bluuebunny/crossref_metadata_2025_split huggingface dataset:
Membrane-cytoskeletal crosstalk mediated by myosin-I regulates adhesion turnover during phagocytosis
Authors: Barger Sarah R. , Reilly Nicholas S. , Shutova Maria S. , Li Qingsen , Maiuri Paolo , Heddleston John M. , Mooseker Mark S. , Flavell Richard A. , Svitkina Tatyana , Oakes Patrick W. , Krendel Mira , Gauthier Nils C. 
Published: April 2019

AbstractPhagocytosis of invading pathogens or cellular debris requires a dramatic change in cell shape driven by actin polymerization. For antibody-covered targets, phagocytosis is thought to proceed through the sequential engagement of Fc-receptors on the phagocyte with antibodies on the target surface, leading to the extension and closure of the phagocytic cup around the target. We find that two actin-dependent molecular motors, class 1 myosins myosin 1e and myosin 1f, are specifically localized to Fc-receptor adhesions and required for efficient phagocytosis of antibody-opsonized targets. Using primary macrophages lacking both myosin 1e and myosin 1f, we find that without the actin-membrane linkage mediated by these myosins, the organization of individual adhesions is compromised, leading to excessive actin polymerization, slower adhesion turnover, and deficient phagocytic internalization. This work identifies a role for class 1 myosins in coordinated adhesion turnover during phagocytosis and supports a mechanism involving membrane-cytoskeletal crosstalk for phagocytic cup closure.
Distinct G protein-coupled receptor phosphorylation motifs modulate arrestin affinity and activation and global conformation
Authors: Mayer Daniel , Damberger Fred F. , Samarasimhareddy Mamidi , Feldmueller Miki , Vuckovic Ziva , Flock Tilman , Bauer Brian , Mutt Eshita , Zosel Franziska , Allain Frédéric H. T. , Standfuss Jörg , Schertler Gebhard F. X. , Deupi Xavier , Sommer Martha E. , Hurevich Mattan , Friedler Assaf , Veprintsev Dmitry B. 
Published: April 2019

AbstractCellular functions of arrestins are determined in part by the pattern of phosphorylation on the G protein-coupled receptors (GPCRs) to which arrestins bind. Despite high-resolution structural data of arrestins bound to phosphorylated receptor C-termini, the functional role of each phosphorylation site remains obscure. Here, we employ a library of synthetic phosphopeptide analogues of the GPCR rhodopsin C-terminus and determine the ability of these peptides to bind and activate arrestins using a variety of biochemical and biophysical methods. We further characterize how these peptides modulate the conformation of arrestin-1 by nuclear magnetic resonance (NMR). Our results indicate different functional classes of phosphorylation sites: ‘key sites’ required for arrestin binding and activation, an ‘inhibitory site’ that abrogates arrestin binding, and ‘modulator sites’ that influence the global conformation of arrestin. These functional motifs allow a better understanding of how different GPCR phosphorylation patterns might control how arrestin functions in the cell.
How face perception unfolds over time
Authors: Dobs Katharina , Isik Leyla , Pantazis Dimitrios , Kanwisher Nancy 
Published: April 2019

AbstractWithin a fraction of a second of viewing a face, we have already determined its gender, age and identity. A full understanding of this remarkable feat will require a characterization of the computational steps it entails, along with the representations extracted at each. Here, we used magnetoencephalography (MEG) to measure the time course of neural responses to faces, thereby addressing two fundamental questions about how face processing unfolds over time. First, using representational similarity analysis, we found that facial gender and age information emerged before identity information, suggesting a coarse-to-fine processing of face dimensions. Second, identity and gender representations of familiar faces were enhanced very early on, suggesting that the behavioral benefit for familiar faces results from tuning of early feed-forward processing mechanisms. These findings start to reveal the time course of face processing in humans, and provide powerful new constraints on computational theories of face perception.
Simulations suggest a constrictive force is required for Gram-negative bacterial cell division
Authors: Nguyen Lam T. , Oikonomou Catherine M. , Ding H. Jane , Kaplan Mohammed , Yao Qing , Chang Yi-Wei , Beeby Morgan , Jensen Grant J. 
Published: April 2019

