bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virus-host protein-protein interactions of mycobacteriophage Giles
Authors: Mehla Jitender , Dedrick Rebekah M. , Caufield J. Harry , Wagemans Jeroen , Sakhawalkar Neha , Johnson Allison , Hatfull Graham F. , Uetz Peter 
Published: November 2017

AbstractMycobacteriophage are viruses that infect mycobacteria. More than 1,400 mycobacteriophage genomes have been sequenced, coding for over one hundred thousand proteins of unknown functions. Here we investigate mycobacteriophage Giles-host protein-protein interactions (PPIs) using yeast two-hybrid screening (Y2H). A total of 25 reproducible PPIs were found for a selected set of 10 Giles proteins, including a putative virion assembly protein (gp17), the phage integrase (gp29), the endolysin (gp31), the phage repressor (gp47), and six proteins of unknown function (gp34, gp35, gp54, gp56, gp64, and gp65). We note that overexpression of the proteins is toxic to M. smegmatis, although whether this toxicity and the associated changes in cellular morphology are related to the putative interactions revealed in the Y2H screen is unclear.
2D/3D Microanalysis by Energy Dispersive X-ray Absorption Spectroscopy Tomography
Authors: Sanchez Dario Ferreira , Simionovici Alexandre S. , Lemelle Laurence , Cuartero Vera , Mathon Olivier , Pascarelli Sakura , Bonnin Anne , Shapiro Russell , Konhauser Kurt , Grolimund Daniel , Bleuet Pierre 
Published: November 2017

AbstractX-ray spectroscopic techniques have proven to be particularly useful in elucidating the molecular and electronic structural information of chemically heterogeneous and complex micro- and nano-structured materials. However, spatially resolved chemical characterization at the micrometre scale remains a challenge. Here, we report the novel hyperspectral technique of micro Energy Dispersive X-ray Absorption Spectroscopy (μED-XAS) tomography which can resolve in both 2D and 3D the spatial distribution of chemical species through the reconstruction of XANES spectra. To document the capability of the technique in resolving chemical species, we first analyse a sample containing 2–30 μm grains of various ferrous- and ferric-iron containing minerals, including hypersthene, magnetite and hematite, distributed in a light matrix of a resin. We accurately obtain the XANES spectra at the Fe K-edge of these four standards, with spatial resolution of 3 μm. Subsequently, a sample of ~1.9 billion-year-old microfossil from the Gunflint Formation in Canada is investigated, and for the first time ever, we are able to locally identify the oxidation state of iron compounds encrusting the 5 to 10 μm microfossils. Our results highlight the potential for attaining new insights into Precambrian ecosystems and the composition of Earth’s earliest life forms.
Deciphering how Cpl-7 cell wall-binding repeats recognize the bacterial peptidoglycan
Authors: Bustamante Noemí , Iglesias-Bexiga Manuel , Bernardo-García Noelia , Silva-Martín Noella , García Guadalupe , Campanero-Rhodes María A. , García Esther , Usón Isabel , Buey Rubén M. , García Pedro , Hermoso Juan A. , Bruix Marta , Menéndez Margarita 
Published: November 2017

AbstractEndolysins, the cell wall lytic enzymes encoded by bacteriophages to release the phage progeny, are among the top alternatives to fight against multiresistant pathogenic bacteria; one of the current biggest challenges to global health. Their narrow range of susceptible bacteria relies, primarily, on targeting specific cell-wall receptors through specialized modules. The cell wall-binding domain of Cpl-7 endolysin, made of three CW_7 repeats, accounts for its extended-range of substrates. Using as model system the cell wall-binding domain of Cpl-7, here we describe the molecular basis for the bacterial cell wall recognition by the CW_7 motif, which is widely represented in sequences of cell wall hydrolases. We report the crystal and solution structure of the full-length domain, identifyN-acetyl-D-glucosaminyl-(β1,4)-N-acetylmuramyl-L-alanyl-D-isoglutamine (GMDP) as the peptidoglycan (PG) target recognized by the CW_7 motifs, and characterize feasible GMDP-CW_7 contacts. Our data suggest that Cpl-7 cell wall-binding domain might simultaneously bind to three PG chains, and also highlight the potential use of CW_7-containing lysins as novel anti-infectives.
Bacterial alterations in salivary microbiota and their association in oral cancer
Authors: Lee Wei-Hsiang , Chen Hui-Mei , Yang Shun-Fa , Liang Chao , Peng Chih-Yu , Lin Feng-Mao , Tsai Lo-Lin , Wu Buor-Chang , Hsin Chung-Han , Chuang Chun-Yi , Yang Ting , Yang Tzu-Ling , Ho Shinn-Ying , Chen Wen-Liang , Ueng Kwo-Chang , Huang Hsien-Da , Huang Chien-Ning , Jong Yuh-Jyh 
Published: November 2017

