordered-nonlinear-wave-propagation
#17
Davide Pierangeli, Andrea Tavani, Fabrizio Di Mei, Aharon J Agranat, Claudio Conti, Eugenio DelRe
A landmark of statistical mechanics, spin-glass theory describes critical phenomena in disordered systems that range from condensed matter to biophysics and social dynamics. The most fascinating concept is the breaking of replica symmetry: identical copies of the randomly interacting system that manifest completely different dynamics. Replica symmetry breaking has been predicted in nonlinear wave propagation, including Bose-Einstein condensates and optics, but it has never been observed. Here, we report the experimental evidence of replica symmetry breaking in optical wave propagation, a phenomenon that emerges from the interplay of disorder and nonlinearity...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142256/quantitative-analysis-of-protein-protein-interactions-and-post-translational-modifications-in-rare-immune-populations
#18
Ayelet Avin, Maayan Levy, Ziv Porat, Jakub Abramson
In spite of recent advances in proteomics, quantitative analyses of protein-protein interactions (PPIs) or post-translational modifications (PTMs) in rare cell populations remain challenging. This is in particular true for analyses of rare immune and/or stem cell populations that are directly isolated from humans or animal models, and which are often characterized by multiple surface markers. To overcome these limitations, here we have developed proximity ligation imaging cytometry (PLIC), a protocol for proteomic analysis of rare cells...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142253/protruding-organic-surfaces-triggered-by-in-plane-electric-fields
#19
Danqing Liu, Nicholas B Tito, Dirk J Broer
Coatings with a dynamic surface topography are of interest for applications in haptics, soft robotics, cell growth in biology, hydro- and air dynamics and tribology. Here we propose a design for creating oscillating surface topographies in thin liquid crystal polymer network coatings under an electric field. By applying an alternating electric field, the coating surface deforms, and pre-designed local corrugations appear. The continuous AC electric field further initiates oscillations superimposed on the formed topographies...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142242/emergent-patterns-of-collective-cell-migration-under-tubular-confinement
#20
Wang Xi, Surabhi Sonam, Thuan Beng Saw, Benoit Ladoux, Chwee Teck Lim
Collective epithelial behaviors are essential for the development of lumens in organs. However, conventional assays of planar systems fail to replicate cell cohorts of tubular structures that advance in concerted ways on out-of-plane curved and confined surfaces, such as ductal elongation in vivo. Here, we mimic such coordinated tissue migration by forming lumens of epithelial cell sheets inside microtubes of 1-10 cell lengths in diameter. We show that these cell tubes reproduce the physiological apical-basal polarity, and have actin alignment, cell orientation, tissue organization, and migration modes that depend on the extent of tubular confinement and/or curvature...
November 15, 2017: Nature Communications
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