AbstractTo divide, Gram-negative bacterial cells must remodel cell wall at the division site. It remains debated, however, whether this cell wall remodeling alone can drive membrane constriction, or if a constrictive force from the tubulin homolog FtsZ is required. Previously, we constructed software (REMODELER 1) to simulate cell wall remodeling during growth. Here, we expanded this software to explore cell wall division (REMODELER 2). We found that simply organizing cell wall synthesis complexes at the midcell is not sufficient to cause invagination, even with the implementation of a make-before-break mechanism, in which new hoops of cell wall are made inside the existing hoops before bonds are cleaved. Division can occur, however, when a constrictive force brings the midcell into a compressed state before new hoops of relaxed cell wall are incorporated between existing hoops. Adding a make-before-break mechanism drives division with a smaller constrictive force sufficient to bring the midcell into a relaxed, but not necessarily compressed, state.
Controllable ion transport by surface-charged graphene oxide membrane
Authors: Zhang Mengchen , Guan Kecheng , Ji Yufan , Liu Gongping , Jin Wanqin , Xu Nanping 
Published: April 2019

AbstractIon transport is crucial for biological systems and membrane-based technology. Atomic-thick two-dimensional materials, especially graphene oxide (GO), have emerged as ideal building blocks for developing synthetic membranes for ion transport. However, the exclusion of small ions in a pressured filtration process remains a challenge for GO membranes. Here we report manipulation of membrane surface charge to control ion transport through GO membranes. The highly charged GO membrane surface repels high-valent co-ions owing to its high interaction energy barrier while concomitantly restraining permeation of electrostatically attracted low-valent counter-ions based on balancing overall solution charge. The deliberately regulated surface-charged GO membranes demonstrate remarkable enhancement of ion rejection with intrinsically high water permeance that exceeds the performance limits of state-of-the-art nanofiltration membranes. This facile and scalable surface charge control approach opens opportunities in selective ion transport for the fields of water transport, biomimetic ion channels and biosensors, ion batteries and energy conversions.
Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1
Authors: Harnoš Jakub , Cañizal Maria Consuelo Alonso , Jurásek Miroslav , Kumar Jitender , Holler Cornelia , Schambony Alexandra , Hanáková Kateřina , Bernatík Ondřej , Zdráhal Zbyněk , Gömöryová Kristína , Gybeľ Tomáš , Radaszkiewicz Tomasz Witold , Kravec Marek , Trantírek Lukáš , Ryneš Jan , Dave Zankruti , Fernández-Llamazares Ana Iris , Vácha Robert , Tripsianes Konstantinos , Hoffmann Carsten , Bryja Vítězslav 
Published: April 2019

AbstractDishevelled (DVL) is the key component of the Wnt signaling pathway. Currently, DVL conformational dynamics under native conditions is unknown. To overcome this limitation, we develop the Fluorescein Arsenical Hairpin Binder- (FlAsH-) based FRET in vivo approach to study DVL conformation in living cells. Using this single-cell FRET approach, we demonstrate that (i) Wnt ligands induce open DVL conformation, (ii) DVL variants that are predominantly open, show more even subcellular localization and more efficient membrane recruitment by Frizzled (FZD) and (iii) Casein kinase 1 ɛ (CK1ɛ) has a key regulatory function in DVL conformational dynamics. In silico modeling and in vitro biophysical methods explain how CK1ɛ-specific phosphorylation events control DVL conformations via modulation of the PDZ domain and its interaction with DVL C-terminus. In summary, our study describes an experimental tool for DVL conformational sampling in living cells and elucidates the essential regulatory role of CK1ɛ in DVL conformational dynamics.
Femtosecond time synchronization of optical clocks off of a flying quadcopter
Authors: Bergeron Hugo , Sinclair Laura C. , Swann William C. , Khader Isaac , Cossel Kevin C. , Cermak Michael , Deschênes Jean-Daniel , Newbury Nathan R. 
Published: April 2019