AbstractOral squamous cell carcinoma (OSCC) is the most common malignant neoplasm of the oral cavity and the fourth leading malignancy and cause of cancer-related death in the male population of Taiwan. Most cases are detected at advanced stages, resulting in poor prognosis. Therefore, improved detection of early oral health disorders is indispensable. The involvement of oral bacteria in inflammation and their association with OSCC progression provide a feasible target for diagnosis. Due to the nature of oral neoplasms, the diagnosis of epithelial precursor lesions is relatively easy compared with that of other types of cancer. However, the transition from an epithelial precursor lesion to cancer is slow and requires further and continuous follow-up. In this study, we investigated microbiota differences between normal individuals, epithelial precursor lesion patients, and cancer patients with different lifestyle habits, such as betel chewing and smoking, using next-generation sequencing. Overall, the oral microbiome compositions of five genera, Bacillus, Enterococcus, Parvimonas, Peptostreptococcus, and Slackia, revealed significant differences between epithelial precursor lesion and cancer patients and correlated with their classification into two clusters. These composition changes might have the potential to constitute a biomarker to help in monitoring the oral carcinogenesis transition from epithelial precursor lesion to cancer.
Quantitative, in situ analysis of mRNAs and proteins with subcellular resolution
Authors: Kwon Sunjong , Chin Koei , Nederlof Michel , Gray Joe W. 
Published: November 2017

AbstractWe describe here a method, termed immunoFISH, for simultaneous in situ analysis of the composition and distribution of proteins and individual RNA transcripts in single cells. Individual RNA molecules are labeled by hybridization and target proteins are concurrently stained using immunofluorescence. Multicolor fluorescence images are acquired and analyzed to determine the abundance, composition, and distribution of hybridized probes and immunofluorescence. We assessed the ability of immunoFISH to simultaneous quantify protein and transcript levels and distribution in cultured HER2 positive breast cancer cells and human breast tumor samples. We demonstrated the utility of this assay in several applications including demonstration of the existence of a layer of normal myoepithelial KRT14 expressing cells that separate HER2+ cancer cells from the stromal and immune microenvironment in HER2+ invasive breast cancer. Our studies show that immunoFISH provides quantitative information about the spatial heterogeneity in transcriptional and proteomic features that exist between and within cells.
Dynamics of Intact MexAB-OprM Efflux Pump: Focusing on the MexA-OprM Interface
Authors: López Cesar A. , Travers Timothy , Pos Klaas M. , Zgurskaya Helen I. , Gnanakaran S. 
Published: November 2017

AbstractAntibiotic efflux is one of the most critical mechanisms leading to bacterial multidrug resistance. Antibiotics are effluxed out of the bacterial cell by a tripartite efflux pump, a complex machinery comprised of outer membrane, periplasmic adaptor, and inner membrane protein components. Understanding the mechanism of efflux pump assembly and its dynamics could facilitate discovery of novel approaches to counteract antibiotic resistance in bacteria. We built here an intact atomistic model of the Pseudomonas aeruginosa MexAB-OprM pump in a Gram-negative membrane model that contained both inner and outer membranes separated by a periplasmic space. All-atom molecular dynamics (MD) simulations confirm that the fully assembled pump is stable in the microsecond timescale. Using a combination of all-atom and coarse-grained MD simulations and sequence covariation analysis, we characterized the interface between MexA and OprM in the context of the entire efflux pump. These analyses suggest a plausible mechanism by which OprM is activated via opening of its periplasmic aperture through a concerted interaction with MexA.
Circularly-polarized, semitransparent and double-sided holograms based on helical photonic structures
Authors: Kobashi Junji , Yoshida Hiroyuki , Ozaki Masanori 
Published: November 2017

AbstractRecent advances in nanofabrication techniques are opening new frontiers in holographic devices, with the capability to integrate various optical functions in a single device. However, while most efficient holograms are achieved in reflection-mode configurations, they are in general opaque because of the reflective substrate that must be used, and therefore, have limited applicability. Here, we present a semi-transparent, reflective computer-generated hologram that is circularly-polarization dependent, and reconstructs different wavefronts when viewed from different sides. The integrated functionality is realized using a single thin-film of liquid crystal with a self-organized helical structure that Bragg reflects circularly-polarized light over a certain band of wavelengths. Asymmetry depending on the viewing side is achieved by exploiting the limited penetration depth of light in the helical structure as well as the nature of liquid crystals to conform to different orientational patterns imprinted on the two substrates sandwiching the material. Also, because the operation wavelength is determined by the reflection band position, pseudo-color holograms can be made by simply stacking layers with different designs. The unique characteristics of this hologram may find applications in polarization-encoded security holograms and see-through holographic signage where different information need to be displayed depending on the viewing direction.
Correlates of compliance with recommended levels of physical activity in children
Authors: Gomes Thayse Natacha , Katzmarzyk Peter T. , Hedeker Donald , Fogelholm Mikael , Standage Martyn , Onywera Vincent , Lambert Estelle V. , Tremblay Mark S. , Chaput Jean-Philippe , Tudor-Locke Catrine , Sarmiento Olga , Matsudo Victor , Kurpad Anura , Kuriyan Rebecca , Zhao Pei , Hu Gang , Olds Timothy , Maher Carol , Maia José 
Published: November 2017

AbstractThe purpose of this study was to describe children’s daily compliance with moderate-to-vigorous physical activity (MVPA) recommendations across a week in different parts of the world, and to identify individual- and school-level correlates that may explain differences in daily MVPA compliance. The sample included 6553 children aged 9–11 years from 12 countries, and multilevel statistical analyses were used, including both child- and school-level variables. Most children did not comply with the MVPA guidelines on a daily basis: Chinese children complied the least, whereas Finnish, Australian, Colombian, UK, and Kenyan children complied the most. Boys (rate ratio [RR] = 1.47) and children with higher unhealthy diet scores (RR = 1.08) complied more, but overweight/obese children (RR = 0.81), earlier maturing children (RR = 0.93), and those who spent more time in screen activities (RR = 0.98) and sleeping (RR = 0.96) had the lowest compliance. At the school level, children with access to playground or sport equipment (RR = 0.88, for both) tended to comply less, whereas those with access to a gymnasium outside the school hours complied more with the MVPA guidelines (RR = 1.14). Significant between-country differences in children’s daily MVPA compliance were observed, reflecting not only site characteristics, but also the importance of individual traits and local school contexts.
The structural, magnetic and optical properties of TMn@(ZnO)42 (TM = Fe, Co and Ni) hetero-nanostructure
Authors: Hu Yaowen , Ji Chuting , Wang Xiaoxu , Huo Jinrong , Liu Qing , Song Yipu 
Published: November 2017

AbstractThe magnetic transition-metal (TM) @ oxide nanoparticles have been of great interest due to their wide range of applications, from medical sensors in magnetic resonance imaging to photo-catalysis. Although several studies on small clusters of TM@oxide have been reported, the understanding of the physical electronic properties of TMn@(ZnO)42 is far from sufficient. In this work, the electronic, magnetic and optical properties of TMn@(ZnO)42 (TM = Fe, Co and Ni) hetero-nanostructure are investigated using the density functional theory (DFT). It has been found that the core-shell nanostructure Fe13@(ZnO)42, Co15@(ZnO)42 and Ni15@(ZnO)42 are the most stable structures. Moreover, it is also predicted that the variation of the magnetic moment and magnetism of Fe, Co and Ni in TMn@ZnO42 hetero-nanostructure mainly stems from effective hybridization between core TM-3d orbitals and shell O-2p orbitals, and a magnetic moment inversion for Fe15@(ZnO)42 is investigated. Finally, optical properties studied by calculations show a red shift phenomenon in the absorption spectrum compared with the case of (ZnO)48.
Circulating complement component 4d (C4d) correlates with tumor volume, chemotherapeutic response and survival in patients with malignant pleural mesothelioma
Authors: Klikovits Thomas , Stockhammer Paul , Laszlo Viktoria , Dong Yawen , Hoda Mir Alireza , Ghanim Bahil , Opitz Isabelle , Frauenfelder Thomas , Nguyen-Kim Thi Dan Linh , Weder Walter , Berger Walter , Grusch Michael , Aigner Clemens , Klepetko Walter , Dome Balazs , Renyi-Vamos Ferenc , Oehler Rudolf , Hegedus Balazs 
Published: November 2017