AbstractFuture optical clock networks will require free-space optical time-frequency transfer between flying clocks. However, simple one-way or standard two-way time transfer between flying clocks will completely break down because of the time-of-flight variations and Doppler shifts associated with the strongly time-varying link distances. Here, we demonstrate an advanced, frequency comb-based optical two-way time-frequency transfer (O-TWTFT) that can successfully synchronize the optical timescales at two sites connected via a time-varying turbulent air path. The link between the two sites is established using either a quadcopter-mounted retroreflector or a swept delay line at speeds up to 24 ms−1. Despite 50-ps breakdown in time-of-flight reciprocity, the sites’ timescales are synchronized to < 1 fs in time deviation. The corresponding sites’ frequencies agree to ~ 10−18 despite 10−7 Doppler shifts. This work demonstrates comb-based O-TWTFT can enable free-space optical networks between airborne or satellite-borne optical clocks for precision navigation, timing and probes of fundamental science.
Machine-learned multi-system surrogate models for materials prediction
Authors: Nyshadham Chandramouli , Rupp Matthias , Bekker Brayden , Shapeev Alexander V. , Mueller Tim , Rosenbrock Conrad W. , Csányi Gábor , Wingate David W. , Hart Gus L. W. 
Published: April 2019

AbstractSurrogate machine-learning models are transforming computational materials science by predicting properties of materials with the accuracy of ab initio methods at a fraction of the computational cost. We demonstrate surrogate models that simultaneously interpolate energies of different materials on a dataset of 10 binary alloys (AgCu, AlFe, AlMg, AlNi, AlTi, CoNi, CuFe, CuNi, FeV, and NbNi) with 10 different species and all possible fcc, bcc, and hcp structures up to eight atoms in the unit cell, 15,950 structures in total. We find that the deviation of prediction errors when increasing the number of simultaneously modeled alloys is <1 meV/atom. Several state-of-the-art materials representations and learning algorithms were found to qualitatively agree on the prediction errors of formation enthalpy with relative errors of <2.5% for all systems.
Control of electrical conductivity of highly stacked zinc oxide nanocrystals by ultraviolet treatment
Authors: Han Wooje , Kim Jiwan , Park Hyung-Ho 
Published: April 2019

AbstractZinc oxide (ZnO) nanocrystals (NCs) were synthesized using a modified sol-gel method. Ultraviolet (UV) treatment was performed under various atmospheres on the highly stacked ZnO NCs. The prepared NCs were characterized using Fourier transform infrared spectroscopy, scanning electron microscopy, X-ray diffraction, photoluminescence spectroscopy, and atomic force microscopy to investigate their structural, electrical, and electrochemical properties. Through these analyses, the effect of the UV treatment on the chemical and electrical characteristics of ZnO NCs was established. According to the analyses, the organic ligands in the NCs were decomposed, and the particles were densified. The mobility of UV-treated ZnO NCs thin films increased to 1.4 cm2/Vs, almost 2 orders higher than the UV untreated ZnO thin films. It was confirmed that the recombination from oxygen vacancies of ZnO could be controlled by UV irradiation. As decreased oxygen vacancies, the band gap of ZnO NCs was increased from 3.2 eV to 3.27 eV.
Cell-penetrating peptide sequence and modification dependent uptake and subcellular distribution of green florescent protein in different cell lines
Authors: Patel Sanjay G. , Sayers Edward J. , He Lin , Narayan Rohan , Williams Thomas L. , Mills Emily M. , Allemann Rudolf K. , Luk Louis Y. P. , Jones Arwyn T. , Tsai Yu-Hsuan 
Published: April 2019

AbstractProtein therapy holds great promise for treating a variety of diseases. To act on intracellular targets, therapeutic proteins must cross the plasma membrane. This has previously been achieved by covalent attachment to a variety of cell-penetrating peptides (CPPs). However, there is limited information on the relative performance of CPPs in delivering proteins to cells, specifically the cytosol and other intracellular locations. Here we use green fluorescent protein (GFP) as a model cargo to compare delivery capacity of five CPP sequences (Penetratin, R8, TAT, Transportan, Xentry) and cyclic derivatives in different human cell lines (HeLa, HEK, 10T1/2, HepG2) representing different tissues. Confocal microscopy analysis indicates that most fusion proteins when incubated with cells at 10 µM localise to endosomes. Quantification of cellular uptake by flow cytometry reveals that uptake depends on both cell type (10T1/2 > HepG2 > HeLa > HEK), and CPP sequence (Transportan > R8 > Penetratin≈TAT > Xentry). CPP sequence cyclisation or addition of a HA-sequence increased cellular uptake, but fluorescence was still contained in vesicles with no evidence of endosomal escape. Our results provide a guide to select CPP for endosomal/lysosomal delivery and a basis for developing more efficient CPPs in the future.
Natural arsenic with a unique order structure: potential for new quantum materials
Authors: Yoshiasa Akira , Tokuda Makoto , Misawa Masaaki , Shimojo Fuyuki , Momma Koichi , Miyawaki Ritsuro , Matsubara Satoshi , Nakatsuka Akihiko , Sugiyama Kazumasa 
Published: April 2019