AbstractOnly limited information is available on the role of complement activation in malignant pleural mesothelioma (MPM). Thus, we investigated the circulating and tissue levels of the complement component 4d (C4d) in MPM. Plasma samples from 55 MPM patients, 21 healthy volunteers (HV) and 14 patients with non-malignant pleural diseases (NMPD) were measured by ELISA for C4d levels. Tissue specimens from 32 patients were analyzed by C4d immunohistochemistry. Tumor volumetry was measured in 20 patients. We found no C4d labeling on tumor cells, but on ectopic lymphoid structures within the tumor stroma. Plasma C4d levels did not significantly differ between MPM, HV or NMPD. Late-stage MPM patients had higher plasma C4d levels compared to early-stage (p = 0.079). High circulating C4d was associated with a higher tumor volume (p = 0.047). Plasma C4d levels following induction chemotherapy were significantly higher in patients with stable/progressive disease compared to those with partial/major response (p = 0.005). Strikingly, patients with low C4d levels at diagnosis had a significantly better overall survival, confirmed in a multivariate cox regression model (hazard ratio 0.263, p = 0.01). Our findings suggest that circulating plasma C4d is a promising new prognostic biomarker in patients with MPM and, moreover, helps to select patients for surgery following induction chemotherapy.
The flexibility and dynamics of the tubules in the endoplasmic reticulum
Authors: Georgiades Pantelis , Allan Victoria J. , Wright Graham D. , Woodman Philip G. , Udommai Parinya , Chung Manloeng A. , Waigh Thomas A. 
Published: November 2017

AbstractThe endoplasmic reticulum (ER) is a single organelle in eukaryotic cells that extends throughout the cell and is involved in a large number of cellular functions. Using a combination of fixed and live cells (human MRC5 lung cells) in diffraction limited and super-resolved fluorescence microscopy (STORM) experiments, we determined that the average persistence length of the ER tubules was 3.03 ± 0.24 μm. Removing the branched network junctions from the analysis caused a slight increase in the average persistence length to 4.71 ± 0.14 μm, and provides the tubule’s persistence length with a moderate length scale dependence. The average radius of the tubules was 44.1 ± 3.2 nm. The bending rigidity of the ER tubule membranes was found to be 10.9 ± 1.2kT(17.0 ± 1.3kTwithout branch points). We investigated the dynamic behaviour of ER tubules in live cells, and found that the ER tubules behaved like semi-flexible fibres under tension. The majority of the ER tubules experienced equilibrium transverse fluctuations under tension, whereas a minority number of them had active super-diffusive motions driven by motor proteins. Cells thus actively modulate the dynamics of the ER in a well-defined manner, which is expected in turn to impact on its many functions.
Ecto-ADP-ribosyltransferase ARTC2.1 functionally modulates FcγR1 and FcγR2B on murine microglia
Authors: Rissiek Björn , Menzel Stephan , Leutert Mario , Cordes Maike , Behr Sarah , Jank Larissa , Ludewig Peter , Gelderblom Mathias , Rissiek Anne , Adriouch Sahil , Haag Friedrich , Hottiger Michael O. , Koch-Nolte Friedrich , Magnus Tim 
Published: November 2017

AbstractMammalian ecto-ADP-ribosyltransferases (ecto-ARTs or also ARTCs) catalyze the ADP-ribosylation of cell surface proteins using extracellular nicotinamide adenine dinucleotide (NAD+) as substrate. By this post-translational protein modification, ecto-ARTs modulate the function of various target proteins. A functional role of ARTC2 has been demonstrated for peripheral immune cells such as T cells and macrophages. Yet, little is known about the role of ecto-ARTs in the central nervous system and on microglia. Here, we identified ARTC2.1 as the major ecto-ART expressed on murine microglia. ARTC2.1 expression was strongly upregulated on microglia upon co-stimulation with LPS and an ERK1/2 inhibitor or upon IFNβ stimulation. We identified several target proteins modified by ARTC2.1 on microglia with a recently developed mass spectrometry approach, including two receptors for immunoglobulin G (IgG), FcγR1 and FcγR2B. Both proteins were verified as targets of ARTC2.1in vitrousing a radiolabeling assay with32P-NAD+as substrate. Moreover, ADP-ribosylation of both targets strongly inhibited their capacity to bind IgG. In concordance, ARTC2.1 induction in WT microglia and subsequent cell surface ADP-ribosylation significantly reduced the phagocytosis of IgG-coated latex beads, which was unimpaired in NAD+/DTT treated microglia from ARTC2.1−/−mice. Hence, induction of ARTC2.1 expression under inflammatory conditions, and subsequent ADP-ribosylation of cell surface target proteins could represent a hitherto unnoticed mechanism to regulate the immune response of murine microglia.
A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community
Authors: Herschend Jakob , Damholt Zacharias B. V. , Marquard Andrea M. , Svensson Birte , Sørensen Søren J. , Hägglund Per , Burmølle Mette 
Published: November 2017