AbstractStudy of arsenic (As) provides guidelines for the development of next-generation materials. We clarify the unique structure of the third crystalline polymorph of natural As (Pnm21-As) by crystallographical experiment and the electronic structure by first-principles computational method. The crystal structure of Pnm21-As is a novel structure in which the basic portions of semi-metalic grey-As and semi-conductor black-As are alternately arranged at the atomic level. For both covalent and van der Waals bonding, the contributions of sd and pd hybridizations are important. Van der Waals bonding characteristics and d orbital contributions can be varied by control of layer stacking. Total charges are clearly divided into positive and negative in the same elements for the grey-As and black-As portions, respectively, is of importance. The sequence in which one-dimensional electron donor and acceptor portions alternate in the layer will be the first description.
Chlamydia pecorum prevalence in South Australian koala (Phascolarctos cinereus) populations: Identification and modelling of a population free from infection
Authors: Fabijan Jessica , Caraguel Charles , Jelocnik Martina , Polkinghorne Adam , Boardman Wayne S. J. , Nishimoto Elisa , Johnsson Greg , Molsher Robyn , Woolford Lucy , Timms Peter , Simmons Greg , Hemmatzadeh Farhid , Trott Darren J. , Speight Natasha 
Published: April 2019

AbstractChlamydia pecorum is an established and prevalent infection that produces severe clinical disease in many koala populations, contributing to dramatic population declines. In wild South Australian koala populations, C. pecorum occurrence and distribution is unknown. Here, C. pecorum-specific real-time quantitative PCR (qPCR) was applied to ocular and urogenital swabs from targeted surveys of wild koalas from the mainland Mount Lofty Ranges (MLR) (n = 75) and Kangaroo Island (KI) (n = 170) populations. Historical data from 13,081 KI koalas (1997–2018) provided additional evidence for assessing the absence of C. pecorum infection. In the MLR population, 46.7% (CI: 35.1–58.6%) of koalas were C. pecorum positive by qPCR but only 4% had grade 3 clinical disease. MLR koala fertility was significantly reduced by C. pecorum infection; all reproductively active females (n = 16) were C. pecorum negative, whereas 85.2% of inactive females (n = 23) were positive (P < 0.001). KI koalas were C. pecorum negative and the population was demonstrated to be free of C. pecorum infection with 95% confidence. C. pecorum is a real threat for the sustainability of the koala and KI is possibly the last isolated, large C. pecorum-free population remaining in Australia. These koalas could provide a safeguard against this serious disease threat to an iconic Australian species.
Superlubricity of glycerol by self-sustained chemical polishing
Authors: Long Yun , Bouchet Maria-Isabel De Barros , Lubrecht Ton , Onodera Tasuku , Martin Jean Michel 
Published: April 2019

AbstractAn impressive superlow coefficient of friction (CoF) as low as 0.004 (nearly equivalent to the rolling coefficient) was obtained by sliding a steel ball against a tetrahedral amorphous diamond-like carbon (ta-C) coating in glycerol under a boundary lubrication regime. X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) revealed substantial changes in the surface chemistry and topography in the friction track. As shown by XPS analysis, a transfer of iron atoms from the steel ball to the ta-C layer occurred, forming iron oxy-hydroxide (FeOOH) termination on both surfaces. Between them, theoretical calculations show that a nanometre-thick fluid film consisting of glycerol and its degradation products prevents direct contact between the solid surfaces by nm-thick film EHL lubrication and results in the superlow friction, in agreement with the experiment. Furthermore, molecular dynamics (MD) simulations reveal that hydrogen atoms act as “low-friction brushes” between sliding layers of crystalline FeOOH, resulting also in low friction. A new model of sustainable green superlubricity is proposed. The tribo-formation of FeOOH with glycerol leads to a unique polishing process, which in turn leads to a self-sustained Elasto-Hydrodynamic Lubrication (EHL) regime until the very thin fluid film is no more than a few nanometres thick. At lower thicknesses, the hydroxide layer takes over. Wear of the ta-C coating is negligible, while wear on the steel ball is very moderate and acceptable for many practical applications, such as bio-tribology and the food industry, in which green lubrication is especially needed.
Facilitation of allocentric coding by virtue of object-semantics
Authors: Karimpur Harun , Morgenstern Yaniv , Fiehler Katja 
Published: April 2019