AbstractMicrobial biofilms are omnipresent in nature and relevant to a broad spectrum of industries ranging from bioremediation and food production to biomedical applications. To date little is understood about how multi-species biofilm communities develop and function on a molecular level, due to the complexity of these biological systems. Here we apply a meta-proteomics approach to investigate the mechanisms influencing biofilm formation in a model consortium of four bacterial soil isolates;Stenotrophomonas rhizophila,Xanthomonas retroflexus,Microbacterium oxydansandPaenibacillus amylolyticus. Protein abundances in community and single species biofilms were compared to describe occurring inter-species interactions and the resulting changes in active metabolic pathways. To obtain full taxonomic resolution between closely related species and empower correct protein quantification, we developed a novel pipeline for generating reduced reference proteomes for spectral database searches. Meta-proteomics profiling indicated that community development is dependent on cooperative interactions between community members facilitating cross-feeding on specific amino acids. Opposite regulation patterns of fermentation and nitrogen pathways inPaenibacillus amylolyticusandXanthomonas retroflexusmay, however, indicate that competition for limited resources also affects community development. Overall our results demonstrate the multitude of pathways involved in biofilm formation in mixed communities.
Non-invasive and invasive diagnoses of aspergillosis in a rat model by mass spectrometry
Authors: Luptáková Dominika , Pluháček Tomáš , Petřík Miloš , Novák Jiří , Palyzová Andrea , Sokolová Lucie , Škríba Anton , Šedivá Blanka , Lemr Karel , Havlíček Vladimír 
Published: November 2017

AbstractInvasive pulmonary aspergillosis results in 450,000 deaths per year and complicates cancer chemotherapy, transplantations and the treatment of other immunosuppressed patients. Using a rat model of experimental aspergillosis, the fungal siderophores ferricrocin and triacetylfusarinine C were identified as markers of aspergillosis and quantified in urine, serum and lung tissues. Biomarkers were analyzed by matrix-assisted laser desorption ionization (MALDI) and electrospray ionization mass spectrometry using a 12T SolariX Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. The limits of detection of the ferri-forms of triacetylfusarinine C and ferricrocin in the rat serum were 0.28 and 0.36 ng/mL, respectively. In the rat urine the respective limits of detection achieved 0.02 and 0.03 ng/mL. In the sera of infected animals, triacetylfusarinine C was not detected but ferricrocin concentration fluctuated in the 3–32 ng/mL range. Notably, the mean concentrations of triacetylfusarinine C and ferricrocin in the rat urine were 0.37 and 0.63 μg/mL, respectively. The MALDI FTICR mass spectrometry imaging illustrated the actual microbial ferricrocin distribution in the lung tissues and resolved the false-positive results obtained by the light microscopy and histological staining. Ferricrocin and triacetylfusarinine C detection in urine represents an innovative non-invasive indication of Aspergillus infection in a host.
Percolation channels: a universal idea to describe the atomic structure and dynamics of glasses and melts
Authors: Le Losq Charles , Neuville Daniel R. , Chen Wenlin , Florian Pierre , Massiot Dominique , Zhou Zhongfu , Greaves George N. 
Published: November 2017

AbstractUnderstanding the links between chemical composition, nano-structure and the dynamic properties of silicate melts and glasses is fundamental to both Earth and Materials Sciences. Central to this is whether the distribution of mobile metallic ions is random or not. In silicate systems, such as window glass, it is well-established that the short-range structure is not random but metal ions cluster, forming percolation channels through a partly broken network of corner-sharing SiO4 tetrahedra. In alumino-silicate glasses and melts, extensively used in industry and representing most of the Earth magmas, metal ions compensate the electrical charge deficit of AlO4− tetrahedra, but until now clustering has not been confirmed. Here we report how major changes in melt viscosity, together with glass Raman and Nuclear Magnetic Resonance measurements and Molecular Dynamics simulations, demonstrate that metal ions nano-segregate into percolation channels, making this a universal phenomenon of oxide glasses and melts. Furthermore, we can explain how, in both single and mixed alkali compositions, metal ion clustering and percolation radically affect melt mobility, central to understanding industrial and geological processes.