AbstractIn the field of spatial coding it is well established that we mentally represent objects for action not only relative to ourselves, egocentrically, but also relative to other objects (landmarks), allocentrically. Several factors facilitate allocentric coding, for example, when objects are task-relevant or constitute stable and reliable spatial configurations. What is unknown, however, is how object-semantics facilitate the formation of these spatial configurations and thus allocentric coding. Here we demonstrate that (i) we can quantify the semantic similarity of objects and that (ii) semantically similar objects can serve as a cluster of landmarks that are allocentrically coded. Participants arranged a set of objects based on their semantic similarity. These arrangements were then entered into a similarity analysis. Based on the results, we created two semantic classes of objects, natural and man-made, that we used in a virtual reality experiment. Participants were asked to perform memory-guided reaching movements toward the initial position of a target object in a scene while either semantically congruent or incongruent landmarks were shifted. We found that the reaching endpoints systematically deviated in the direction of landmark shift. Importantly, this effect was stronger for shifts of semantically congruent landmarks. Our findings suggest that object-semantics facilitate allocentric coding by creating stable spatial configurations.
New insights into the ORF2 capsid protein, a key player of the hepatitis E virus lifecycle
Authors: Ankavay Maliki , Montpellier Claire , Sayed Ibrahim M. , Saliou Jean-Michel , Wychowski Czeslaw , Saas Laure , Duvet Sandrine , Aliouat-Denis Cécile-Marie , Farhat Rayan , de Masson d’Autume Valentin , Meuleman Philip , Dubuisson Jean , Cocquerel Laurence 
Published: April 2019

AbstractHepatitis E Virus (HEV) genome encodes three proteins including the ORF2 capsid protein. Recently, we demonstrated that HEV produces three different forms of ORF2: (i) the ORF2i form (infectious ORF2) which is the component of infectious particles, (ii) the secreted ORF2g (glycosylated ORF2) and ORF2c (cleaved ORF2) forms that are not associated with infectious particles, but are the major antigens in HEV-infected patient sera. The ORF2 protein sequence contains three highly conserved potential N-glycosylation sites (N1, N2 and N3). The status and biological relevance of ORF2 N-glycosylation in HEV lifecycle remain to be elucidated. Here, we generated and extensively characterized a series of ORF2 mutants in which the three N-glycosylation sites were mutated individually or in combination. We demonstrated that the ORF2g/c protein is N-glycosylated on N1 and N3 sites but not on the N2 site. We showed that N-glycosylation of ORF2 protein does not play any role in replication and assembly of infectious HEV particles. We found that glycosylated ORF2g/c forms are very stable proteins which are targeted by patient antibodies. We also demonstrated that the ORF2i protein is translocated into the nucleus of infected cells. Hence, our study led to new insights into the molecular mechanisms of ORF2 expression.
A functional Magnetic Resonance Imaging study of patients with Polar Type II/III complex shoulder instability
Authors: Howard Anthony , Powell Joanne L. , Gibson Jo , Hawkes David , Kemp Graham J. , Frostick Simon P. 
Published: April 2019

AbstractThe pathophysiology of Stanmore Classification Polar type II/III shoulder instability is not well understood. Functional Magnetic Resonance Imaging was used to measure brain activity in response to forward flexion and abduction in 16 patients with Polar Type II/III shoulder instability and 16 age-matched controls. When a cluster level correction was applied patients showed significantly greater brain activity than controls in primary motor cortex (BA4), supramarginal gyrus (BA40), inferior frontal gyrus (BA44), precentral gyrus (BA6) and middle frontal gyrus (BA6): the latter region is considered premotor cortex. Using voxel level correction within these five regions a unique activation was found in the primary motor cortex (BA4) at MNI coordinates -38 -26 56. Activation was greater in controls compared to patients in the parahippocampal gyrus (BA27) and perirhinal cortex (BA36). These findings show, for the first time, neural differences in patients with complex shoulder instability, and suggest that patients are in some sense working harder or differently to maintain shoulder stability, with brain activity similar to early stage motor sequence learning. It will help to understand the condition, design better therapies and improve treatment of this group; avoiding the common clinical misconception that their recurrent shoulder dislocations are a form of attention-seeking.